Starting phenix.real_space_refine on Mon Jun 16 06:50:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yd4_39164/06_2025/8yd4_39164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yd4_39164/06_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_39164/06_2025/8yd4_39164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yd4_39164/06_2025/8yd4_39164.map" model { file = "/net/cci-nas-00/data/ceres_data/8yd4_39164/06_2025/8yd4_39164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yd4_39164/06_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-5710/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: 5.82, per 1000 atoms: 0.31 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: 4.00 Conformation dependent library (CDL) restraints added in 2.2 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: 2.12 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: 5.84 Time building geometry restraints manager: 4.84 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: 0.15 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 35.550 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- 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 : 1.900 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: 0.3193 time to fit residues: 160.7665 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 : 2.120 ------------------------------------------------------------------------------- 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 = 0.150510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.130755 restraints weight = 19959.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.133460 restraints weight = 14163.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.135424 restraints weight = 10932.088| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 4.62818 ( 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 : 1.961 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: 0.8611 (t) REVERT: C 113 TYR cc_start: 0.8604 (m-80) cc_final: 0.8319 (m-80) REVERT: E 113 TYR cc_start: 0.8668 (m-80) cc_final: 0.8289 (m-80) REVERT: F 26 SER cc_start: 0.8757 (m) cc_final: 0.8526 (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: 0.7529 (ptm) REVERT: H 39 GLU cc_start: 0.7890 (tt0) cc_final: 0.7499 (tt0) REVERT: H 107 GLN cc_start: 0.8244 (pm20) cc_final: 0.7927 (pt0) REVERT: I 39 GLU cc_start: 0.7770 (tt0) cc_final: 0.7424 (tt0) REVERT: I 107 GLN cc_start: 0.8386 (pm20) cc_final: 0.8082 (pt0) REVERT: J 74 MET cc_start: 0.8874 (ttm) cc_final: 0.8486 (ttt) REVERT: J 107 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: K 39 GLU cc_start: 0.7843 (tt0) cc_final: 0.7510 (tt0) REVERT: L 93 MET cc_start: 0.8501 (mtm) cc_final: 0.8259 (mtp) REVERT: L 107 GLN cc_start: 0.8329 (pm20) cc_final: 0.8001 (pt0) REVERT: M 39 GLU cc_start: 0.7852 (tt0) cc_final: 0.7457 (tt0) REVERT: N 74 MET cc_start: 0.8851 (ttm) cc_final: 0.8512 (ttt) REVERT: N 107 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8048 (pt0) outliers start: 32 outliers final: 15 residues processed: 287 average time/residue: 0.3348 time to fit residues: 141.3958 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 : 1.805 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.150939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.131337 restraints weight = 19744.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.134259 restraints weight = 13916.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.136385 restraints weight = 10688.395| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 18984 Z= 0.110 Angle : 0.449 5.674 25655 Z= 0.232 Chirality : 0.040 0.143 2989 Planarity : 0.003 0.042 3325 Dihedral : 4.023 33.678 2647 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.94 % Allowed : 13.47 % 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: -2.36 (0.16), residues: 2380 helix: -0.98 (0.14), residues: 1253 sheet: -2.96 (0.25), residues: 315 loop : -1.60 (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 I 135 PHE 0.005 0.001 PHE B 31 TYR 0.014 0.001 TYR F 183 ARG 0.005 0.000 ARG K 97 Details of bonding type rmsd hydrogen bonds : bond 0.02728 ( 763) hydrogen bonds : angle 4.18805 ( 2310) covalent geometry : bond 0.00254 (18984) covalent geometry : angle 0.44882 (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 285 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 2.103 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: 0.8521 (mttt) cc_final: 0.8259 (mttm) REVERT: B 113 TYR cc_start: 0.8622 (m-80) cc_final: 0.8416 (m-80) REVERT: C 26 SER cc_start: 0.8786 (m) cc_final: 0.8576 (t) REVERT: C 113 TYR cc_start: 0.8628 (m-80) cc_final: 0.8309 (m-80) REVERT: E 113 TYR cc_start: 0.8683 (m-80) cc_final: 0.8355 (m-80) REVERT: F 26 SER cc_start: 0.8811 (m) cc_final: 0.8522 (t) REVERT: G 26 SER cc_start: 0.8720 (m) cc_final: 0.8496 (t) REVERT: H 39 GLU cc_start: 0.7841 (tt0) cc_final: 0.7435 (tt0) REVERT: H 107 GLN cc_start: 0.8225 (pm20) cc_final: 0.7978 (pt0) REVERT: I 39 GLU cc_start: 0.7804 (tt0) cc_final: 0.7428 (tt0) REVERT: I 107 GLN cc_start: 0.8312 (pm20) cc_final: 0.8047 (pt0) REVERT: J 74 MET cc_start: 0.8823 (ttm) cc_final: 0.8519 (ttt) REVERT: J 107 GLN cc_start: 0.8198 (pm20) cc_final: 0.7949 (pt0) REVERT: K 39 GLU cc_start: 0.7917 (tt0) cc_final: 0.7521 (tt0) REVERT: K 74 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8117 (ttt) REVERT: K 97 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.7082 (mtt180) REVERT: L 39 GLU cc_start: 0.7442 (tt0) cc_final: 0.7227 (tt0) REVERT: L 107 GLN cc_start: 0.8290 (pm20) cc_final: 0.7990 (pt0) REVERT: M 39 GLU cc_start: 0.7817 (tt0) cc_final: 0.7437 (tt0) REVERT: N 39 GLU cc_start: 0.7788 (tt0) cc_final: 0.7496 (tt0) REVERT: N 74 MET cc_start: 0.8831 (ttm) cc_final: 0.8505 (ttt) outliers start: 38 outliers final: 23 residues processed: 272 average time/residue: 0.3335 time to fit residues: 134.7158 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 : 1.867 ------------------------------------------------------------------------------- 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 C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 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 K residue 74 MET Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 180 optimal weight: 0.0470 chunk 48 optimal weight: 0.0670 chunk 111 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.152617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.134189 restraints weight = 19805.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.136792 restraints weight = 13967.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.138862 restraints weight = 10798.912| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18984 Z= 0.095 Angle : 0.430 8.650 25655 Z= 0.222 Chirality : 0.040 0.135 2989 Planarity : 0.003 0.033 3325 Dihedral : 3.888 31.318 2647 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.09 % Allowed : 13.06 % Favored : 84.85 % 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: -1.84 (0.17), residues: 2380 helix: -0.58 (0.14), residues: 1253 sheet: -2.68 (0.26), residues: 315 loop : -1.34 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.002 0.000 HIS E 123 PHE 0.004 0.001 PHE B 31 TYR 0.011 0.001 TYR E 183 ARG 0.003 0.000 ARG K 97 Details of bonding type rmsd hydrogen bonds : bond 0.02377 ( 763) hydrogen bonds : angle 3.95827 ( 2310) covalent geometry : bond 0.00216 (18984) covalent geometry : angle 0.43043 (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 282 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 2.043 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: C 113 TYR cc_start: 0.8620 (m-80) cc_final: 0.8311 (m-80) REVERT: E 113 TYR cc_start: 0.8672 (m-80) cc_final: 0.8346 (m-80) REVERT: F 26 SER cc_start: 0.8798 (m) cc_final: 0.8537 (t) REVERT: H 39 GLU cc_start: 0.7839 (tt0) cc_final: 0.7449 (tt0) REVERT: H 107 GLN cc_start: 0.8187 (pm20) cc_final: 0.7962 (pt0) REVERT: I 39 GLU cc_start: 0.7814 (tt0) cc_final: 0.7427 (tt0) REVERT: I 107 GLN cc_start: 0.8284 (pm20) cc_final: 0.8010 (pt0) REVERT: J 107 GLN cc_start: 0.8160 (pm20) cc_final: 0.7921 (pt0) REVERT: K 39 GLU cc_start: 0.7920 (tt0) cc_final: 0.7536 (tt0) REVERT: K 107 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: L 39 GLU cc_start: 0.7589 (tt0) cc_final: 0.7325 (tt0) REVERT: L 107 GLN cc_start: 0.8269 (pm20) cc_final: 0.8012 (pt0) REVERT: M 39 GLU cc_start: 0.7836 (tt0) cc_final: 0.7454 (tt0) REVERT: N 39 GLU cc_start: 0.7800 (tt0) cc_final: 0.7510 (tt0) REVERT: N 74 MET cc_start: 0.8827 (ttm) cc_final: 0.8485 (ttt) outliers start: 41 outliers final: 22 residues processed: 265 average time/residue: 0.3289 time to fit residues: 130.5068 Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain K residue 107 GLN 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: 1.9990 chunk 115 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 202 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.137955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3265 r_free = 0.3265 target = 0.127113 restraints weight = 20115.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.126787 restraints weight = 18942.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.126777 restraints weight = 18309.574| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2856 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= 0.117 Angle : 0.455 6.099 25655 Z= 0.235 Chirality : 0.041 0.148 2989 Planarity : 0.003 0.029 3325 Dihedral : 4.061 32.354 2647 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.04 % Allowed : 13.62 % Favored : 84.34 % 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: -1.51 (0.17), residues: 2380 helix: -0.31 (0.15), residues: 1253 sheet: -2.51 (0.27), residues: 315 loop : -1.19 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.002 0.001 HIS M 135 PHE 0.006 0.001 PHE F 175 TYR 0.013 0.001 TYR F 183 ARG 0.002 0.000 ARG K 97 Details of bonding type rmsd hydrogen bonds : bond 0.02470 ( 763) hydrogen bonds : angle 3.95657 ( 2310) covalent geometry : bond 0.00274 (18984) covalent geometry : angle 0.45544 (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 269 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 1.848 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: C 113 TYR cc_start: 0.8557 (m-80) cc_final: 0.8229 (m-80) REVERT: E 113 TYR cc_start: 0.8634 (m-80) cc_final: 0.8318 (m-80) REVERT: F 26 SER cc_start: 0.8837 (m) cc_final: 0.8517 (t) REVERT: H 39 GLU cc_start: 0.7840 (tt0) cc_final: 0.7486 (tt0) REVERT: H 107 GLN cc_start: 0.8185 (pm20) cc_final: 0.7955 (pt0) REVERT: I 39 GLU cc_start: 0.7845 (tt0) cc_final: 0.7489 (tt0) REVERT: I 107 GLN cc_start: 0.8301 (pm20) cc_final: 0.8020 (pt0) REVERT: J 107 GLN cc_start: 0.8183 (pm20) cc_final: 0.7963 (pt0) REVERT: K 39 GLU cc_start: 0.7895 (tt0) cc_final: 0.7539 (tt0) REVERT: K 107 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: L 39 GLU cc_start: 0.7614 (tt0) cc_final: 0.7323 (tt0) REVERT: L 107 GLN cc_start: 0.8216 (pm20) cc_final: 0.7999 (pt0) REVERT: M 39 GLU cc_start: 0.7836 (tt0) cc_final: 0.7522 (tt0) REVERT: N 39 GLU cc_start: 0.7791 (tt0) cc_final: 0.7544 (tt0) REVERT: N 74 MET cc_start: 0.8832 (ttm) cc_final: 0.8521 (ttt) outliers start: 40 outliers final: 27 residues processed: 253 average time/residue: 0.3169 time to fit residues: 120.8073 Evaluate side-chains 249 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 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 165 ILE 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 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 J residue 202 THR Chi-restraints excluded: chain K residue 107 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 114 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN G 123 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.131517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.122843 restraints weight = 20629.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.122341 restraints weight = 29954.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.117291 restraints weight = 34054.637| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18984 Z= 0.220 Angle : 0.577 7.403 25655 Z= 0.298 Chirality : 0.045 0.166 2989 Planarity : 0.004 0.033 3325 Dihedral : 4.821 39.257 2647 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.76 % Allowed : 14.49 % Favored : 82.76 % 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: -1.69 (0.17), residues: 2380 helix: -0.50 (0.14), residues: 1218 sheet: -2.52 (0.24), residues: 385 loop : -1.03 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 174 HIS 0.005 0.001 HIS H 135 PHE 0.011 0.002 PHE F 102 TYR 0.021 0.002 TYR B 91 ARG 0.004 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 763) hydrogen bonds : angle 4.43759 ( 2310) covalent geometry : bond 0.00524 (18984) covalent geometry : angle 0.57690 (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 283 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 2.041 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: B 113 TYR cc_start: 0.8741 (m-80) cc_final: 0.8535 (m-80) REVERT: H 107 GLN cc_start: 0.8461 (pm20) cc_final: 0.8141 (pt0) REVERT: I 39 GLU cc_start: 0.8042 (tt0) cc_final: 0.7689 (tt0) REVERT: I 107 GLN cc_start: 0.8449 (pm20) cc_final: 0.8086 (pt0) REVERT: J 107 GLN cc_start: 0.8353 (pm20) cc_final: 0.8068 (pt0) REVERT: K 39 GLU cc_start: 0.8038 (tt0) cc_final: 0.7686 (tt0) REVERT: L 39 GLU cc_start: 0.7819 (tt0) cc_final: 0.7438 (tt0) REVERT: L 107 GLN cc_start: 0.8422 (pm20) cc_final: 0.8154 (pt0) REVERT: M 39 GLU cc_start: 0.8026 (tt0) cc_final: 0.7686 (tt0) REVERT: N 39 GLU cc_start: 0.7986 (tt0) cc_final: 0.7760 (tt0) REVERT: N 74 MET cc_start: 0.8863 (ttm) cc_final: 0.8570 (ttt) outliers start: 54 outliers final: 37 residues processed: 265 average time/residue: 0.3050 time to fit residues: 124.0477 Evaluate side-chains 262 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 B residue 26 SER 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 D residue 165 ILE 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 202 THR Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 74 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 65 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 205 optimal weight: 0.0060 chunk 186 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS H 135 HIS I 135 HIS J 135 HIS K 135 HIS L 135 HIS M 135 HIS N 135 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.121657 restraints weight = 20296.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.120597 restraints weight = 28325.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.120842 restraints weight = 29099.618| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18984 Z= 0.184 Angle : 0.523 7.019 25655 Z= 0.273 Chirality : 0.043 0.151 2989 Planarity : 0.003 0.034 3325 Dihedral : 4.734 37.843 2647 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.65 % Allowed : 14.95 % Favored : 82.40 % 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: -0.41 (0.15), residues: 1197 sheet: -2.25 (0.27), residues: 336 loop : -1.07 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 174 HIS 0.006 0.001 HIS J 135 PHE 0.009 0.001 PHE B 102 TYR 0.016 0.001 TYR F 183 ARG 0.004 0.000 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 763) hydrogen bonds : angle 4.28759 ( 2310) covalent geometry : bond 0.00438 (18984) covalent geometry : angle 0.52267 (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 283 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 1.902 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: B 122 MET cc_start: 0.6793 (tpt) cc_final: 0.6176 (tpt) REVERT: F 26 SER cc_start: 0.8931 (m) cc_final: 0.8542 (t) REVERT: H 39 GLU cc_start: 0.7843 (tt0) cc_final: 0.7576 (tt0) REVERT: H 107 GLN cc_start: 0.8284 (pm20) cc_final: 0.8057 (pt0) REVERT: I 39 GLU cc_start: 0.7838 (tt0) cc_final: 0.7537 (tt0) REVERT: K 39 GLU cc_start: 0.7901 (tt0) cc_final: 0.7598 (tt0) REVERT: K 94 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8779 (mm110) REVERT: K 107 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: L 39 GLU cc_start: 0.7709 (tt0) cc_final: 0.7354 (tt0) REVERT: L 107 GLN cc_start: 0.8324 (pm20) cc_final: 0.8121 (pt0) REVERT: M 39 GLU cc_start: 0.7867 (tt0) cc_final: 0.7577 (tt0) REVERT: N 39 GLU cc_start: 0.7806 (tt0) cc_final: 0.7599 (tt0) REVERT: N 74 MET cc_start: 0.8852 (ttm) cc_final: 0.8568 (ttt) outliers start: 52 outliers final: 37 residues processed: 266 average time/residue: 0.3086 time to fit residues: 126.2421 Evaluate side-chains 268 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain E residue 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 124 GLN Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 202 THR 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 73 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N 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: 2.9990 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 224 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 HIS I 135 HIS J 135 HIS K 135 HIS L 135 HIS M 135 HIS N 135 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.137758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.128492 restraints weight = 20035.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.127815 restraints weight = 29608.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.128253 restraints weight = 30116.061| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18984 Z= 0.091 Angle : 0.445 8.148 25655 Z= 0.233 Chirality : 0.040 0.138 2989 Planarity : 0.003 0.032 3325 Dihedral : 4.214 31.115 2647 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.09 % Allowed : 16.12 % Favored : 81.79 % 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: -1.09 (0.17), residues: 2380 helix: 0.00 (0.15), residues: 1211 sheet: -2.32 (0.25), residues: 385 loop : -0.72 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 174 HIS 0.006 0.001 HIS J 135 PHE 0.005 0.001 PHE F 31 TYR 0.012 0.001 TYR F 183 ARG 0.002 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.02258 ( 763) hydrogen bonds : angle 3.91205 ( 2310) covalent geometry : bond 0.00205 (18984) covalent geometry : angle 0.44515 (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 276 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 2.120 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: 0.8936 (m) cc_final: 0.8475 (t) REVERT: E 113 TYR cc_start: 0.8639 (m-80) cc_final: 0.8355 (m-80) REVERT: E 183 TYR cc_start: 0.9109 (t80) cc_final: 0.8885 (t80) REVERT: F 26 SER cc_start: 0.8804 (m) cc_final: 0.8522 (t) REVERT: H 39 GLU cc_start: 0.7806 (tt0) cc_final: 0.7511 (tt0) REVERT: H 107 GLN cc_start: 0.8162 (pm20) cc_final: 0.7955 (pt0) REVERT: I 39 GLU cc_start: 0.7794 (tt0) cc_final: 0.7550 (tt0) REVERT: J 39 GLU cc_start: 0.7745 (tt0) cc_final: 0.7444 (tt0) REVERT: K 39 GLU cc_start: 0.7851 (tt0) cc_final: 0.7616 (tt0) REVERT: K 107 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: L 39 GLU cc_start: 0.7716 (tt0) cc_final: 0.7366 (tt0) REVERT: M 39 GLU cc_start: 0.7777 (tt0) cc_final: 0.7568 (tt0) REVERT: N 74 MET cc_start: 0.8767 (ttm) cc_final: 0.8456 (ttt) outliers start: 41 outliers final: 30 residues processed: 262 average time/residue: 0.3113 time to fit residues: 123.5660 Evaluate side-chains 257 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain E residue 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 191 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 119 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.136529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.126517 restraints weight = 20047.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.125591 restraints weight = 29169.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.126514 restraints weight = 26616.768| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3349 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= 0.117 Angle : 0.469 8.829 25655 Z= 0.243 Chirality : 0.041 0.145 2989 Planarity : 0.003 0.033 3325 Dihedral : 4.263 32.246 2647 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.24 % Allowed : 16.02 % Favored : 81.73 % 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: -0.95 (0.17), residues: 2380 helix: 0.13 (0.15), residues: 1190 sheet: -2.22 (0.25), residues: 385 loop : -0.69 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 174 HIS 0.002 0.000 HIS F 123 PHE 0.006 0.001 PHE F 175 TYR 0.015 0.001 TYR F 183 ARG 0.002 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.02420 ( 763) hydrogen bonds : angle 3.94948 ( 2310) covalent geometry : bond 0.00272 (18984) covalent geometry : angle 0.46897 (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 266 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 2.018 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: 0.8952 (m) cc_final: 0.8493 (t) REVERT: B 122 MET cc_start: 0.6790 (tpt) cc_final: 0.6269 (tpt) REVERT: E 113 TYR cc_start: 0.8665 (m-80) cc_final: 0.8362 (m-80) REVERT: F 26 SER cc_start: 0.8842 (m) cc_final: 0.8519 (t) REVERT: F 93 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7384 (mmm) REVERT: H 39 GLU cc_start: 0.7831 (tt0) cc_final: 0.7534 (tt0) REVERT: H 107 GLN cc_start: 0.8195 (pm20) cc_final: 0.7982 (pt0) REVERT: I 39 GLU cc_start: 0.7835 (tt0) cc_final: 0.7579 (tt0) REVERT: J 39 GLU cc_start: 0.7810 (tt0) cc_final: 0.7538 (tt0) REVERT: K 39 GLU cc_start: 0.7865 (tt0) cc_final: 0.7624 (tt0) REVERT: K 107 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: L 39 GLU cc_start: 0.7756 (tt0) cc_final: 0.7400 (tt0) REVERT: M 39 GLU cc_start: 0.7845 (tt0) cc_final: 0.7610 (tt0) REVERT: N 74 MET cc_start: 0.8784 (ttm) cc_final: 0.8462 (ttt) outliers start: 44 outliers final: 35 residues processed: 251 average time/residue: 0.3236 time to fit residues: 122.8047 Evaluate side-chains 260 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain 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 93 MET 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 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 73 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain N residue 57 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 167 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.132373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.120872 restraints weight = 20280.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.121066 restraints weight = 19491.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.121167 restraints weight = 17690.679| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 18984 Z= 0.198 Angle : 0.555 10.235 25655 Z= 0.286 Chirality : 0.044 0.154 2989 Planarity : 0.003 0.035 3325 Dihedral : 4.704 36.365 2647 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.14 % Allowed : 16.33 % Favored : 81.53 % 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: -1.12 (0.17), residues: 2380 helix: -0.21 (0.15), residues: 1211 sheet: -2.05 (0.28), residues: 336 loop : -0.67 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 174 HIS 0.002 0.001 HIS F 123 PHE 0.010 0.001 PHE D 102 TYR 0.019 0.002 TYR B 91 ARG 0.002 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 763) hydrogen bonds : angle 4.25624 ( 2310) covalent geometry : bond 0.00474 (18984) covalent geometry : angle 0.55463 (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 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 1.890 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 122 MET cc_start: 0.6761 (tpt) cc_final: 0.6110 (tpt) REVERT: C 113 TYR cc_start: 0.8639 (m-80) cc_final: 0.8308 (m-80) REVERT: D 99 MET cc_start: 0.8951 (mmm) cc_final: 0.8717 (tpt) REVERT: F 26 SER cc_start: 0.8942 (m) cc_final: 0.8559 (t) REVERT: F 93 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7446 (mmm) REVERT: H 107 GLN cc_start: 0.8294 (pm20) cc_final: 0.8038 (pt0) REVERT: I 39 GLU cc_start: 0.7909 (tt0) cc_final: 0.7554 (tt0) REVERT: J 39 GLU cc_start: 0.7911 (tt0) cc_final: 0.7584 (tt0) REVERT: K 39 GLU cc_start: 0.7948 (tt0) cc_final: 0.7544 (tt0) REVERT: K 107 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: L 39 GLU cc_start: 0.7805 (tt0) cc_final: 0.7415 (tt0) REVERT: M 39 GLU cc_start: 0.7948 (tt0) cc_final: 0.7662 (tt0) REVERT: N 74 MET cc_start: 0.8842 (ttm) cc_final: 0.8585 (ttt) outliers start: 42 outliers final: 37 residues processed: 258 average time/residue: 0.3178 time to fit residues: 124.6439 Evaluate side-chains 268 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain 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 93 MET 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 191 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain J residue 74 MET 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 73 THR Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain N residue 57 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 72 optimal weight: 0.0040 chunk 218 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 HIS I 135 HIS J 135 HIS K 135 HIS L 135 HIS M 135 HIS N 135 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.138683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.126235 restraints weight = 20025.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.126066 restraints weight = 22985.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.126675 restraints weight = 21376.346| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3439 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= 0.097 Angle : 0.465 8.931 25655 Z= 0.241 Chirality : 0.040 0.141 2989 Planarity : 0.003 0.032 3325 Dihedral : 4.252 31.166 2647 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.09 % Allowed : 16.43 % Favored : 81.48 % 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: -0.79 (0.18), residues: 2380 helix: 0.22 (0.15), residues: 1211 sheet: -2.18 (0.26), residues: 385 loop : -0.52 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 174 HIS 0.006 0.001 HIS J 135 PHE 0.010 0.001 PHE K 83 TYR 0.013 0.001 TYR F 183 ARG 0.002 0.000 ARG I 161 Details of bonding type rmsd hydrogen bonds : bond 0.02286 ( 763) hydrogen bonds : angle 3.90366 ( 2310) covalent geometry : bond 0.00222 (18984) covalent geometry : angle 0.46520 (25655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5256.41 seconds wall clock time: 92 minutes 37.91 seconds (5557.91 seconds total)