Starting phenix.real_space_refine on Mon May 19 09:58:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yd4_39164/05_2025/8yd4_39164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yd4_39164/05_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_39164/05_2025/8yd4_39164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yd4_39164/05_2025/8yd4_39164.map" model { file = "/net/cci-nas-00/data/ceres_data/8yd4_39164/05_2025/8yd4_39164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yd4_39164/05_2025/8yd4_39164.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "I" 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: C, B, E, D, G, F, H, K, J, M, L, N Time building chain proxies: 6.10, per 1000 atoms: 0.33 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: 4.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.51 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: 5.92 Time building geometry restraints manager: 5.18 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 37.060 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.001 0.000 TRP D 174 HIS 0.001 0.000 HIS E 123 PHE 0.002 0.000 PHE K 37 TYR 0.003 0.000 TYR E 91 ARG 0.002 0.000 ARG M 40 Details of bonding type rmsd hydrogen bonds : bond 0.25138 ( 763) hydrogen bonds : angle 7.76838 ( 2310) covalent geometry : bond 0.00151 (18984) covalent geometry : angle 0.39893 (25655) *********************** 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 : 1.800 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: 0.8160 (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: 0.7296 (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: 0.8206 (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: 0.3191 time to fit residues: 160.0430 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 : 1.963 ------------------------------------------------------------------------------- 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 200 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 A 142 GLN B 117 HIS B 139 GLN B 142 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 107 GLN J 171 HIS K 171 HIS L 171 HIS M 171 HIS N 107 GLN N 171 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.150509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.130528 restraints weight = 19959.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.133466 restraints weight = 14186.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.135343 restraints weight = 10958.619| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2251 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= 0.170 Angle : 0.512 6.090 25655 Z= 0.270 Chirality : 0.042 0.162 2989 Planarity : 0.004 0.027 3325 Dihedral : 4.277 36.917 2659 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 11.02 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.15), residues: 2380 helix: -1.60 (0.13), residues: 1246 sheet: -3.38 (0.23), residues: 322 loop : -2.02 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.004 0.001 HIS C 123 PHE 0.009 0.002 PHE B 102 TYR 0.010 0.001 TYR C 91 ARG 0.004 0.000 ARG H 40 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 763) hydrogen bonds : angle 4.62819 ( 2310) covalent geometry : bond 0.00400 (18984) covalent geometry : angle 0.51224 (25655) *********************** 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 296 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 1.803 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: A 109 LYS cc_start: 0.8539 (mttt) cc_final: 0.8269 (mttm) REVERT: C 26 SER cc_start: 0.8819 (m) cc_final: 0.8612 (t) REVERT: C 113 TYR cc_start: 0.8604 (m-80) cc_final: 0.8321 (m-80) REVERT: E 113 TYR cc_start: 0.8668 (m-80) cc_final: 0.8291 (m-80) REVERT: F 26 SER cc_start: 0.8757 (m) cc_final: 0.8527 (t) REVERT: G 26 SER cc_start: 0.8724 (m) cc_final: 0.8494 (t) REVERT: G 95 MET cc_start: 0.7782 (tmm) cc_final: 0.7530 (ptm) REVERT: H 39 GLU cc_start: 0.7892 (tt0) cc_final: 0.7499 (tt0) REVERT: H 107 GLN cc_start: 0.8243 (pm20) cc_final: 0.7923 (pt0) REVERT: I 39 GLU cc_start: 0.7772 (tt0) cc_final: 0.7424 (tt0) REVERT: I 107 GLN cc_start: 0.8387 (pm20) cc_final: 0.8082 (pt0) REVERT: J 74 MET cc_start: 0.8873 (ttm) cc_final: 0.8485 (ttt) REVERT: J 107 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: K 39 GLU cc_start: 0.7847 (tt0) cc_final: 0.7511 (tt0) REVERT: L 93 MET cc_start: 0.8500 (mtm) cc_final: 0.8256 (mtp) REVERT: L 107 GLN cc_start: 0.8331 (pm20) cc_final: 0.8002 (pt0) REVERT: M 39 GLU cc_start: 0.7854 (tt0) cc_final: 0.7457 (tt0) REVERT: N 74 MET cc_start: 0.8851 (ttm) cc_final: 0.8510 (ttt) REVERT: N 107 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8046 (pt0) outliers start: 32 outliers final: 15 residues processed: 287 average time/residue: 0.3249 time to fit residues: 137.5638 Evaluate side-chains 251 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 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 E residue 36 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 107 GLN Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 157 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 224 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 189 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN D 142 GLN E 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.155088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.135780 restraints weight = 19600.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.138683 restraints weight = 13839.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.140840 restraints weight = 10602.636| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2342 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= 0.087 Angle : 0.427 5.327 25655 Z= 0.221 Chirality : 0.039 0.139 2989 Planarity : 0.003 0.042 3325 Dihedral : 3.860 32.294 2647 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.94 % Allowed : 13.32 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.16), residues: 2380 helix: -0.92 (0.14), residues: 1253 sheet: -2.89 (0.25), residues: 315 loop : -1.58 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.002 0.000 HIS D 123 PHE 0.005 0.001 PHE E 31 TYR 0.013 0.001 TYR E 183 ARG 0.005 0.000 ARG K 97 Details of bonding type rmsd hydrogen bonds : bond 0.02566 ( 763) hydrogen bonds : angle 4.09964 ( 2310) covalent geometry : bond 0.00193 (18984) covalent geometry : angle 0.42697 (25655) *********************** 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 283 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 1.976 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: 0.8507 (mttt) cc_final: 0.8223 (mttm) REVERT: C 113 TYR cc_start: 0.8604 (m-80) cc_final: 0.8283 (m-80) REVERT: E 113 TYR cc_start: 0.8657 (m-80) cc_final: 0.8277 (m-80) REVERT: F 26 SER cc_start: 0.8743 (m) cc_final: 0.8486 (t) REVERT: H 39 GLU cc_start: 0.7803 (tt0) cc_final: 0.7414 (tt0) REVERT: H 107 GLN cc_start: 0.8123 (pm20) cc_final: 0.7863 (pt0) REVERT: I 39 GLU cc_start: 0.7769 (tt0) cc_final: 0.7389 (tt0) REVERT: I 107 GLN cc_start: 0.8260 (pm20) cc_final: 0.8034 (pt0) REVERT: J 74 MET cc_start: 0.8814 (ttm) cc_final: 0.8481 (ttt) REVERT: J 107 GLN cc_start: 0.8120 (pm20) cc_final: 0.7862 (pt0) REVERT: K 39 GLU cc_start: 0.7869 (tt0) cc_final: 0.7457 (tt0) REVERT: K 97 ARG cc_start: 0.7313 (mtm-85) cc_final: 0.7071 (mtt180) REVERT: L 107 GLN cc_start: 0.8212 (pm20) cc_final: 0.7910 (pt0) REVERT: M 39 GLU cc_start: 0.7787 (tt0) cc_final: 0.7409 (tt0) REVERT: N 39 GLU cc_start: 0.7764 (tt0) cc_final: 0.7493 (tt0) REVERT: N 74 MET cc_start: 0.8806 (ttm) cc_final: 0.8480 (ttt) outliers start: 38 outliers final: 24 residues processed: 269 average time/residue: 0.3140 time to fit residues: 125.8070 Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 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 C residue 145 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 42 ASN Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 145 VAL 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 165 ILE Chi-restraints excluded: chain G residue 166 GLU 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 180 optimal weight: 0.0670 chunk 48 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.7120 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.144540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.125143 restraints weight = 20031.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.127862 restraints weight = 14448.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.129858 restraints weight = 11279.062| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18984 Z= 0.135 Angle : 0.471 5.361 25655 Z= 0.243 Chirality : 0.041 0.147 2989 Planarity : 0.003 0.032 3325 Dihedral : 4.117 33.617 2647 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.19 % Allowed : 13.21 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2380 helix: -0.64 (0.14), residues: 1253 sheet: -2.75 (0.25), residues: 315 loop : -1.34 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 174 HIS 0.003 0.001 HIS M 135 PHE 0.006 0.001 PHE G 102 TYR 0.014 0.001 TYR C 183 ARG 0.005 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.02761 ( 763) hydrogen bonds : angle 4.12490 ( 2310) covalent geometry : bond 0.00320 (18984) covalent geometry : angle 0.47102 (25655) *********************** 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 272 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 2.052 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: 0.8691 (m-80) cc_final: 0.8368 (m-80) REVERT: F 26 SER cc_start: 0.8871 (m) cc_final: 0.8549 (t) REVERT: H 39 GLU cc_start: 0.7944 (tt0) cc_final: 0.7538 (tt0) REVERT: H 107 GLN cc_start: 0.8247 (pm20) cc_final: 0.7977 (pt0) REVERT: I 39 GLU cc_start: 0.7852 (tt0) cc_final: 0.7469 (tt0) REVERT: I 107 GLN cc_start: 0.8341 (pm20) cc_final: 0.8051 (pt0) REVERT: J 39 GLU cc_start: 0.7645 (tt0) cc_final: 0.7438 (tt0) REVERT: J 74 MET cc_start: 0.8813 (ttm) cc_final: 0.8424 (ttt) REVERT: J 107 GLN cc_start: 0.8229 (pm20) cc_final: 0.7985 (pt0) REVERT: K 39 GLU cc_start: 0.7965 (tt0) cc_final: 0.7558 (tt0) REVERT: K 97 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.7083 (mtt180) REVERT: L 107 GLN cc_start: 0.8288 (pm20) cc_final: 0.8017 (pt0) REVERT: M 39 GLU cc_start: 0.7875 (tt0) cc_final: 0.7533 (tt0) REVERT: N 39 GLU cc_start: 0.7848 (tt0) cc_final: 0.7552 (tt0) REVERT: N 74 MET cc_start: 0.8840 (ttm) cc_final: 0.8509 (ttt) outliers start: 43 outliers final: 22 residues processed: 253 average time/residue: 0.3174 time to fit residues: 120.1727 Evaluate side-chains 243 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 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 E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 165 ILE 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 L residue 202 THR Chi-restraints excluded: chain M residue 74 MET 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 106 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.139546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.127477 restraints weight = 20047.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.127830 restraints weight = 17431.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.127910 restraints weight = 15783.262| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2879 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= 0.112 Angle : 0.445 5.087 25655 Z= 0.230 Chirality : 0.040 0.144 2989 Planarity : 0.003 0.031 3325 Dihedral : 4.085 32.034 2647 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.24 % Allowed : 13.16 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2380 helix: -0.34 (0.15), residues: 1253 sheet: -2.51 (0.27), residues: 315 loop : -1.16 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.002 0.000 HIS M 135 PHE 0.006 0.001 PHE F 175 TYR 0.013 0.001 TYR F 183 ARG 0.003 0.000 ARG K 97 Details of bonding type rmsd hydrogen bonds : bond 0.02416 ( 763) hydrogen bonds : angle 3.96105 ( 2310) covalent geometry : bond 0.00262 (18984) covalent geometry : angle 0.44489 (25655) *********************** 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 278 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 1.886 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: B 26 SER cc_start: 0.8795 (m) cc_final: 0.8592 (t) REVERT: E 113 TYR cc_start: 0.8681 (m-80) cc_final: 0.8358 (m-80) REVERT: F 26 SER cc_start: 0.8868 (m) cc_final: 0.8563 (t) REVERT: H 39 GLU cc_start: 0.7927 (tt0) cc_final: 0.7513 (tt0) REVERT: H 107 GLN cc_start: 0.8273 (pm20) cc_final: 0.7989 (pt0) REVERT: I 39 GLU cc_start: 0.7932 (tt0) cc_final: 0.7520 (tt0) REVERT: I 107 GLN cc_start: 0.8312 (pm20) cc_final: 0.8011 (pt0) REVERT: J 39 GLU cc_start: 0.7790 (tt0) cc_final: 0.7515 (tt0) REVERT: J 74 MET cc_start: 0.8812 (ttm) cc_final: 0.8396 (ttt) REVERT: J 107 GLN cc_start: 0.8206 (pm20) cc_final: 0.7964 (pt0) REVERT: K 39 GLU cc_start: 0.7962 (tt0) cc_final: 0.7552 (tt0) REVERT: K 97 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7077 (mtt180) REVERT: K 107 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: L 107 GLN cc_start: 0.8260 (pm20) cc_final: 0.7998 (pt0) REVERT: M 39 GLU cc_start: 0.7924 (tt0) cc_final: 0.7565 (tt0) REVERT: N 39 GLU cc_start: 0.7905 (tt0) cc_final: 0.7632 (tt0) REVERT: N 74 MET cc_start: 0.8848 (ttm) cc_final: 0.8515 (ttt) outliers start: 44 outliers final: 27 residues processed: 260 average time/residue: 0.3059 time to fit residues: 119.8862 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 : 1.881 ------------------------------------------------------------------------------- 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 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 I residue 74 MET Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain L 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 114 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 112 optimal weight: 0.0970 chunk 159 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.137430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.124515 restraints weight = 20231.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.125581 restraints weight = 16949.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.126726 restraints weight = 14657.589| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18984 Z= 0.138 Angle : 0.476 7.625 25655 Z= 0.245 Chirality : 0.041 0.151 2989 Planarity : 0.003 0.030 3325 Dihedral : 4.213 32.769 2647 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.45 % Allowed : 13.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2380 helix: -0.26 (0.15), residues: 1253 sheet: -2.43 (0.27), residues: 315 loop : -1.08 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.003 0.001 HIS H 135 PHE 0.006 0.001 PHE F 175 TYR 0.014 0.001 TYR F 183 ARG 0.002 0.000 ARG K 97 Details of bonding type rmsd hydrogen bonds : bond 0.02546 ( 763) hydrogen bonds : angle 4.02524 ( 2310) covalent geometry : bond 0.00326 (18984) covalent geometry : angle 0.47577 (25655) *********************** 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 274 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 2.066 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: E 113 TYR cc_start: 0.8699 (m-80) cc_final: 0.8424 (m-80) REVERT: F 26 SER cc_start: 0.8907 (m) cc_final: 0.8576 (t) REVERT: H 39 GLU cc_start: 0.7961 (tt0) cc_final: 0.7534 (tt0) REVERT: H 107 GLN cc_start: 0.8320 (pm20) cc_final: 0.8030 (pt0) REVERT: I 39 GLU cc_start: 0.7935 (tt0) cc_final: 0.7538 (tt0) REVERT: I 107 GLN cc_start: 0.8370 (pm20) cc_final: 0.8001 (pt0) REVERT: J 39 GLU cc_start: 0.7822 (tt0) cc_final: 0.7538 (tt0) REVERT: J 74 MET cc_start: 0.8789 (ttm) cc_final: 0.8372 (ttt) REVERT: J 107 GLN cc_start: 0.8278 (pm20) cc_final: 0.8005 (pt0) REVERT: K 39 GLU cc_start: 0.7995 (tt0) cc_final: 0.7609 (tt0) REVERT: K 97 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.7173 (mtt180) REVERT: K 107 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7724 (pt0) REVERT: L 107 GLN cc_start: 0.8329 (pm20) cc_final: 0.8072 (pt0) REVERT: M 39 GLU cc_start: 0.7945 (tt0) cc_final: 0.7599 (tt0) REVERT: N 39 GLU cc_start: 0.7957 (tt0) cc_final: 0.7701 (tt0) REVERT: N 74 MET cc_start: 0.8863 (ttm) cc_final: 0.8531 (ttt) outliers start: 48 outliers final: 35 residues processed: 257 average time/residue: 0.3160 time to fit residues: 121.9258 Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 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 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 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain I 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 K residue 202 THR Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 74 MET 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 65 optimal weight: 0.0370 chunk 116 optimal weight: 5.9990 chunk 9 optimal weight: 0.0570 chunk 135 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 214 optimal weight: 8.9990 chunk 41 optimal weight: 0.0970 chunk 163 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 overall best weight: 0.4174 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.143094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.130700 restraints weight = 19611.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.130690 restraints weight = 21986.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.131425 restraints weight = 20824.434| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2976 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= 0.074 Angle : 0.422 8.424 25655 Z= 0.219 Chirality : 0.039 0.132 2989 Planarity : 0.003 0.030 3325 Dihedral : 3.863 29.956 2647 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.99 % Allowed : 14.13 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2380 helix: 0.17 (0.15), residues: 1260 sheet: -2.12 (0.28), residues: 315 loop : -1.02 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.001 0.000 HIS C 123 PHE 0.004 0.001 PHE D 31 TYR 0.010 0.001 TYR F 183 ARG 0.003 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.02042 ( 763) hydrogen bonds : angle 3.70336 ( 2310) covalent geometry : bond 0.00159 (18984) covalent geometry : angle 0.42193 (25655) *********************** 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 270 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 2.015 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 26 SER cc_start: 0.8946 (m) cc_final: 0.8485 (t) REVERT: C 113 TYR cc_start: 0.8538 (m-80) cc_final: 0.8181 (m-80) REVERT: E 113 TYR cc_start: 0.8608 (m-80) cc_final: 0.8296 (m-80) REVERT: E 183 TYR cc_start: 0.9134 (t80) cc_final: 0.8925 (t80) REVERT: F 26 SER cc_start: 0.8791 (m) cc_final: 0.8543 (t) REVERT: H 39 GLU cc_start: 0.7788 (tt0) cc_final: 0.7514 (tt0) REVERT: I 39 GLU cc_start: 0.7796 (tt0) cc_final: 0.7498 (tt0) REVERT: I 107 GLN cc_start: 0.8189 (pm20) cc_final: 0.7939 (pt0) REVERT: I 192 GLU cc_start: 0.8522 (tp30) cc_final: 0.8169 (mm-30) REVERT: J 39 GLU cc_start: 0.7750 (tt0) cc_final: 0.7410 (tt0) REVERT: K 39 GLU cc_start: 0.7848 (tt0) cc_final: 0.7528 (tt0) REVERT: K 97 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.7101 (mtt180) REVERT: K 107 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: L 107 GLN cc_start: 0.8135 (pm20) cc_final: 0.7934 (pt0) REVERT: M 39 GLU cc_start: 0.7794 (tt0) cc_final: 0.7559 (tt0) REVERT: N 39 GLU cc_start: 0.7816 (tt0) cc_final: 0.7608 (tt0) REVERT: N 74 MET cc_start: 0.8790 (ttm) cc_final: 0.8454 (ttt) outliers start: 39 outliers final: 23 residues processed: 256 average time/residue: 0.3255 time to fit residues: 124.0924 Evaluate side-chains 247 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 145 VAL Chi-restraints excluded: chain E residue 190 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 166 GLU Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain L residue 57 MET 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 91 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.140735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.128617 restraints weight = 19925.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.128470 restraints weight = 22473.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.128812 restraints weight = 21175.360| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18984 Z= 0.099 Angle : 0.448 8.198 25655 Z= 0.228 Chirality : 0.040 0.145 2989 Planarity : 0.003 0.028 3325 Dihedral : 3.929 31.318 2647 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.14 % Allowed : 14.39 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2380 helix: 0.32 (0.15), residues: 1260 sheet: -2.10 (0.28), residues: 315 loop : -0.89 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 174 HIS 0.002 0.000 HIS J 135 PHE 0.005 0.001 PHE F 175 TYR 0.012 0.001 TYR F 183 ARG 0.002 0.000 ARG K 97 Details of bonding type rmsd hydrogen bonds : bond 0.02234 ( 763) hydrogen bonds : angle 3.76021 ( 2310) covalent geometry : bond 0.00230 (18984) covalent geometry : angle 0.44830 (25655) *********************** 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 265 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 1.953 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 26 SER cc_start: 0.8948 (m) cc_final: 0.8474 (t) REVERT: C 113 TYR cc_start: 0.8561 (m-80) cc_final: 0.8205 (m-80) REVERT: E 113 TYR cc_start: 0.8632 (m-80) cc_final: 0.8333 (m-80) REVERT: F 26 SER cc_start: 0.8827 (m) cc_final: 0.8539 (t) REVERT: G 93 MET cc_start: 0.8101 (tpp) cc_final: 0.6974 (tpp) REVERT: H 39 GLU cc_start: 0.7812 (tt0) cc_final: 0.7540 (tt0) REVERT: I 39 GLU cc_start: 0.7817 (tt0) cc_final: 0.7537 (tt0) REVERT: I 107 GLN cc_start: 0.8230 (pm20) cc_final: 0.7981 (pt0) REVERT: J 39 GLU cc_start: 0.7791 (tt0) cc_final: 0.7451 (tt0) REVERT: K 39 GLU cc_start: 0.7885 (tt0) cc_final: 0.7585 (tt0) REVERT: K 107 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: M 39 GLU cc_start: 0.7854 (tt0) cc_final: 0.7586 (tt0) REVERT: N 74 MET cc_start: 0.8780 (ttm) cc_final: 0.8447 (ttt) outliers start: 42 outliers final: 29 residues processed: 251 average time/residue: 0.3193 time to fit residues: 120.2636 Evaluate side-chains 251 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 182 GLU 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 165 ILE 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 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 57 MET Chi-restraints excluded: chain L residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 119 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.138304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.125433 restraints weight = 19979.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.126531 restraints weight = 16544.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.127646 restraints weight = 14310.870| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18984 Z= 0.123 Angle : 0.476 8.034 25655 Z= 0.243 Chirality : 0.041 0.144 2989 Planarity : 0.003 0.029 3325 Dihedral : 4.166 32.314 2647 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.04 % Allowed : 14.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2380 helix: 0.33 (0.15), residues: 1253 sheet: -2.11 (0.28), residues: 315 loop : -0.72 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.003 0.001 HIS J 135 PHE 0.005 0.001 PHE F 31 TYR 0.020 0.001 TYR E 183 ARG 0.002 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.02439 ( 763) hydrogen bonds : angle 3.88769 ( 2310) covalent geometry : bond 0.00289 (18984) covalent geometry : angle 0.47569 (25655) *********************** 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 268 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 1.950 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: A 26 SER cc_start: 0.9013 (m) cc_final: 0.8523 (t) REVERT: E 113 TYR cc_start: 0.8704 (m-80) cc_final: 0.8387 (m-80) REVERT: F 26 SER cc_start: 0.8848 (m) cc_final: 0.8543 (t) REVERT: G 93 MET cc_start: 0.8167 (tpp) cc_final: 0.7114 (tpp) REVERT: H 39 GLU cc_start: 0.7972 (tt0) cc_final: 0.7592 (tt0) REVERT: I 39 GLU cc_start: 0.7957 (tt0) cc_final: 0.7592 (tt0) REVERT: I 107 GLN cc_start: 0.8322 (pm20) cc_final: 0.8029 (pt0) REVERT: J 39 GLU cc_start: 0.7892 (tt0) cc_final: 0.7513 (tt0) REVERT: K 39 GLU cc_start: 0.8003 (tt0) cc_final: 0.7665 (tt0) REVERT: K 107 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: M 39 GLU cc_start: 0.7996 (tt0) cc_final: 0.7644 (tt0) REVERT: N 74 MET cc_start: 0.8802 (ttm) cc_final: 0.8443 (ttt) outliers start: 40 outliers final: 31 residues processed: 254 average time/residue: 0.3297 time to fit residues: 125.1120 Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 D residue 182 GLU 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 E residue 191 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 165 ILE 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 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 K residue 202 THR Chi-restraints excluded: chain L 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 167 optimal weight: 6.9990 chunk 82 optimal weight: 0.0870 chunk 103 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 209 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.137355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.125048 restraints weight = 19946.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.125734 restraints weight = 17248.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.125929 restraints weight = 15028.947| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18984 Z= 0.136 Angle : 0.492 9.534 25655 Z= 0.251 Chirality : 0.041 0.145 2989 Planarity : 0.003 0.028 3325 Dihedral : 4.246 32.679 2647 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.04 % Allowed : 14.74 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2380 helix: 0.28 (0.15), residues: 1260 sheet: -2.13 (0.28), residues: 315 loop : -0.73 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.003 0.001 HIS J 135 PHE 0.006 0.001 PHE F 175 TYR 0.019 0.001 TYR E 183 ARG 0.005 0.000 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.02493 ( 763) hydrogen bonds : angle 3.93615 ( 2310) covalent geometry : bond 0.00321 (18984) covalent geometry : angle 0.49211 (25655) ********************** 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 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 2.042 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: 0.8717 (m-80) cc_final: 0.8438 (m-80) REVERT: F 26 SER cc_start: 0.8865 (m) cc_final: 0.8554 (t) REVERT: G 93 MET cc_start: 0.8147 (tpp) cc_final: 0.7144 (tpp) REVERT: H 39 GLU cc_start: 0.7984 (tt0) cc_final: 0.7618 (tt0) REVERT: I 39 GLU cc_start: 0.7960 (tt0) cc_final: 0.7614 (tt0) REVERT: I 107 GLN cc_start: 0.8315 (pm20) cc_final: 0.8002 (pt0) REVERT: J 39 GLU cc_start: 0.7961 (tt0) cc_final: 0.7626 (tt0) REVERT: K 39 GLU cc_start: 0.8000 (tt0) cc_final: 0.7660 (tt0) REVERT: K 107 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: M 39 GLU cc_start: 0.8006 (tt0) cc_final: 0.7632 (tt0) REVERT: N 74 MET cc_start: 0.8802 (ttm) cc_final: 0.8445 (ttt) outliers start: 40 outliers final: 31 residues processed: 250 average time/residue: 0.3307 time to fit residues: 124.6425 Evaluate side-chains 253 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 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 D residue 182 GLU 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 E residue 191 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 165 ILE 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 G residue 190 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 74 MET 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 72 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 140 optimal weight: 0.0020 chunk 209 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.137346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.125059 restraints weight = 20111.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.126046 restraints weight = 16459.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.126196 restraints weight = 13371.544| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18984 Z= 0.136 Angle : 0.496 9.645 25655 Z= 0.254 Chirality : 0.042 0.146 2989 Planarity : 0.003 0.028 3325 Dihedral : 4.329 33.170 2647 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.89 % Allowed : 14.85 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 2380 helix: 0.32 (0.15), residues: 1239 sheet: -2.17 (0.28), residues: 315 loop : -0.74 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.003 0.001 HIS H 135 PHE 0.006 0.001 PHE E 175 TYR 0.019 0.001 TYR E 183 ARG 0.002 0.000 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.02529 ( 763) hydrogen bonds : angle 3.96165 ( 2310) covalent geometry : bond 0.00322 (18984) covalent geometry : angle 0.49613 (25655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4862.81 seconds wall clock time: 86 minutes 15.51 seconds (5175.51 seconds total)