Starting phenix.real_space_refine on Thu Sep 18 16:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yd4_39164/09_2025/8yd4_39164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yd4_39164/09_2025/8yd4_39164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yd4_39164/09_2025/8yd4_39164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yd4_39164/09_2025/8yd4_39164.map" model { file = "/net/cci-nas-00/data/ceres_data/8yd4_39164/09_2025/8yd4_39164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yd4_39164/09_2025/8yd4_39164.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.063 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 119 5.16 5 C 11781 2.51 5 N 3199 2.21 5 O 3626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18725 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1352 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain breaks: 1 Chain: "H" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1323 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, I, J, K, L, M, N Time building chain proxies: 2.52, per 1000 atoms: 0.13 Number of scatterers: 18725 At special positions: 0 Unit cell: (117.04, 118.8, 104.72, 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 119 16.00 O 3626 8.00 N 3199 7.00 C 11781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 929.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4578 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 28 sheets defined 50.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 removed outlier: 3.731A pdb=" N TYR A 21 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 55 Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.995A pdb=" N ALA A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.840A pdb=" N LEU A 103 " --> pdb=" O MET A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 159 removed outlier: 3.509A pdb=" N ILE A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 4.056A pdb=" N ILE A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.510A pdb=" N LEU A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 removed outlier: 3.732A pdb=" N TYR B 21 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 22 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 55 Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.995A pdb=" N ALA B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 105 removed outlier: 3.839A pdb=" N LEU B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 159 removed outlier: 3.510A pdb=" N ILE B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 4.056A pdb=" N ILE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.510A pdb=" N LEU B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 26 removed outlier: 3.731A pdb=" N TYR C 21 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 70 through 84 removed outlier: 3.995A pdb=" N ALA C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.840A pdb=" N LEU C 103 " --> pdb=" O MET C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 159 removed outlier: 3.509A pdb=" N ILE C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 149 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 155 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 4.056A pdb=" N ILE C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 removed outlier: 3.509A pdb=" N LEU C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 26 removed outlier: 3.731A pdb=" N TYR D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 55 Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.995A pdb=" N ALA D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.840A pdb=" N LEU D 103 " --> pdb=" O MET D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 159 removed outlier: 3.509A pdb=" N ILE D 146 " --> pdb=" O GLN D 142 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 155 " --> pdb=" O PHE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 4.055A pdb=" N ILE D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 3.510A pdb=" N LEU D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 26 removed outlier: 3.732A pdb=" N TYR E 21 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU E 22 " --> pdb=" O ASP E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 55 Processing helix chain 'E' and resid 70 through 84 removed outlier: 3.995A pdb=" N ALA E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.839A pdb=" N LEU E 103 " --> pdb=" O MET E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 159 removed outlier: 3.510A pdb=" N ILE E 146 " --> pdb=" O GLN E 142 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU E 149 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 155 " --> pdb=" O PHE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 169 removed outlier: 4.055A pdb=" N ILE E 165 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 3.510A pdb=" N LEU E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 removed outlier: 3.731A pdb=" N TYR F 21 " --> pdb=" O THR F 17 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU F 22 " --> pdb=" O ASP F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 55 Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.996A pdb=" N ALA F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.840A pdb=" N LEU F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 159 removed outlier: 3.510A pdb=" N ILE F 146 " --> pdb=" O GLN F 142 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU F 149 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 155 " --> pdb=" O PHE F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 169 removed outlier: 4.055A pdb=" N ILE F 165 " --> pdb=" O PRO F 161 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 184 removed outlier: 3.510A pdb=" N LEU F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 26 removed outlier: 3.731A pdb=" N TYR G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU G 22 " --> pdb=" O ASP G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 55 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.995A pdb=" N ALA G 76 " --> pdb=" O SER G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 105 removed outlier: 3.839A pdb=" N LEU G 103 " --> pdb=" O MET G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 159 removed outlier: 3.509A pdb=" N ILE G 146 " --> pdb=" O GLN G 142 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G 155 " --> pdb=" O PHE G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 169 removed outlier: 4.056A pdb=" N ILE G 165 " --> pdb=" O PRO G 161 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU G 166 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 184 removed outlier: 3.510A pdb=" N LEU G 181 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 39 removed outlier: 3.558A pdb=" N LYS H 35 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 67 removed outlier: 3.916A pdb=" N ILE H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU H 61 " --> pdb=" O MET H 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.617A pdb=" N ASP H 91 " --> pdb=" O MET H 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 118 removed outlier: 4.033A pdb=" N LEU H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 173 removed outlier: 3.592A pdb=" N HIS H 171 " --> pdb=" O THR H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 184 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.617A pdb=" N LYS H 195 " --> pdb=" O ALA H 191 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 196' Processing helix chain 'I' and resid 31 through 39 removed outlier: 3.559A pdb=" N LYS I 35 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU I 39 " --> pdb=" O LYS I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 67 removed outlier: 3.916A pdb=" N ILE I 56 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU I 61 " --> pdb=" O MET I 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 94 removed outlier: 3.617A pdb=" N ASP I 91 " --> pdb=" O MET I 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR I 92 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 118 removed outlier: 4.033A pdb=" N LEU I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 173 removed outlier: 3.593A pdb=" N HIS I 171 " --> pdb=" O THR I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 184 Processing helix chain 'I' and resid 191 through 196 removed outlier: 3.616A pdb=" N LYS I 195 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP I 196 " --> pdb=" O GLU I 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 191 through 196' Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.559A pdb=" N LYS J 35 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU J 39 " --> pdb=" O LYS J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 67 removed outlier: 3.917A pdb=" N ILE J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU J 61 " --> pdb=" O MET J 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 94 removed outlier: 3.617A pdb=" N ASP J 91 " --> pdb=" O MET J 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR J 92 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 removed outlier: 4.033A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 173 removed outlier: 3.592A pdb=" N HIS J 171 " --> pdb=" O THR J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 184 Processing helix chain 'J' and resid 191 through 196 removed outlier: 3.618A pdb=" N LYS J 195 " --> pdb=" O ALA J 191 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP J 196 " --> pdb=" O GLU J 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 191 through 196' Processing helix chain 'K' and resid 31 through 39 removed outlier: 3.560A pdb=" N LYS K 35 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU K 39 " --> pdb=" O LYS K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 67 removed outlier: 3.917A pdb=" N ILE K 56 " --> pdb=" O SER K 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 94 removed outlier: 3.616A pdb=" N ASP K 91 " --> pdb=" O MET K 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 removed outlier: 4.033A pdb=" N LEU K 115 " --> pdb=" O ALA K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 173 removed outlier: 3.593A pdb=" N HIS K 171 " --> pdb=" O THR K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 184 Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.617A pdb=" N LYS K 195 " --> pdb=" O ALA K 191 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP K 196 " --> pdb=" O GLU K 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 191 through 196' Processing helix chain 'L' and resid 31 through 39 removed outlier: 3.559A pdb=" N LYS L 35 " --> pdb=" O ASN L 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU L 39 " --> pdb=" O LYS L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 67 removed outlier: 3.916A pdb=" N ILE L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU L 61 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU L 64 " --> pdb=" O LEU L 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER L 65 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 94 removed outlier: 3.617A pdb=" N ASP L 91 " --> pdb=" O MET L 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 118 removed outlier: 4.033A pdb=" N LEU L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 173 removed outlier: 3.593A pdb=" N HIS L 171 " --> pdb=" O THR L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 184 Processing helix chain 'L' and resid 191 through 196 removed outlier: 3.617A pdb=" N LYS L 195 " --> pdb=" O ALA L 191 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP L 196 " --> pdb=" O GLU L 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 191 through 196' Processing helix chain 'M' and resid 31 through 39 removed outlier: 3.559A pdb=" N LYS M 35 " --> pdb=" O ASN M 31 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 67 removed outlier: 3.916A pdb=" N ILE M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU M 61 " --> pdb=" O MET M 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER M 65 " --> pdb=" O LEU M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 removed outlier: 3.616A pdb=" N ASP M 91 " --> pdb=" O MET M 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 118 removed outlier: 4.033A pdb=" N LEU M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 173 removed outlier: 3.593A pdb=" N HIS M 171 " --> pdb=" O THR M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 184 Processing helix chain 'M' and resid 191 through 196 removed outlier: 3.616A pdb=" N LYS M 195 " --> pdb=" O ALA M 191 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 191 through 196' Processing helix chain 'N' and resid 31 through 39 removed outlier: 3.559A pdb=" N LYS N 35 " --> pdb=" O ASN N 31 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU N 39 " --> pdb=" O LYS N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 67 removed outlier: 3.916A pdb=" N ILE N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU N 61 " --> pdb=" O MET N 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU N 64 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 94 removed outlier: 3.617A pdb=" N ASP N 91 " --> pdb=" O MET N 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 118 removed outlier: 4.032A pdb=" N LEU N 115 " --> pdb=" O ALA N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 173 removed outlier: 3.594A pdb=" N HIS N 171 " --> pdb=" O THR N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 184 Processing helix chain 'N' and resid 191 through 196 removed outlier: 3.616A pdb=" N LYS N 195 " --> pdb=" O ALA N 191 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP N 196 " --> pdb=" O GLU N 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 191 through 196' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.254A pdb=" N ILE A 60 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR A 91 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 62 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET A 93 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 64 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N MET A 95 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG A 119 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY A 94 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU A 121 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.255A pdb=" N ILE B 60 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 91 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 62 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET B 93 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE B 64 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N MET B 95 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG B 119 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY B 94 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU B 121 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA B 96 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.254A pdb=" N ILE C 60 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR C 91 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 62 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET C 93 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 64 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N MET C 95 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG C 119 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY C 94 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU C 121 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 96 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 113 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.255A pdb=" N ILE D 60 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR D 91 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU D 62 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET D 93 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE D 64 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N MET D 95 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG D 119 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY D 94 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LEU D 121 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA D 96 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 113 through 114 Processing sheet with id=AA9, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.255A pdb=" N ILE E 60 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR E 91 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU E 62 " --> pdb=" O TYR E 91 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET E 93 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE E 64 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N MET E 95 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG E 119 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY E 94 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU E 121 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA E 96 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 113 through 114 Processing sheet with id=AB2, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.254A pdb=" N ILE F 60 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR F 91 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU F 62 " --> pdb=" O TYR F 91 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET F 93 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE F 64 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N MET F 95 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG F 119 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY F 94 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU F 121 " --> pdb=" O GLY F 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA F 96 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AB4, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.254A pdb=" N ILE G 60 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR G 91 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU G 62 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET G 93 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE G 64 " --> pdb=" O MET G 93 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N MET G 95 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG G 119 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY G 94 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU G 121 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA G 96 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 113 through 114 Processing sheet with id=AB6, first strand: chain 'H' and resid 41 through 43 removed outlier: 6.722A pdb=" N ILE H 72 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL H 103 " --> pdb=" O ILE H 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET H 74 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU H 105 " --> pdb=" O MET H 74 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE H 76 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN H 107 " --> pdb=" O ILE H 76 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER H 78 " --> pdb=" O GLN H 107 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA H 109 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG H 131 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY H 106 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU H 133 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 41 through 43 removed outlier: 6.722A pdb=" N ILE H 72 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL H 103 " --> pdb=" O ILE H 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET H 74 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU H 105 " --> pdb=" O MET H 74 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE H 76 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN H 107 " --> pdb=" O ILE H 76 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER H 78 " --> pdb=" O GLN H 107 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA H 109 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N MET H 125 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR H 102 " --> pdb=" O MET H 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA H 126 " --> pdb=" O THR H 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE I 72 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL I 103 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET I 74 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU I 105 " --> pdb=" O MET I 74 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE I 76 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN I 107 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER I 78 " --> pdb=" O GLN I 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA I 109 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG I 131 " --> pdb=" O CYS I 104 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY I 106 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU I 133 " --> pdb=" O GLY I 106 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA I 108 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE I 72 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL I 103 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET I 74 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU I 105 " --> pdb=" O MET I 74 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE I 76 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN I 107 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER I 78 " --> pdb=" O GLN I 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA I 109 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N MET I 125 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR I 102 " --> pdb=" O MET I 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA I 126 " --> pdb=" O THR I 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE J 72 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL J 103 " --> pdb=" O ILE J 72 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET J 74 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU J 105 " --> pdb=" O MET J 74 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE J 76 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN J 107 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER J 78 " --> pdb=" O GLN J 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA J 109 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG J 131 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY J 106 " --> pdb=" O ARG J 131 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU J 133 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA J 108 " --> pdb=" O LEU J 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE J 72 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL J 103 " --> pdb=" O ILE J 72 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET J 74 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU J 105 " --> pdb=" O MET J 74 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE J 76 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN J 107 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER J 78 " --> pdb=" O GLN J 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA J 109 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N MET J 125 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR J 102 " --> pdb=" O MET J 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J 126 " --> pdb=" O THR J 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE K 72 " --> pdb=" O GLN K 101 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL K 103 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET K 74 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU K 105 " --> pdb=" O MET K 74 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE K 76 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN K 107 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER K 78 " --> pdb=" O GLN K 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA K 109 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG K 131 " --> pdb=" O CYS K 104 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY K 106 " --> pdb=" O ARG K 131 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU K 133 " --> pdb=" O GLY K 106 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA K 108 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE K 72 " --> pdb=" O GLN K 101 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL K 103 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET K 74 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU K 105 " --> pdb=" O MET K 74 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE K 76 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN K 107 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER K 78 " --> pdb=" O GLN K 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA K 109 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N MET K 125 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR K 102 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA K 126 " --> pdb=" O THR K 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE L 72 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL L 103 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET L 74 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU L 105 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE L 76 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN L 107 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER L 78 " --> pdb=" O GLN L 107 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA L 109 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG L 131 " --> pdb=" O CYS L 104 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY L 106 " --> pdb=" O ARG L 131 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU L 133 " --> pdb=" O GLY L 106 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ALA L 108 " --> pdb=" O LEU L 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE L 72 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL L 103 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET L 74 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU L 105 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE L 76 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN L 107 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER L 78 " --> pdb=" O GLN L 107 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA L 109 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N MET L 125 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR L 102 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 126 " --> pdb=" O THR L 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 41 through 43 removed outlier: 6.722A pdb=" N ILE M 72 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL M 103 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET M 74 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU M 105 " --> pdb=" O MET M 74 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE M 76 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN M 107 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER M 78 " --> pdb=" O GLN M 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA M 109 " --> pdb=" O SER M 78 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG M 131 " --> pdb=" O CYS M 104 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY M 106 " --> pdb=" O ARG M 131 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU M 133 " --> pdb=" O GLY M 106 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA M 108 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 41 through 43 removed outlier: 6.722A pdb=" N ILE M 72 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL M 103 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET M 74 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU M 105 " --> pdb=" O MET M 74 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE M 76 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN M 107 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER M 78 " --> pdb=" O GLN M 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA M 109 " --> pdb=" O SER M 78 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N MET M 125 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR M 102 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA M 126 " --> pdb=" O THR M 202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE N 72 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL N 103 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET N 74 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU N 105 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE N 76 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN N 107 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER N 78 " --> pdb=" O GLN N 107 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA N 109 " --> pdb=" O SER N 78 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG N 131 " --> pdb=" O CYS N 104 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY N 106 " --> pdb=" O ARG N 131 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU N 133 " --> pdb=" O GLY N 106 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA N 108 " --> pdb=" O LEU N 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 41 through 43 removed outlier: 6.721A pdb=" N ILE N 72 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL N 103 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET N 74 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU N 105 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE N 76 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN N 107 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER N 78 " --> pdb=" O GLN N 107 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA N 109 " --> pdb=" O SER N 78 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N MET N 125 " --> pdb=" O ILE N 100 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR N 102 " --> pdb=" O MET N 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA N 126 " --> pdb=" O THR N 202 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.51 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: 6349 1.34 - 1.46: 3540 1.46 - 1.58: 8878 1.58 - 1.69: 0 1.69 - 1.81: 217 Bond restraints: 18984 Sorted by residual: bond pdb=" CB GLU L 165 " pdb=" CG GLU L 165 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.26e-01 bond pdb=" CB GLU H 165 " pdb=" CG GLU H 165 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.20e-01 bond pdb=" CB GLU M 165 " pdb=" CG GLU M 165 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.15e-01 bond pdb=" CB GLU N 165 " pdb=" CG GLU N 165 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CB GLU K 165 " pdb=" CG GLU K 165 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 ... (remaining 18979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 24999 1.03 - 2.07: 505 2.07 - 3.10: 123 3.10 - 4.13: 21 4.13 - 5.17: 7 Bond angle restraints: 25655 Sorted by residual: angle pdb=" N ASP H 49 " pdb=" CA ASP H 49 " pdb=" C ASP H 49 " ideal model delta sigma weight residual 108.07 110.94 -2.87 1.38e+00 5.25e-01 4.33e+00 angle pdb=" N ASP N 49 " pdb=" CA ASP N 49 " pdb=" C ASP N 49 " ideal model delta sigma weight residual 108.07 110.91 -2.84 1.38e+00 5.25e-01 4.23e+00 angle pdb=" N ASP I 49 " pdb=" CA ASP I 49 " pdb=" C ASP I 49 " ideal model delta sigma weight residual 108.07 110.91 -2.84 1.38e+00 5.25e-01 4.23e+00 angle pdb=" N ASP J 49 " pdb=" CA ASP J 49 " pdb=" C ASP J 49 " ideal model delta sigma weight residual 108.07 110.91 -2.84 1.38e+00 5.25e-01 4.22e+00 angle pdb=" N ASP M 49 " pdb=" CA ASP M 49 " pdb=" C ASP M 49 " ideal model delta sigma weight residual 108.07 110.88 -2.81 1.38e+00 5.25e-01 4.15e+00 ... (remaining 25650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 10923 16.81 - 33.62: 522 33.62 - 50.42: 98 50.42 - 67.23: 35 67.23 - 84.04: 49 Dihedral angle restraints: 11627 sinusoidal: 4557 harmonic: 7070 Sorted by residual: dihedral pdb=" CA ASP L 182 " pdb=" CB ASP L 182 " pdb=" CG ASP L 182 " pdb=" OD1 ASP L 182 " ideal model delta sinusoidal sigma weight residual -30.00 -86.21 56.21 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP H 182 " pdb=" CB ASP H 182 " pdb=" CG ASP H 182 " pdb=" OD1 ASP H 182 " ideal model delta sinusoidal sigma weight residual -30.00 -86.19 56.19 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASP K 182 " pdb=" CB ASP K 182 " pdb=" CG ASP K 182 " pdb=" OD1 ASP K 182 " ideal model delta sinusoidal sigma weight residual -30.00 -86.15 56.15 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 11624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1812 0.025 - 0.050: 758 0.050 - 0.075: 218 0.075 - 0.100: 106 0.100 - 0.125: 95 Chirality restraints: 2989 Sorted by residual: chirality pdb=" CA ILE M 72 " pdb=" N ILE M 72 " pdb=" C ILE M 72 " pdb=" CB ILE M 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE N 72 " pdb=" N ILE N 72 " pdb=" C ILE N 72 " pdb=" CB ILE N 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE H 72 " pdb=" N ILE H 72 " pdb=" C ILE H 72 " pdb=" CB ILE H 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 2986 not shown) Planarity restraints: 3325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 66 " -0.014 5.00e-02 4.00e+02 2.06e-02 6.80e-01 pdb=" N PRO C 67 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 66 " -0.014 5.00e-02 4.00e+02 2.05e-02 6.74e-01 pdb=" N PRO F 67 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO F 67 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO F 67 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 66 " 0.013 5.00e-02 4.00e+02 2.05e-02 6.70e-01 pdb=" N PRO B 67 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " 0.011 5.00e-02 4.00e+02 ... (remaining 3322 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4986 2.80 - 3.33: 17122 3.33 - 3.85: 28760 3.85 - 4.38: 34988 4.38 - 4.90: 60321 Nonbonded interactions: 146177 Sorted by model distance: nonbonded pdb=" NH2 ARG A 23 " pdb=" OE2 GLU G 54 " model vdw 2.278 3.120 nonbonded pdb=" O ALA I 88 " pdb=" OG1 THR I 92 " model vdw 2.331 3.040 nonbonded pdb=" O ALA K 88 " pdb=" OG1 THR K 92 " model vdw 2.331 3.040 nonbonded pdb=" O ALA H 88 " pdb=" OG1 THR H 92 " model vdw 2.332 3.040 nonbonded pdb=" O ALA L 88 " pdb=" OG1 THR L 92 " model vdw 2.332 3.040 ... (remaining 146172 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.002 0.022 18984 Z= 0.084 Angle : 0.399 5.168 25655 Z= 0.244 Chirality : 0.037 0.125 2989 Planarity : 0.002 0.021 3325 Dihedral : 12.132 84.040 7049 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.71 % Allowed : 5.36 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.36 (0.13), residues: 2380 helix: -2.72 (0.11), residues: 1204 sheet: -3.51 (0.24), residues: 287 loop : -2.60 (0.17), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 40 TYR 0.003 0.000 TYR E 91 PHE 0.002 0.000 PHE K 37 TRP 0.001 0.000 TRP D 174 HIS 0.001 0.000 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00151 (18984) covalent geometry : angle 0.39893 (25655) hydrogen bonds : bond 0.25138 ( 763) hydrogen bonds : angle 7.76838 ( 2310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 324 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 TYR cc_start: 0.8377 (m-80) cc_final: 0.8161 (m-80) REVERT: E 113 TYR cc_start: 0.8345 (m-80) cc_final: 0.7886 (m-80) REVERT: F 163 GLU cc_start: 0.7263 (mp0) cc_final: 0.7012 (mp0) REVERT: G 39 GLU cc_start: 0.7155 (tp30) cc_final: 0.6781 (mt-10) REVERT: I 39 GLU cc_start: 0.7617 (tt0) cc_final: 0.7297 (tt0) REVERT: I 74 MET cc_start: 0.8545 (ttm) cc_final: 0.8280 (ttt) REVERT: J 74 MET cc_start: 0.8410 (ttm) cc_final: 0.8134 (ttt) REVERT: L 74 MET cc_start: 0.8444 (ttm) cc_final: 0.8207 (ttt) REVERT: M 39 GLU cc_start: 0.7603 (tt0) cc_final: 0.7212 (tt0) REVERT: N 74 MET cc_start: 0.8428 (ttm) cc_final: 0.8049 (ttt) outliers start: 14 outliers final: 13 residues processed: 338 average time/residue: 0.1575 time to fit residues: 79.4755 Evaluate side-chains 272 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 165 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 139 GLN B 117 HIS B 139 GLN C 117 HIS C 139 GLN C 142 GLN D 117 HIS D 139 GLN E 117 HIS E 139 GLN E 142 GLN F 117 HIS F 139 GLN F 142 GLN G 117 HIS G 139 GLN G 142 GLN H 171 HIS I 171 HIS J 171 HIS K 107 GLN K 171 HIS L 107 GLN L 171 HIS M 171 HIS N 107 GLN N 171 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.161885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.143730 restraints weight = 19716.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.146163 restraints weight = 14293.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.148163 restraints weight = 11287.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.149472 restraints weight = 9347.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.150706 restraints weight = 8038.204| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 18984 Z= 0.114 Angle : 0.441 5.918 25655 Z= 0.233 Chirality : 0.040 0.148 2989 Planarity : 0.003 0.026 3325 Dihedral : 3.801 33.313 2659 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.94 % Allowed : 9.18 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.15), residues: 2380 helix: -1.52 (0.13), residues: 1246 sheet: -3.22 (0.23), residues: 322 loop : -1.99 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 40 TYR 0.008 0.001 TYR A 91 PHE 0.006 0.001 PHE E 31 TRP 0.004 0.001 TRP B 174 HIS 0.002 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00255 (18984) covalent geometry : angle 0.44082 (25655) hydrogen bonds : bond 0.03188 ( 763) hydrogen bonds : angle 4.51227 ( 2310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8456 (mttt) cc_final: 0.8178 (mttm) REVERT: C 113 TYR cc_start: 0.8549 (m-80) cc_final: 0.8327 (m-80) REVERT: D 99 MET cc_start: 0.8740 (tpp) cc_final: 0.8277 (tpt) REVERT: E 113 TYR cc_start: 0.8554 (m-80) cc_final: 0.8100 (m-80) REVERT: G 26 SER cc_start: 0.8691 (m) cc_final: 0.8456 (t) REVERT: H 107 GLN cc_start: 0.8102 (pm20) cc_final: 0.7717 (pt0) REVERT: I 39 GLU cc_start: 0.7706 (tt0) cc_final: 0.7364 (tt0) REVERT: I 74 MET cc_start: 0.8849 (ttm) cc_final: 0.8564 (ttt) REVERT: I 107 GLN cc_start: 0.8190 (pm20) cc_final: 0.7944 (pt0) REVERT: J 74 MET cc_start: 0.8783 (ttm) cc_final: 0.8387 (ttt) REVERT: J 107 GLN cc_start: 0.8159 (pm20) cc_final: 0.7835 (pt0) REVERT: K 39 GLU cc_start: 0.7765 (tt0) cc_final: 0.7548 (tt0) REVERT: K 74 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8078 (ttt) REVERT: K 107 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: L 107 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: M 39 GLU cc_start: 0.7773 (tt0) cc_final: 0.7388 (tt0) REVERT: N 74 MET cc_start: 0.8796 (ttm) cc_final: 0.8430 (ttt) outliers start: 38 outliers final: 16 residues processed: 293 average time/residue: 0.1535 time to fit residues: 67.9091 Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain L residue 107 GLN Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 107 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 160 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 101 optimal weight: 0.0060 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN B 142 GLN D 142 GLN E 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.159949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.140708 restraints weight = 19794.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.143625 restraints weight = 14173.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.145673 restraints weight = 10971.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.147109 restraints weight = 9034.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.148277 restraints weight = 7750.824| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18984 Z= 0.095 Angle : 0.426 7.931 25655 Z= 0.218 Chirality : 0.040 0.143 2989 Planarity : 0.003 0.024 3325 Dihedral : 3.745 31.512 2651 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.35 % Allowed : 11.79 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.16), residues: 2380 helix: -0.81 (0.14), residues: 1246 sheet: -2.88 (0.24), residues: 322 loop : -1.62 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.007 0.001 TYR A 91 PHE 0.005 0.001 PHE D 31 TRP 0.005 0.001 TRP C 174 HIS 0.002 0.000 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00212 (18984) covalent geometry : angle 0.42587 (25655) hydrogen bonds : bond 0.02622 ( 763) hydrogen bonds : angle 4.07015 ( 2310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8456 (mttt) cc_final: 0.8166 (mttm) REVERT: B 26 SER cc_start: 0.8759 (m) cc_final: 0.8543 (t) REVERT: C 113 TYR cc_start: 0.8554 (m-80) cc_final: 0.8275 (m-80) REVERT: E 99 MET cc_start: 0.8922 (tpp) cc_final: 0.8518 (tpt) REVERT: E 113 TYR cc_start: 0.8604 (m-80) cc_final: 0.8207 (m-80) REVERT: F 26 SER cc_start: 0.8964 (m) cc_final: 0.8420 (t) REVERT: H 39 GLU cc_start: 0.7838 (tt0) cc_final: 0.7488 (tt0) REVERT: H 107 GLN cc_start: 0.8053 (pm20) cc_final: 0.7783 (pt0) REVERT: I 39 GLU cc_start: 0.7775 (tt0) cc_final: 0.7381 (tt0) REVERT: I 107 GLN cc_start: 0.8228 (pm20) cc_final: 0.7969 (pt0) REVERT: J 74 MET cc_start: 0.8798 (ttm) cc_final: 0.8446 (ttt) REVERT: J 107 GLN cc_start: 0.8185 (pm20) cc_final: 0.7882 (pt0) REVERT: K 39 GLU cc_start: 0.7842 (tt0) cc_final: 0.7458 (tt0) REVERT: L 39 GLU cc_start: 0.7401 (tt0) cc_final: 0.7152 (tt0) REVERT: L 107 GLN cc_start: 0.7896 (pm20) cc_final: 0.7652 (pt0) REVERT: M 39 GLU cc_start: 0.7804 (tt0) cc_final: 0.7428 (tt0) REVERT: N 74 MET cc_start: 0.8786 (ttm) cc_final: 0.8457 (ttt) REVERT: N 107 GLN cc_start: 0.7907 (pm20) cc_final: 0.7701 (pt0) outliers start: 46 outliers final: 26 residues processed: 288 average time/residue: 0.1588 time to fit residues: 67.8122 Evaluate side-chains 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS F 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.131982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.118598 restraints weight = 20798.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.118634 restraints weight = 20767.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.119647 restraints weight = 19187.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.120115 restraints weight = 16720.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.120380 restraints weight = 14852.240| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18984 Z= 0.259 Angle : 0.637 8.332 25655 Z= 0.328 Chirality : 0.046 0.169 2989 Planarity : 0.004 0.037 3325 Dihedral : 5.030 42.370 2649 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.55 % Allowed : 12.65 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.16), residues: 2380 helix: -0.92 (0.14), residues: 1218 sheet: -2.93 (0.23), residues: 385 loop : -1.22 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 97 TYR 0.020 0.002 TYR F 91 PHE 0.016 0.002 PHE E 102 TRP 0.007 0.001 TRP B 174 HIS 0.006 0.001 HIS I 135 Details of bonding type rmsd covalent geometry : bond 0.00620 (18984) covalent geometry : angle 0.63739 (25655) hydrogen bonds : bond 0.03673 ( 763) hydrogen bonds : angle 4.67921 ( 2310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 TYR cc_start: 0.8699 (m-80) cc_final: 0.8416 (m-80) REVERT: H 107 GLN cc_start: 0.8440 (pm20) cc_final: 0.8194 (pt0) REVERT: I 39 GLU cc_start: 0.7946 (tt0) cc_final: 0.7556 (tt0) REVERT: I 74 MET cc_start: 0.8986 (ttm) cc_final: 0.8762 (ttp) REVERT: I 107 GLN cc_start: 0.8485 (pm20) cc_final: 0.8174 (pt0) REVERT: J 39 GLU cc_start: 0.7788 (tt0) cc_final: 0.7521 (tt0) REVERT: J 74 MET cc_start: 0.8884 (ttm) cc_final: 0.8552 (ttt) REVERT: J 107 GLN cc_start: 0.8392 (pm20) cc_final: 0.8123 (pt0) REVERT: K 39 GLU cc_start: 0.7998 (tt0) cc_final: 0.7597 (tt0) REVERT: L 39 GLU cc_start: 0.7736 (tt0) cc_final: 0.7394 (tt0) REVERT: L 107 GLN cc_start: 0.8480 (pm20) cc_final: 0.8160 (pt0) REVERT: M 39 GLU cc_start: 0.7975 (tt0) cc_final: 0.7579 (tt0) REVERT: M 97 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.7002 (mtt180) REVERT: N 39 GLU cc_start: 0.7898 (tt0) cc_final: 0.7607 (tt0) REVERT: N 74 MET cc_start: 0.8870 (ttm) cc_final: 0.8562 (ttt) REVERT: N 107 GLN cc_start: 0.8417 (pm20) cc_final: 0.8089 (pt0) outliers start: 50 outliers final: 27 residues processed: 275 average time/residue: 0.1466 time to fit residues: 61.1359 Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 194 optimal weight: 0.9990 chunk 189 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 193 optimal weight: 0.2980 chunk 170 optimal weight: 2.9990 chunk 201 optimal weight: 0.4980 chunk 209 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN E 42 ASN H 135 HIS I 135 HIS J 135 HIS K 135 HIS L 135 HIS M 135 HIS N 135 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.139112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.131634 restraints weight = 19964.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.131370 restraints weight = 26678.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.129143 restraints weight = 28340.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.128527 restraints weight = 19961.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.129068 restraints weight = 17748.924| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18984 Z= 0.083 Angle : 0.433 4.841 25655 Z= 0.227 Chirality : 0.039 0.132 2989 Planarity : 0.003 0.038 3325 Dihedral : 4.132 33.446 2645 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.14 % Allowed : 13.06 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.17), residues: 2380 helix: -0.43 (0.14), residues: 1260 sheet: -2.56 (0.27), residues: 315 loop : -1.33 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 97 TYR 0.010 0.001 TYR A 91 PHE 0.005 0.001 PHE C 175 TRP 0.004 0.001 TRP E 174 HIS 0.006 0.001 HIS H 135 Details of bonding type rmsd covalent geometry : bond 0.00178 (18984) covalent geometry : angle 0.43288 (25655) hydrogen bonds : bond 0.02274 ( 763) hydrogen bonds : angle 3.94454 ( 2310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 TYR cc_start: 0.8646 (m-80) cc_final: 0.8356 (m-80) REVERT: E 163 GLU cc_start: 0.7345 (mp0) cc_final: 0.7120 (mp0) REVERT: E 183 TYR cc_start: 0.9154 (t80) cc_final: 0.8940 (t80) REVERT: F 26 SER cc_start: 0.9046 (m) cc_final: 0.8493 (t) REVERT: H 39 GLU cc_start: 0.7785 (tt0) cc_final: 0.7523 (tt0) REVERT: H 107 GLN cc_start: 0.8200 (pm20) cc_final: 0.7991 (pt0) REVERT: I 39 GLU cc_start: 0.7807 (tt0) cc_final: 0.7502 (tt0) REVERT: I 107 GLN cc_start: 0.8255 (pm20) cc_final: 0.7969 (pt0) REVERT: J 39 GLU cc_start: 0.7689 (tt0) cc_final: 0.7417 (tt0) REVERT: K 39 GLU cc_start: 0.7903 (tt0) cc_final: 0.7589 (tt0) REVERT: L 39 GLU cc_start: 0.7628 (tt0) cc_final: 0.7318 (tt0) REVERT: L 107 GLN cc_start: 0.8244 (pm20) cc_final: 0.8019 (pt0) REVERT: M 39 GLU cc_start: 0.7798 (tt0) cc_final: 0.7506 (tt0) REVERT: M 97 ARG cc_start: 0.7228 (mtm-85) cc_final: 0.6941 (mtt180) REVERT: N 39 GLU cc_start: 0.7743 (tt0) cc_final: 0.7535 (tt0) REVERT: N 74 MET cc_start: 0.8842 (ttm) cc_final: 0.8506 (ttt) outliers start: 42 outliers final: 28 residues processed: 269 average time/residue: 0.1311 time to fit residues: 53.0400 Evaluate side-chains 251 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 163 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 186 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.138528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.127440 restraints weight = 19890.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.127983 restraints weight = 17781.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.128269 restraints weight = 15906.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.129087 restraints weight = 15177.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.129469 restraints weight = 13817.348| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18984 Z= 0.101 Angle : 0.450 5.510 25655 Z= 0.233 Chirality : 0.040 0.139 2989 Planarity : 0.003 0.040 3325 Dihedral : 4.061 31.928 2645 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.40 % Allowed : 13.32 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.17), residues: 2380 helix: -0.15 (0.15), residues: 1253 sheet: -2.37 (0.27), residues: 315 loop : -1.05 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 97 TYR 0.013 0.001 TYR F 183 PHE 0.005 0.001 PHE F 175 TRP 0.004 0.001 TRP G 174 HIS 0.001 0.000 HIS M 135 Details of bonding type rmsd covalent geometry : bond 0.00232 (18984) covalent geometry : angle 0.45017 (25655) hydrogen bonds : bond 0.02306 ( 763) hydrogen bonds : angle 3.87729 ( 2310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 TYR cc_start: 0.8651 (m-80) cc_final: 0.8359 (m-80) REVERT: F 26 SER cc_start: 0.9057 (m) cc_final: 0.8502 (t) REVERT: H 39 GLU cc_start: 0.7862 (tt0) cc_final: 0.7545 (tt0) REVERT: H 107 GLN cc_start: 0.8217 (pm20) cc_final: 0.7999 (pt0) REVERT: I 39 GLU cc_start: 0.7814 (tt0) cc_final: 0.7533 (tt0) REVERT: I 107 GLN cc_start: 0.8280 (pm20) cc_final: 0.8029 (pt0) REVERT: J 39 GLU cc_start: 0.7713 (tt0) cc_final: 0.7432 (tt0) REVERT: J 64 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7427 (tm-30) REVERT: K 39 GLU cc_start: 0.7905 (tt0) cc_final: 0.7589 (tt0) REVERT: L 39 GLU cc_start: 0.7685 (tt0) cc_final: 0.7380 (tt0) REVERT: L 107 GLN cc_start: 0.8247 (pm20) cc_final: 0.8029 (pt0) REVERT: M 39 GLU cc_start: 0.7856 (tt0) cc_final: 0.7572 (tt0) REVERT: M 97 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.6957 (mtt180) REVERT: N 39 GLU cc_start: 0.7783 (tt0) cc_final: 0.7558 (tt0) REVERT: N 74 MET cc_start: 0.8824 (ttm) cc_final: 0.8497 (ttt) outliers start: 47 outliers final: 30 residues processed: 256 average time/residue: 0.1302 time to fit residues: 50.2715 Evaluate side-chains 249 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 129 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 163 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.129731 restraints weight = 19880.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.129665 restraints weight = 22909.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.129816 restraints weight = 21688.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.129990 restraints weight = 19427.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.130797 restraints weight = 18427.086| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18984 Z= 0.092 Angle : 0.443 5.750 25655 Z= 0.230 Chirality : 0.040 0.136 2989 Planarity : 0.003 0.047 3325 Dihedral : 3.995 30.526 2645 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.30 % Allowed : 13.62 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2380 helix: 0.09 (0.15), residues: 1260 sheet: -2.21 (0.28), residues: 315 loop : -1.02 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 97 TYR 0.012 0.001 TYR F 183 PHE 0.006 0.001 PHE D 31 TRP 0.004 0.001 TRP B 174 HIS 0.001 0.000 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00210 (18984) covalent geometry : angle 0.44328 (25655) hydrogen bonds : bond 0.02196 ( 763) hydrogen bonds : angle 3.79127 ( 2310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8945 (m) cc_final: 0.8466 (t) REVERT: E 113 TYR cc_start: 0.8641 (m-80) cc_final: 0.8341 (m-80) REVERT: F 26 SER cc_start: 0.9048 (m) cc_final: 0.8497 (t) REVERT: H 39 GLU cc_start: 0.7836 (tt0) cc_final: 0.7503 (tt0) REVERT: I 39 GLU cc_start: 0.7808 (tt0) cc_final: 0.7527 (tt0) REVERT: I 107 GLN cc_start: 0.8216 (pm20) cc_final: 0.7975 (pt0) REVERT: J 39 GLU cc_start: 0.7691 (tt0) cc_final: 0.7418 (tt0) REVERT: K 39 GLU cc_start: 0.7845 (tt0) cc_final: 0.7559 (tt0) REVERT: L 39 GLU cc_start: 0.7702 (tt0) cc_final: 0.7392 (tt0) REVERT: L 107 GLN cc_start: 0.8207 (pm20) cc_final: 0.8006 (pt0) REVERT: M 39 GLU cc_start: 0.7808 (tt0) cc_final: 0.7539 (tt0) REVERT: M 97 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6906 (mtt180) REVERT: N 39 GLU cc_start: 0.7799 (tt0) cc_final: 0.7577 (tt0) REVERT: N 74 MET cc_start: 0.8790 (ttm) cc_final: 0.8433 (ttt) outliers start: 45 outliers final: 29 residues processed: 253 average time/residue: 0.1354 time to fit residues: 51.2909 Evaluate side-chains 248 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 218 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 158 optimal weight: 0.0870 chunk 132 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.139056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.126501 restraints weight = 19939.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.127686 restraints weight = 16398.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.128824 restraints weight = 14134.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.129478 restraints weight = 12565.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.130171 restraints weight = 11457.811| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18984 Z= 0.114 Angle : 0.466 7.610 25655 Z= 0.240 Chirality : 0.041 0.142 2989 Planarity : 0.003 0.031 3325 Dihedral : 4.092 31.952 2645 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.50 % Allowed : 13.67 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.17), residues: 2380 helix: 0.15 (0.15), residues: 1260 sheet: -2.19 (0.28), residues: 315 loop : -0.89 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 97 TYR 0.013 0.001 TYR F 183 PHE 0.005 0.001 PHE D 31 TRP 0.004 0.001 TRP B 174 HIS 0.001 0.000 HIS H 135 Details of bonding type rmsd covalent geometry : bond 0.00266 (18984) covalent geometry : angle 0.46577 (25655) hydrogen bonds : bond 0.02373 ( 763) hydrogen bonds : angle 3.85571 ( 2310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8993 (m) cc_final: 0.8491 (t) REVERT: E 113 TYR cc_start: 0.8700 (m-80) cc_final: 0.8382 (m-80) REVERT: F 26 SER cc_start: 0.9104 (m) cc_final: 0.8533 (t) REVERT: H 39 GLU cc_start: 0.7984 (tt0) cc_final: 0.7579 (tt0) REVERT: I 39 GLU cc_start: 0.7936 (tt0) cc_final: 0.7587 (tt0) REVERT: I 107 GLN cc_start: 0.8320 (pm20) cc_final: 0.8032 (pt0) REVERT: J 39 GLU cc_start: 0.7845 (tt0) cc_final: 0.7456 (tt0) REVERT: K 39 GLU cc_start: 0.7978 (tt0) cc_final: 0.7654 (tt0) REVERT: L 39 GLU cc_start: 0.7867 (tt0) cc_final: 0.7443 (tt0) REVERT: L 57 MET cc_start: 0.8608 (ttm) cc_final: 0.8366 (mtp) REVERT: L 107 GLN cc_start: 0.8327 (pm20) cc_final: 0.7968 (pt0) REVERT: M 39 GLU cc_start: 0.7992 (tt0) cc_final: 0.7622 (tt0) REVERT: M 97 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6888 (mtt180) REVERT: N 39 GLU cc_start: 0.7957 (tt0) cc_final: 0.7710 (tt0) REVERT: N 74 MET cc_start: 0.8783 (ttm) cc_final: 0.8411 (ttt) outliers start: 49 outliers final: 34 residues processed: 256 average time/residue: 0.1310 time to fit residues: 50.5483 Evaluate side-chains 254 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 162 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 68 optimal weight: 0.0270 chunk 235 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.141000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.129286 restraints weight = 19755.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.129334 restraints weight = 21074.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.129486 restraints weight = 20472.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.129753 restraints weight = 19895.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.129970 restraints weight = 17290.117| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18984 Z= 0.091 Angle : 0.449 8.464 25655 Z= 0.230 Chirality : 0.040 0.138 2989 Planarity : 0.003 0.031 3325 Dihedral : 3.986 31.337 2645 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.79 % Allowed : 14.44 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.18), residues: 2380 helix: 0.32 (0.15), residues: 1267 sheet: -2.04 (0.29), residues: 315 loop : -0.89 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 97 TYR 0.012 0.001 TYR F 183 PHE 0.004 0.001 PHE G 31 TRP 0.004 0.001 TRP B 174 HIS 0.001 0.000 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00208 (18984) covalent geometry : angle 0.44932 (25655) hydrogen bonds : bond 0.02166 ( 763) hydrogen bonds : angle 3.73151 ( 2310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8951 (m) cc_final: 0.8508 (t) REVERT: E 113 TYR cc_start: 0.8661 (m-80) cc_final: 0.8352 (m-80) REVERT: F 26 SER cc_start: 0.9045 (m) cc_final: 0.8498 (t) REVERT: G 93 MET cc_start: 0.8117 (tpp) cc_final: 0.7762 (mmm) REVERT: H 39 GLU cc_start: 0.7893 (tt0) cc_final: 0.7522 (tt0) REVERT: I 39 GLU cc_start: 0.7837 (tt0) cc_final: 0.7560 (tt0) REVERT: I 107 GLN cc_start: 0.8212 (pm20) cc_final: 0.7968 (pt0) REVERT: J 39 GLU cc_start: 0.7792 (tt0) cc_final: 0.7484 (tt0) REVERT: K 39 GLU cc_start: 0.7866 (tt0) cc_final: 0.7617 (tt0) REVERT: L 39 GLU cc_start: 0.7783 (tt0) cc_final: 0.7420 (tt0) REVERT: L 57 MET cc_start: 0.8508 (ttm) cc_final: 0.8297 (mtp) REVERT: L 107 GLN cc_start: 0.8239 (pm20) cc_final: 0.7954 (pt0) REVERT: M 39 GLU cc_start: 0.7858 (tt0) cc_final: 0.7566 (tt0) REVERT: M 97 ARG cc_start: 0.7090 (mtm-85) cc_final: 0.6838 (mtt180) REVERT: N 74 MET cc_start: 0.8757 (ttm) cc_final: 0.8410 (ttt) outliers start: 35 outliers final: 29 residues processed: 248 average time/residue: 0.1301 time to fit residues: 49.0002 Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 160 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.139503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.127030 restraints weight = 19807.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.127995 restraints weight = 16484.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.129061 restraints weight = 14228.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.129547 restraints weight = 12662.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.130224 restraints weight = 11667.842| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18984 Z= 0.112 Angle : 0.473 8.716 25655 Z= 0.240 Chirality : 0.041 0.141 2989 Planarity : 0.003 0.031 3325 Dihedral : 4.082 32.136 2645 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.63 % Allowed : 14.64 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.18), residues: 2380 helix: 0.35 (0.15), residues: 1267 sheet: -2.04 (0.29), residues: 315 loop : -0.83 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 97 TYR 0.013 0.001 TYR F 183 PHE 0.004 0.001 PHE E 175 TRP 0.005 0.001 TRP B 174 HIS 0.001 0.000 HIS H 135 Details of bonding type rmsd covalent geometry : bond 0.00261 (18984) covalent geometry : angle 0.47315 (25655) hydrogen bonds : bond 0.02321 ( 763) hydrogen bonds : angle 3.80676 ( 2310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8996 (m) cc_final: 0.8510 (t) REVERT: E 113 TYR cc_start: 0.8711 (m-80) cc_final: 0.8387 (m-80) REVERT: F 26 SER cc_start: 0.9111 (m) cc_final: 0.8549 (t) REVERT: H 39 GLU cc_start: 0.8002 (tt0) cc_final: 0.7561 (tt0) REVERT: I 39 GLU cc_start: 0.7960 (tt0) cc_final: 0.7612 (tt0) REVERT: I 107 GLN cc_start: 0.8289 (pm20) cc_final: 0.7985 (pt0) REVERT: J 39 GLU cc_start: 0.7882 (tt0) cc_final: 0.7548 (tt0) REVERT: K 39 GLU cc_start: 0.7988 (tt0) cc_final: 0.7667 (tt0) REVERT: K 107 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: L 39 GLU cc_start: 0.7893 (tt0) cc_final: 0.7469 (tt0) REVERT: L 107 GLN cc_start: 0.8349 (pm20) cc_final: 0.7991 (pt0) REVERT: M 39 GLU cc_start: 0.8011 (tt0) cc_final: 0.7643 (tt0) REVERT: M 97 ARG cc_start: 0.7173 (mtm-85) cc_final: 0.6915 (mtt180) REVERT: N 74 MET cc_start: 0.8763 (ttm) cc_final: 0.8363 (ttt) outliers start: 32 outliers final: 27 residues processed: 249 average time/residue: 0.1291 time to fit residues: 48.7162 Evaluate side-chains 253 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 6 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.135154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.122124 restraints weight = 20389.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.123441 restraints weight = 16973.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.124281 restraints weight = 14702.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.125172 restraints weight = 13133.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.125559 restraints weight = 12066.036| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18984 Z= 0.174 Angle : 0.550 8.991 25655 Z= 0.279 Chirality : 0.043 0.152 2989 Planarity : 0.003 0.032 3325 Dihedral : 4.583 36.340 2645 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.73 % Allowed : 14.90 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.17), residues: 2380 helix: 0.24 (0.15), residues: 1197 sheet: -2.06 (0.26), residues: 385 loop : -0.60 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 97 TYR 0.017 0.002 TYR B 91 PHE 0.007 0.001 PHE G 102 TRP 0.006 0.001 TRP B 174 HIS 0.002 0.001 HIS M 135 Details of bonding type rmsd covalent geometry : bond 0.00414 (18984) covalent geometry : angle 0.54985 (25655) hydrogen bonds : bond 0.02837 ( 763) hydrogen bonds : angle 4.14046 ( 2310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.71 seconds wall clock time: 42 minutes 58.09 seconds (2578.09 seconds total)