Starting phenix.real_space_refine on Tue Mar 19 03:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tej_25847/03_2024/7tej_25847.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tej_25847/03_2024/7tej_25847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tej_25847/03_2024/7tej_25847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tej_25847/03_2024/7tej_25847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tej_25847/03_2024/7tej_25847.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tej_25847/03_2024/7tej_25847.pdb" } resolution = 2.74 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= 0.006 sd= 0.148 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: 5 Type Number sf(0) Gaussians S 146 5.16 5 C 29029 2.51 5 N 7772 2.21 5 O 8801 1.98 5 H 45742 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 91490 Number of models: 1 Model: "" Number of chains: 28 Chain: "1" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3163 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain breaks: 2 Chain: "2" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3412 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "A" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3732 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3743 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "C" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3547 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 2 Chain: "D" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3132 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 4 Chain: "E" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2656 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain breaks: 6 Chain: "F" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3438 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 2 Chain: "G" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3608 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 8, 'TRANS': 223} Chain breaks: 2 Chain: "H" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2786 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 176} Chain breaks: 2 Chain: "I" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3131 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain breaks: 2 Chain: "J" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3142 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "K" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3111 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "L" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3120 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain breaks: 2 Chain: "M" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3163 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain breaks: 2 Chain: "N" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3412 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "O" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3732 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "P" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3743 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "Q" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3596 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Chain: "R" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3132 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 4 Chain: "S" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2656 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain breaks: 6 Chain: "T" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3438 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 2 Chain: "U" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3607 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 8, 'TRANS': 223} Chain breaks: 2 Chain: "V" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2786 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 176} Chain breaks: 2 Chain: "W" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3131 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain breaks: 2 Chain: "X" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3142 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "Y" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3111 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "Z" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3120 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain breaks: 2 Time building chain proxies: 29.37, per 1000 atoms: 0.32 Number of scatterers: 91490 At special positions: 0 Unit cell: (187.62, 196.1, 136.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 146 16.00 O 8801 8.00 N 7772 7.00 C 29029 6.00 H 45742 1.00 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 - 3.50 Amino acid : False - 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: 57.65 Conformation dependent library (CDL) restraints added in 7.5 seconds 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10822 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 70 sheets defined 40.0% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.19 Creating SS restraints... Processing helix chain '1' and resid 76 through 98 Processing helix chain '1' and resid 104 through 116 Processing helix chain '1' and resid 161 through 174 Proline residue: 1 167 - end of helix Processing helix chain '1' and resid 195 through 214 Processing helix chain '2' and resid 90 through 108 removed outlier: 3.837A pdb=" N ALA 2 108 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 137 Processing helix chain '2' and resid 178 through 182 Processing helix chain '2' and resid 183 through 190 removed outlier: 3.839A pdb=" N LEU 2 187 " --> pdb=" O MET 2 183 " (cutoff:3.500A) Processing helix chain '2' and resid 194 through 201 Proline residue: 2 199 - end of helix Processing helix chain '2' and resid 202 through 221 Processing helix chain '2' and resid 252 through 257 removed outlier: 3.506A pdb=" N ASP 2 257 " --> pdb=" O PHE 2 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.553A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 131 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.652A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'B' and resid 18 through 31 removed outlier: 3.695A pdb=" N ASP B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.551A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.540A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 248 Processing helix chain 'C' and resid 17 through 30 Processing helix chain 'C' and resid 78 through 101 Processing helix chain 'C' and resid 105 through 121 removed outlier: 3.659A pdb=" N TYR C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 121 " --> pdb=" O GLN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 removed outlier: 3.676A pdb=" N LYS C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'C' and resid 225 through 241 removed outlier: 3.515A pdb=" N TYR C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 30 Processing helix chain 'D' and resid 78 through 100 removed outlier: 3.680A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.517A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 85 through 104 Processing helix chain 'E' and resid 108 through 114 Processing helix chain 'E' and resid 175 through 187 removed outlier: 3.839A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.596A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.806A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 180 removed outlier: 5.044A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 removed outlier: 3.651A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'G' and resid 20 through 32 removed outlier: 3.591A pdb=" N GLU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 107 through 122 Processing helix chain 'G' and resid 167 through 181 removed outlier: 3.538A pdb=" N LYS G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 204 removed outlier: 3.639A pdb=" N LYS G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU G 204 " --> pdb=" O TYR G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 removed outlier: 3.763A pdb=" N LEU G 235 " --> pdb=" O LYS G 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 90 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 147 through 152 Processing helix chain 'H' and resid 153 through 161 Processing helix chain 'H' and resid 166 through 185 Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'I' and resid 88 through 100 Processing helix chain 'I' and resid 104 through 119 Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.542A pdb=" N VAL I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 Processing helix chain 'J' and resid 3 through 8 removed outlier: 4.420A pdb=" N ASN J 7 " --> pdb=" O PRO J 3 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY J 8 " --> pdb=" O SER J 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 3 through 8' Processing helix chain 'J' and resid 55 through 78 Processing helix chain 'J' and resid 82 through 96 Processing helix chain 'J' and resid 141 through 153 Processing helix chain 'J' and resid 158 through 176 removed outlier: 3.744A pdb=" N ARG J 176 " --> pdb=" O ASN J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 71 Processing helix chain 'K' and resid 75 through 91 Processing helix chain 'K' and resid 135 through 147 removed outlier: 5.608A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU K 142 " --> pdb=" O TYR K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 130 through 145 Processing helix chain 'L' and resid 150 through 165 Processing helix chain 'L' and resid 207 through 219 removed outlier: 3.560A pdb=" N VAL L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER L 217 " --> pdb=" O GLY L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 243 Processing helix chain 'L' and resid 268 through 280 removed outlier: 3.842A pdb=" N TRP L 273 " --> pdb=" O GLY L 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 99 Processing helix chain 'M' and resid 104 through 116 Processing helix chain 'M' and resid 161 through 174 Proline residue: M 167 - end of helix Processing helix chain 'M' and resid 195 through 214 Processing helix chain 'N' and resid 90 through 108 removed outlier: 3.937A pdb=" N ALA N 108 " --> pdb=" O VAL N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 137 Processing helix chain 'N' and resid 179 through 190 removed outlier: 3.591A pdb=" N MET N 183 " --> pdb=" O PHE N 179 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) Proline residue: N 186 - end of helix Processing helix chain 'N' and resid 194 through 201 Proline residue: N 199 - end of helix Processing helix chain 'N' and resid 202 through 221 Processing helix chain 'N' and resid 252 through 257 Processing helix chain 'O' and resid 25 through 36 removed outlier: 3.570A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN O 36 " --> pdb=" O PHE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 86 through 109 Processing helix chain 'O' and resid 113 through 131 Processing helix chain 'O' and resid 174 through 189 Processing helix chain 'O' and resid 198 through 215 removed outlier: 3.598A pdb=" N VAL O 202 " --> pdb=" O SER O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 250 Processing helix chain 'P' and resid 18 through 30 Processing helix chain 'P' and resid 58 through 61 Processing helix chain 'P' and resid 78 through 96 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.560A pdb=" N LYS P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 198 Processing helix chain 'P' and resid 218 through 222 Processing helix chain 'P' and resid 239 through 248 Processing helix chain 'Q' and resid 17 through 30 Processing helix chain 'Q' and resid 78 through 100 removed outlier: 3.582A pdb=" N ARG Q 97 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 123 removed outlier: 3.600A pdb=" N TYR Q 120 " --> pdb=" O VAL Q 116 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR Q 121 " --> pdb=" O GLN Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 177 removed outlier: 3.515A pdb=" N LYS Q 177 " --> pdb=" O GLU Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 201 Processing helix chain 'Q' and resid 225 through 241 Processing helix chain 'R' and resid 18 through 30 Processing helix chain 'R' and resid 78 through 100 removed outlier: 3.699A pdb=" N ILE R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG R 97 " --> pdb=" O ALA R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 121 removed outlier: 3.543A pdb=" N TYR R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR R 121 " --> pdb=" O GLN R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 179 removed outlier: 3.556A pdb=" N VAL R 171 " --> pdb=" O ASN R 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS R 177 " --> pdb=" O GLU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 200 Processing helix chain 'R' and resid 225 through 235 Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 85 through 104 Processing helix chain 'S' and resid 108 through 116 removed outlier: 3.706A pdb=" N GLN S 114 " --> pdb=" O GLU S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 187 removed outlier: 4.435A pdb=" N ALA S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 206 Processing helix chain 'S' and resid 236 through 242 Processing helix chain 'T' and resid 19 through 30 removed outlier: 3.564A pdb=" N ILE T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS T 30 " --> pdb=" O LEU T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 Processing helix chain 'T' and resid 104 through 120 removed outlier: 3.832A pdb=" N LYS T 118 " --> pdb=" O ASP T 114 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR T 120 " --> pdb=" O ALA T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 180 removed outlier: 5.051A pdb=" N ASP T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 199 removed outlier: 3.725A pdb=" N GLN T 199 " --> pdb=" O GLU T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 234 removed outlier: 3.573A pdb=" N ALA T 229 " --> pdb=" O ASP T 226 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS T 232 " --> pdb=" O ALA T 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.533A pdb=" N GLU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN U 32 " --> pdb=" O LYS U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 102 Processing helix chain 'U' and resid 107 through 122 removed outlier: 3.541A pdb=" N HIS U 122 " --> pdb=" O TYR U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 167 through 182 removed outlier: 3.681A pdb=" N LYS U 177 " --> pdb=" O ALA U 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 204 removed outlier: 3.640A pdb=" N LYS U 193 " --> pdb=" O ARG U 189 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU U 204 " --> pdb=" O TYR U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 244 removed outlier: 3.785A pdb=" N LEU U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 90 Processing helix chain 'V' and resid 93 through 105 Processing helix chain 'V' and resid 147 through 152 Processing helix chain 'V' and resid 153 through 161 Processing helix chain 'V' and resid 166 through 185 Processing helix chain 'V' and resid 208 through 213 Processing helix chain 'W' and resid 88 through 100 Processing helix chain 'W' and resid 104 through 119 Processing helix chain 'W' and resid 159 through 171 removed outlier: 3.573A pdb=" N VAL W 166 " --> pdb=" O ALA W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 195 Processing helix chain 'X' and resid 2 through 6 Processing helix chain 'X' and resid 55 through 78 Processing helix chain 'X' and resid 82 through 96 Processing helix chain 'X' and resid 141 through 153 Processing helix chain 'X' and resid 158 through 176 removed outlier: 3.531A pdb=" N GLU X 164 " --> pdb=" O GLU X 160 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG X 176 " --> pdb=" O ASN X 172 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 71 removed outlier: 4.376A pdb=" N VAL Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 91 Processing helix chain 'Y' and resid 134 through 147 removed outlier: 3.924A pdb=" N TYR Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU Y 142 " --> pdb=" O TYR Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 130 through 145 Processing helix chain 'Z' and resid 150 through 165 Processing helix chain 'Z' and resid 207 through 219 removed outlier: 3.848A pdb=" N SER Z 217 " --> pdb=" O GLY Z 213 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 243 Processing helix chain 'Z' and resid 268 through 280 removed outlier: 3.755A pdb=" N TRP Z 273 " --> pdb=" O GLY Z 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 155 through 158 Processing sheet with id=AA2, first strand: chain '1' and resid 48 through 50 removed outlier: 6.752A pdb=" N ASN 1 48 " --> pdb=" O ASN 1 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 63 through 64 removed outlier: 3.884A pdb=" N VAL 1 141 " --> pdb=" O GLU 1 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 66 through 69 removed outlier: 5.417A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 66 through 69 removed outlier: 5.417A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 174 through 176 removed outlier: 5.737A pdb=" N PHE 2 228 " --> pdb=" O ASN 2 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN 2 244 " --> pdb=" O PHE 2 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA8, first strand: chain 'A' and resid 72 through 73 removed outlier: 4.106A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY A 165 " --> pdb=" O MET B 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.772A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU B 211 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.492A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.446A pdb=" N THR B 225 " --> pdb=" O TYR I 215 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG I 217 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN I 218 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL I 202 " --> pdb=" O ASN I 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.546A pdb=" N VAL C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.571A pdb=" N GLU D 211 " --> pdb=" O CYS D 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.617A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.510A pdb=" N ALA E 37 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.327A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AC1, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.341A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 161 through 164 Processing sheet with id=AC3, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.909A pdb=" N TRP G 157 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 143 through 146 Processing sheet with id=AC5, first strand: chain 'H' and resid 39 through 41 removed outlier: 6.946A pdb=" N THR H 39 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 54 through 57 removed outlier: 6.664A pdb=" N ILE H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL H 129 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.734A pdb=" N SER I 49 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.470A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 241 through 247 removed outlier: 6.371A pdb=" N TYR J 198 " --> pdb=" O LEU I 242 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU I 244 " --> pdb=" O LYS J 196 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS J 196 " --> pdb=" O GLU I 244 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE I 246 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL J 194 " --> pdb=" O ILE I 246 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.463A pdb=" N SER J 30 " --> pdb=" O GLY J 34 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLY J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 42 through 45 removed outlier: 3.810A pdb=" N VAL J 48 " --> pdb=" O TYR J 45 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE J 123 " --> pdb=" O PRO J 106 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE J 120 " --> pdb=" O ALA J 132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 129 through 131 removed outlier: 4.560A pdb=" N VAL K 180 " --> pdb=" O VAL K 191 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.645A pdb=" N ARG K 22 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.334A pdb=" N THR K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 201 through 204 removed outlier: 6.240A pdb=" N VAL L 250 " --> pdb=" O ASN L 265 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN L 265 " --> pdb=" O VAL L 250 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU L 252 " --> pdb=" O HIS L 263 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.737A pdb=" N ALA L 95 " --> pdb=" O ALA L 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 109 through 111 removed outlier: 4.331A pdb=" N ILE L 187 " --> pdb=" O GLY L 199 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 155 through 158 Processing sheet with id=AE1, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.726A pdb=" N ASN M 48 " --> pdb=" O ASN M 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 63 through 64 removed outlier: 3.850A pdb=" N ASN M 74 " --> pdb=" O HIS M 127 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL M 141 " --> pdb=" O GLU M 153 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 66 through 69 removed outlier: 5.492A pdb=" N LEU N 67 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR N 63 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR N 82 " --> pdb=" O VAL N 78 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 66 through 69 removed outlier: 5.492A pdb=" N LEU N 67 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR N 63 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 174 through 177 removed outlier: 4.110A pdb=" N VAL N 44 " --> pdb=" O THR N 177 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE N 228 " --> pdb=" O ASN N 244 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN N 244 " --> pdb=" O PHE N 228 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 168 through 171 removed outlier: 4.712A pdb=" N VAL O 225 " --> pdb=" O LEU O 236 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 72 through 74 removed outlier: 4.129A pdb=" N ILE O 154 " --> pdb=" O TYR O 166 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY O 165 " --> pdb=" O MET P 57 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 161 through 164 removed outlier: 3.819A pdb=" N GLY P 42 " --> pdb=" O ALA P 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 64 through 68 removed outlier: 6.506A pdb=" N ILE P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 224 through 225 removed outlier: 6.383A pdb=" N THR P 225 " --> pdb=" O TYR W 215 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ARG W 217 " --> pdb=" O THR P 225 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN W 218 " --> pdb=" O VAL W 202 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL W 202 " --> pdb=" O ASN W 218 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id=AF3, first strand: chain 'Q' and resid 65 through 68 removed outlier: 6.590A pdb=" N VAL Q 71 " --> pdb=" O ILE Q 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 161 through 164 removed outlier: 3.531A pdb=" N GLU R 211 " --> pdb=" O CYS R 46 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 65 through 68 removed outlier: 6.594A pdb=" N VAL R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 169 through 173 Processing sheet with id=AF7, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.352A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR S 165 " --> pdb=" O HIS S 157 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF9, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.356A pdb=" N MET T 70 " --> pdb=" O CYS T 66 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 161 through 164 Processing sheet with id=AG2, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.548A pdb=" N THR U 135 " --> pdb=" O LEU U 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP U 157 " --> pdb=" O MET U 149 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 143 through 146 Processing sheet with id=AG4, first strand: chain 'V' and resid 39 through 41 removed outlier: 7.010A pdb=" N THR V 39 " --> pdb=" O ALA V 46 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 54 through 57 removed outlier: 6.572A pdb=" N ILE V 60 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE V 117 " --> pdb=" O CYS V 63 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL V 129 " --> pdb=" O LEU V 141 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 49 through 51 removed outlier: 6.774A pdb=" N SER W 49 " --> pdb=" O ALA W 56 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 63 through 67 removed outlier: 6.472A pdb=" N ILE W 70 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 241 through 247 removed outlier: 6.369A pdb=" N TYR X 198 " --> pdb=" O LEU W 242 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU W 244 " --> pdb=" O LYS X 196 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS X 196 " --> pdb=" O GLU W 244 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE W 246 " --> pdb=" O VAL X 194 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL X 194 " --> pdb=" O ILE W 246 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE X 10 " --> pdb=" O ASP X 25 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.233A pdb=" N SER X 30 " --> pdb=" O GLY X 34 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY X 34 " --> pdb=" O SER X 30 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'X' and resid 42 through 44 removed outlier: 3.670A pdb=" N PHE X 123 " --> pdb=" O PRO X 106 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 129 through 131 removed outlier: 4.606A pdb=" N VAL Y 180 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.709A pdb=" N ARG Y 22 " --> pdb=" O VAL Y 26 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL Y 26 " --> pdb=" O ARG Y 22 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.374A pdb=" N THR Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 201 through 204 removed outlier: 6.247A pdb=" N VAL Z 250 " --> pdb=" O ASN Z 265 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN Z 265 " --> pdb=" O VAL Z 250 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU Z 252 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 95 through 97 removed outlier: 6.737A pdb=" N ALA Z 95 " --> pdb=" O ALA Z 102 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Z' and resid 109 through 111 removed outlier: 4.295A pdb=" N ILE Z 187 " --> pdb=" O GLY Z 199 " (cutoff:3.500A) 2686 hydrogen bonds defined for protein. 7563 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: 39.37 Time building geometry restraints manager: 60.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 45670 1.13 - 1.30: 7739 1.30 - 1.47: 18224 1.47 - 1.64: 20434 1.64 - 1.81: 220 Bond restraints: 92287 Sorted by residual: bond pdb=" CD2 HIS L 141 " pdb=" HD2 HIS L 141 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE2 GLN Y 54 " pdb="HE21 GLN Y 54 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ALA G 196 " pdb=" H ALA G 196 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LEU B 85 " pdb=" H LEU B 85 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 HIS S 91 " pdb=" HD2 HIS S 91 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 92282 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.55: 702 105.55 - 112.69: 108379 112.69 - 119.83: 26832 119.83 - 126.97: 30359 126.97 - 134.12: 424 Bond angle restraints: 166696 Sorted by residual: angle pdb=" C LEU G 80 " pdb=" N ILE G 81 " pdb=" CA ILE G 81 " ideal model delta sigma weight residual 120.24 122.82 -2.58 6.30e-01 2.52e+00 1.68e+01 angle pdb=" N ASP M 219 " pdb=" CA ASP M 219 " pdb=" C ASP M 219 " ideal model delta sigma weight residual 113.18 107.73 5.45 1.33e+00 5.65e-01 1.68e+01 angle pdb=" CA PRO C 13 " pdb=" N PRO C 13 " pdb=" CD PRO C 13 " ideal model delta sigma weight residual 112.00 106.67 5.33 1.40e+00 5.10e-01 1.45e+01 angle pdb=" C GLU M 37 " pdb=" N ASP M 38 " pdb=" CA ASP M 38 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" N ILE J 126 " pdb=" CA ILE J 126 " pdb=" C ILE J 126 " ideal model delta sigma weight residual 113.00 108.79 4.21 1.30e+00 5.92e-01 1.05e+01 ... (remaining 166691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 38561 17.93 - 35.87: 2620 35.87 - 53.80: 989 53.80 - 71.74: 973 71.74 - 89.67: 100 Dihedral angle restraints: 43243 sinusoidal: 23606 harmonic: 19637 Sorted by residual: dihedral pdb=" CA VAL U 59 " pdb=" C VAL U 59 " pdb=" N PRO U 60 " pdb=" CA PRO U 60 " ideal model delta harmonic sigma weight residual -180.00 -155.20 -24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLU Y 48 " pdb=" C GLU Y 48 " pdb=" N ALA Y 49 " pdb=" CA ALA Y 49 " ideal model delta harmonic sigma weight residual 180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LEU S 142 " pdb=" C LEU S 142 " pdb=" N LEU S 143 " pdb=" CA LEU S 143 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 43240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4554 0.034 - 0.068: 1726 0.068 - 0.102: 526 0.102 - 0.137: 313 0.137 - 0.171: 39 Chirality restraints: 7158 Sorted by residual: chirality pdb=" CA ILE J 136 " pdb=" N ILE J 136 " pdb=" C ILE J 136 " pdb=" CB ILE J 136 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ILE X 136 " pdb=" N ILE X 136 " pdb=" C ILE X 136 " pdb=" CB ILE X 136 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA ILE V 116 " pdb=" N ILE V 116 " pdb=" C ILE V 116 " pdb=" CB ILE V 116 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 7155 not shown) Planarity restraints: 13639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 12 " 0.069 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO C 13 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 13 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 13 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 217 " -0.007 2.00e-02 2.50e+03 1.84e-02 1.35e+01 pdb=" CG TRP G 217 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP G 217 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP G 217 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP G 217 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP G 217 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 217 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 217 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 217 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 217 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP G 217 " -0.051 2.00e-02 2.50e+03 pdb=" HE1 TRP G 217 " 0.021 2.00e-02 2.50e+03 pdb=" HE3 TRP G 217 " 0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 217 " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 217 " -0.009 2.00e-02 2.50e+03 pdb=" HH2 TRP G 217 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 200 " 0.004 2.00e-02 2.50e+03 1.79e-02 9.66e+00 pdb=" CG TYR G 200 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR G 200 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR G 200 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 200 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR G 200 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR G 200 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 200 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 TYR G 200 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 TYR G 200 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR G 200 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR G 200 " 0.014 2.00e-02 2.50e+03 ... (remaining 13636 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.97: 2140 1.97 - 2.63: 112301 2.63 - 3.29: 286399 3.29 - 3.94: 385998 3.94 - 4.60: 583846 Nonbonded interactions: 1370684 Sorted by model distance: nonbonded pdb=" OE1 GLU X 131 " pdb=" HZ1 LYS X 133 " model vdw 1.317 1.850 nonbonded pdb=" OE2 GLU S 197 " pdb=" HH TYR S 231 " model vdw 1.353 1.850 nonbonded pdb=" H SER C 12 " pdb=" O HIS C 16 " model vdw 1.360 1.850 nonbonded pdb=" OD1 ASP N 58 " pdb="HH21 ARG N 74 " model vdw 1.384 1.850 nonbonded pdb=" H SER Q 12 " pdb=" O HIS Q 16 " model vdw 1.394 1.850 ... (remaining 1370679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain 'M' } ncs_group { reference = chain '2' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = (chain 'C' and (resid 17 through 56 or resid 63 through 121 or resid 126 through \ 200 or resid 210 through 235)) selection = chain 'D' selection = (chain 'Q' and (resid 17 through 48 or resid 52 through 56 or resid 63 through 1 \ 21 or resid 126 through 200 or resid 210 through 235)) selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = (chain 'G' and (resid 5 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 73 through 244)) selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.040 Extract box with map and model: 12.830 Check model and map are aligned: 1.320 Set scattering table: 0.640 Process input model: 231.880 Find NCS groups from input model: 3.980 Set up NCS constraints: 0.540 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:9.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 263.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.004 0.085 46545 Z= 0.271 Angle : 0.582 7.852 62903 Z= 0.328 Chirality : 0.045 0.171 7158 Planarity : 0.005 0.101 8041 Dihedral : 12.223 88.931 17097 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 1.11 (0.11), residues: 5705 helix: 1.54 (0.11), residues: 2115 sheet: 0.54 (0.13), residues: 1398 loop : 0.21 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 217 HIS 0.008 0.002 HIS 1 114 PHE 0.023 0.002 PHE H 101 TYR 0.028 0.002 TYR G 200 ARG 0.013 0.001 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 730 time to evaluate : 5.519 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 212 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7699 (mp0) REVERT: D 232 TYR cc_start: 0.6973 (m-80) cc_final: 0.6691 (m-80) REVERT: K 154 GLU cc_start: 0.7400 (mp0) cc_final: 0.7112 (mp0) REVERT: K 158 ASP cc_start: 0.7624 (m-30) cc_final: 0.7357 (m-30) REVERT: N 214 MET cc_start: 0.8707 (mmt) cc_final: 0.7767 (mmt) REVERT: T 90 GLN cc_start: 0.7575 (mt0) cc_final: 0.7371 (tt0) REVERT: V 210 ASP cc_start: 0.7129 (m-30) cc_final: 0.6902 (m-30) REVERT: Y 154 GLU cc_start: 0.7441 (mp0) cc_final: 0.7170 (mp0) REVERT: Y 158 ASP cc_start: 0.7691 (m-30) cc_final: 0.7423 (m-30) outliers start: 0 outliers final: 0 residues processed: 730 average time/residue: 3.1169 time to fit residues: 2789.9491 Evaluate side-chains 467 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 5.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 5.9990 chunk 436 optimal weight: 5.9990 chunk 242 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 451 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 chunk 336 optimal weight: 0.8980 chunk 523 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN F 60 GLN G 181 HIS H 164 ASN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN L 141 HIS M 99 ASN M 114 HIS ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 GLN T 60 GLN W 51 GLN W 173 GLN Z 164 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46545 Z= 0.185 Angle : 0.549 7.214 62903 Z= 0.298 Chirality : 0.044 0.178 7158 Planarity : 0.004 0.059 8041 Dihedral : 5.046 46.955 6339 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.09 % Allowed : 7.07 % Favored : 91.85 % 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: 1.21 (0.11), residues: 5705 helix: 1.95 (0.11), residues: 2123 sheet: 0.23 (0.13), residues: 1441 loop : 0.18 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 130 HIS 0.006 0.001 HIS O 209 PHE 0.021 0.001 PHE F 179 TYR 0.013 0.001 TYR 1 150 ARG 0.006 0.000 ARG Z 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 516 time to evaluate : 5.585 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: 1 125 TYR cc_start: 0.6257 (OUTLIER) cc_final: 0.5746 (m-80) REVERT: 2 190 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7596 (mtmt) REVERT: B 108 LYS cc_start: 0.8030 (tptp) cc_final: 0.7713 (ttpt) REVERT: C 52 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7431 (mt) REVERT: C 149 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: E 20 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5385 (ptt90) REVERT: E 202 LYS cc_start: 0.6947 (ttpp) cc_final: 0.6738 (ttpt) REVERT: H 79 GLN cc_start: 0.7991 (tt0) cc_final: 0.7693 (tt0) REVERT: I 149 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6923 (p0) REVERT: K 64 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: K 154 GLU cc_start: 0.7404 (mp0) cc_final: 0.7124 (mp0) REVERT: K 158 ASP cc_start: 0.7614 (m-30) cc_final: 0.7352 (m-30) REVERT: L 130 TRP cc_start: 0.3617 (OUTLIER) cc_final: 0.1931 (m-90) REVERT: N 190 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7618 (mtmt) REVERT: N 214 MET cc_start: 0.8579 (mmt) cc_final: 0.7741 (mmt) REVERT: P 78 MET cc_start: 0.8499 (mtm) cc_final: 0.8179 (mtm) REVERT: R 181 ARG cc_start: 0.6825 (mmm160) cc_final: 0.6534 (mmm160) REVERT: S 20 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.5281 (ptt90) REVERT: U 19 ARG cc_start: 0.8230 (ptm-80) cc_final: 0.7985 (ptm160) REVERT: U 61 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6757 (tm-30) REVERT: U 125 TYR cc_start: 0.8497 (m-80) cc_final: 0.8200 (m-80) REVERT: V 210 ASP cc_start: 0.7150 (m-30) cc_final: 0.6870 (m-30) REVERT: X 65 MET cc_start: 0.8241 (ttm) cc_final: 0.8009 (ttm) REVERT: X 131 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6114 (tm-30) REVERT: Y 154 GLU cc_start: 0.7447 (mp0) cc_final: 0.7162 (mp0) REVERT: Y 158 ASP cc_start: 0.7663 (m-30) cc_final: 0.7398 (m-30) REVERT: Z 145 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6751 (mp0) outliers start: 54 outliers final: 17 residues processed: 544 average time/residue: 2.8747 time to fit residues: 1953.2809 Evaluate side-chains 483 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 454 time to evaluate : 5.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 125 TYR Chi-restraints excluded: chain 2 residue 190 LYS Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain L residue 130 TRP Chi-restraints excluded: chain N residue 190 LYS Chi-restraints excluded: chain P residue 216 ASP Chi-restraints excluded: chain P residue 240 SER Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain W residue 156 LEU Chi-restraints excluded: chain X residue 131 GLU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 193 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 435 optimal weight: 0.7980 chunk 356 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 524 optimal weight: 0.7980 chunk 566 optimal weight: 1.9990 chunk 466 optimal weight: 0.5980 chunk 519 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 420 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 145 ASN F 60 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 ASN M 114 HIS S 114 GLN T 60 GLN T 90 GLN Z 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 46545 Z= 0.167 Angle : 0.487 6.166 62903 Z= 0.265 Chirality : 0.043 0.162 7158 Planarity : 0.004 0.049 8041 Dihedral : 4.734 36.033 6339 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.11 % Allowed : 8.13 % Favored : 90.76 % 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: 1.37 (0.11), residues: 5705 helix: 2.28 (0.11), residues: 2136 sheet: 0.13 (0.13), residues: 1429 loop : 0.15 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Z 133 HIS 0.005 0.001 HIS E 99 PHE 0.020 0.001 PHE F 179 TYR 0.015 0.001 TYR G 102 ARG 0.011 0.000 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 493 time to evaluate : 5.538 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: 1 166 MET cc_start: 0.8036 (tpt) cc_final: 0.7726 (tpt) REVERT: C 14 ASP cc_start: 0.7781 (p0) cc_final: 0.7550 (p0) REVERT: C 52 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7505 (mt) REVERT: C 149 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: D 56 ASP cc_start: 0.7067 (t70) cc_final: 0.6646 (t70) REVERT: E 20 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5359 (ptt90) REVERT: H 79 GLN cc_start: 0.8001 (tt0) cc_final: 0.7713 (tt0) REVERT: K 64 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: K 154 GLU cc_start: 0.7447 (mp0) cc_final: 0.7120 (mp0) REVERT: K 158 ASP cc_start: 0.7626 (m-30) cc_final: 0.7369 (m-30) REVERT: L 193 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6092 (m-30) REVERT: M 45 ASP cc_start: 0.8569 (p0) cc_final: 0.8316 (p0) REVERT: M 52 TYR cc_start: 0.8104 (m-80) cc_final: 0.7839 (m-80) REVERT: N 190 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7709 (mtmt) REVERT: N 214 MET cc_start: 0.8530 (mmt) cc_final: 0.7495 (mmt) REVERT: P 78 MET cc_start: 0.8559 (mtm) cc_final: 0.8317 (mtm) REVERT: R 17 ILE cc_start: 0.4535 (mm) cc_final: 0.4264 (mt) REVERT: R 143 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: S 20 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.5145 (ptt90) REVERT: U 61 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6645 (tm-30) REVERT: U 125 TYR cc_start: 0.8510 (m-80) cc_final: 0.8212 (m-80) REVERT: X 131 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6080 (tm-30) REVERT: Y 154 GLU cc_start: 0.7447 (mp0) cc_final: 0.7169 (mp0) REVERT: Y 158 ASP cc_start: 0.7692 (m-30) cc_final: 0.7437 (m-30) outliers start: 55 outliers final: 22 residues processed: 523 average time/residue: 2.7147 time to fit residues: 1796.5076 Evaluate side-chains 481 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 450 time to evaluate : 5.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 136 ASP Chi-restraints excluded: chain 1 residue 212 GLU Chi-restraints excluded: chain 2 residue 133 MET Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain H residue 63 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain N residue 190 LYS Chi-restraints excluded: chain P residue 240 SER Chi-restraints excluded: chain Q residue 32 CYS Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 219 ASP Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain X residue 131 GLU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Z residue 193 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 chunk 271 optimal weight: 0.3980 chunk 58 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 351 optimal weight: 4.9990 chunk 525 optimal weight: 0.5980 chunk 556 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 498 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN M 99 ASN M 113 GLN T 52 ASN T 60 GLN U 169 GLN Z 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 46545 Z= 0.208 Angle : 0.489 6.947 62903 Z= 0.265 Chirality : 0.043 0.169 7158 Planarity : 0.004 0.053 8041 Dihedral : 4.644 29.609 6339 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.37 % Allowed : 8.82 % Favored : 89.81 % 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: 1.43 (0.11), residues: 5705 helix: 2.42 (0.11), residues: 2148 sheet: 0.13 (0.13), residues: 1443 loop : 0.09 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 130 HIS 0.005 0.001 HIS O 209 PHE 0.020 0.001 PHE F 179 TYR 0.013 0.001 TYR G 102 ARG 0.004 0.000 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 466 time to evaluate : 5.896 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: symmetry clash revert: symmetry clash REVERT: 1 125 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.5787 (m-80) REVERT: 1 208 THR cc_start: 0.8637 (m) cc_final: 0.8280 (m) REVERT: C 231 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: D 143 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: E 20 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5414 (ptt90) REVERT: E 140 VAL cc_start: 0.5983 (m) cc_final: 0.5607 (t) REVERT: F 27 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7317 (mm-30) REVERT: F 113 CYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7480 (t) REVERT: F 155 GLU cc_start: 0.7731 (tt0) cc_final: 0.7125 (tt0) REVERT: H 79 GLN cc_start: 0.8048 (tt0) cc_final: 0.7744 (tt0) REVERT: K 64 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: K 154 GLU cc_start: 0.7459 (mp0) cc_final: 0.7171 (mp0) REVERT: K 158 ASP cc_start: 0.7663 (m-30) cc_final: 0.7383 (m-30) REVERT: N 214 MET cc_start: 0.8572 (mmt) cc_final: 0.7303 (mmt) REVERT: P 78 MET cc_start: 0.8570 (mtm) cc_final: 0.8296 (mtm) REVERT: P 116 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8031 (ttmm) REVERT: Q 52 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6765 (mt) REVERT: Q 119 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7083 (mtp-110) REVERT: R 17 ILE cc_start: 0.4544 (mm) cc_final: 0.4304 (mt) REVERT: R 235 GLN cc_start: 0.6723 (tm-30) cc_final: 0.6505 (tm-30) REVERT: S 20 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5182 (ptt90) REVERT: T 52 ASN cc_start: 0.5086 (OUTLIER) cc_final: 0.4441 (m-40) REVERT: T 61 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6586 (ptmm) REVERT: U 19 ARG cc_start: 0.8275 (ptm-80) cc_final: 0.7837 (ptm160) REVERT: U 61 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6693 (tm-30) REVERT: U 151 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: V 59 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7500 (mptm) REVERT: Y 154 GLU cc_start: 0.7455 (mp0) cc_final: 0.7137 (mp0) REVERT: Y 158 ASP cc_start: 0.7710 (m-30) cc_final: 0.7443 (m-30) REVERT: Z 120 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6977 (mtm) outliers start: 68 outliers final: 32 residues processed: 500 average time/residue: 2.7175 time to fit residues: 1719.8949 Evaluate side-chains 480 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 434 time to evaluate : 5.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 125 TYR Chi-restraints excluded: chain 1 residue 136 ASP Chi-restraints excluded: chain 1 residue 212 GLU Chi-restraints excluded: chain 1 residue 241 ASP Chi-restraints excluded: chain 2 residue 133 MET Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 63 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain P residue 240 SER Chi-restraints excluded: chain Q residue 32 CYS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 52 ASN Chi-restraints excluded: chain T residue 61 LYS Chi-restraints excluded: chain U residue 151 GLU Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain V residue 59 LYS Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain Z residue 158 LEU Chi-restraints excluded: chain Z residue 193 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 414 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 475 optimal weight: 5.9990 chunk 384 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 499 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 ASN F 60 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN L 164 GLN M 99 ASN M 114 HIS ** V 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 46545 Z= 0.334 Angle : 0.523 6.941 62903 Z= 0.285 Chirality : 0.044 0.172 7158 Planarity : 0.004 0.053 8041 Dihedral : 4.781 25.778 6339 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.63 % Allowed : 9.52 % Favored : 88.85 % 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: 1.23 (0.11), residues: 5705 helix: 2.28 (0.11), residues: 2154 sheet: 0.01 (0.13), residues: 1445 loop : -0.03 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Z 133 HIS 0.005 0.001 HIS T 69 PHE 0.019 0.002 PHE F 179 TYR 0.015 0.002 TYR X 45 ARG 0.007 0.001 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 443 time to evaluate : 5.585 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: 1 125 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5963 (m-80) REVERT: 1 143 SER cc_start: 0.8400 (t) cc_final: 0.8122 (m) REVERT: C 52 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7552 (mt) REVERT: C 149 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: C 231 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: D 143 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: E 140 VAL cc_start: 0.6245 (m) cc_final: 0.5994 (t) REVERT: F 113 CYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7477 (t) REVERT: H 79 GLN cc_start: 0.8090 (tt0) cc_final: 0.7796 (tt0) REVERT: I 227 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7045 (mm-30) REVERT: N 190 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7703 (mtmt) REVERT: N 214 MET cc_start: 0.8611 (mmt) cc_final: 0.7342 (mmt) REVERT: P 78 MET cc_start: 0.8575 (mtm) cc_final: 0.8291 (mtm) REVERT: P 116 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8050 (ttmm) REVERT: Q 52 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6875 (mt) REVERT: Q 119 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7011 (mtp-110) REVERT: R 17 ILE cc_start: 0.4634 (mm) cc_final: 0.4375 (mt) REVERT: S 20 ARG cc_start: 0.5867 (OUTLIER) cc_final: 0.5287 (ptt90) REVERT: T 195 GLU cc_start: 0.6839 (tp30) cc_final: 0.5918 (tp30) REVERT: T 199 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6521 (mp10) REVERT: U 19 ARG cc_start: 0.8355 (ptm-80) cc_final: 0.7848 (ptm160) REVERT: U 61 GLN cc_start: 0.6967 (tm-30) cc_final: 0.6626 (tm-30) REVERT: U 151 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: X 131 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6184 (tm-30) REVERT: Z 145 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6699 (mp0) outliers start: 81 outliers final: 39 residues processed: 485 average time/residue: 2.7519 time to fit residues: 1679.3555 Evaluate side-chains 476 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 422 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 125 TYR Chi-restraints excluded: chain 1 residue 136 ASP Chi-restraints excluded: chain 1 residue 212 GLU Chi-restraints excluded: chain 1 residue 241 ASP Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 63 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain I residue 119 TYR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain N residue 190 LYS Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain P residue 240 SER Chi-restraints excluded: chain Q residue 32 CYS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 199 GLN Chi-restraints excluded: chain T residue 219 ASP Chi-restraints excluded: chain U residue 151 GLU Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain V residue 74 ILE Chi-restraints excluded: chain W residue 119 TYR Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 156 LEU Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 131 GLU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Z residue 145 GLU Chi-restraints excluded: chain Z residue 158 LEU Chi-restraints excluded: chain Z residue 180 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 5.9990 chunk 501 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 326 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 557 optimal weight: 2.9990 chunk 462 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 ASN F 60 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN M 99 ASN Q 209 ASN ** V 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 ASN Z 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 46545 Z= 0.305 Angle : 0.523 7.160 62903 Z= 0.284 Chirality : 0.044 0.174 7158 Planarity : 0.004 0.054 8041 Dihedral : 4.791 23.692 6339 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.69 % Allowed : 10.17 % Favored : 88.14 % 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: 1.16 (0.11), residues: 5705 helix: 2.24 (0.11), residues: 2152 sheet: 0.00 (0.13), residues: 1443 loop : -0.12 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Z 133 HIS 0.005 0.001 HIS G 86 PHE 0.017 0.002 PHE F 179 TYR 0.019 0.002 TYR G 102 ARG 0.007 0.000 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 433 time to evaluate : 5.744 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: 1 125 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: 2 190 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7603 (mtmt) REVERT: C 231 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: F 113 CYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7448 (t) REVERT: H 79 GLN cc_start: 0.8096 (tt0) cc_final: 0.7814 (tt0) REVERT: I 227 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: K 158 ASP cc_start: 0.7613 (m-30) cc_final: 0.7281 (m-30) REVERT: L 193 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6302 (m-30) REVERT: N 214 MET cc_start: 0.8614 (mmt) cc_final: 0.7277 (mmt) REVERT: P 50 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6702 (pttp) REVERT: P 78 MET cc_start: 0.8569 (mtm) cc_final: 0.8281 (mtm) REVERT: P 116 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8110 (ttmm) REVERT: Q 52 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6914 (mt) REVERT: Q 119 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7009 (mtp-110) REVERT: R 17 ILE cc_start: 0.4868 (mm) cc_final: 0.4584 (mt) REVERT: R 143 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: R 235 GLN cc_start: 0.6607 (tm-30) cc_final: 0.6367 (tm-30) REVERT: S 20 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5396 (ptt90) REVERT: T 61 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6902 (ptmm) REVERT: T 113 CYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7615 (t) REVERT: T 199 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6530 (mp10) REVERT: U 19 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.8088 (ptm160) REVERT: U 61 GLN cc_start: 0.6999 (tm-30) cc_final: 0.6652 (tm-30) REVERT: U 151 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: V 59 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7445 (mptm) REVERT: W 119 TYR cc_start: 0.5444 (OUTLIER) cc_final: 0.5151 (t80) REVERT: X 131 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6192 (tm-30) REVERT: Y 114 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: Y 154 GLU cc_start: 0.7630 (mp0) cc_final: 0.7074 (mp0) REVERT: Y 158 ASP cc_start: 0.7666 (m-30) cc_final: 0.7342 (m-30) REVERT: Z 175 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7600 (mpp) outliers start: 84 outliers final: 40 residues processed: 481 average time/residue: 2.7261 time to fit residues: 1658.5008 Evaluate side-chains 471 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 411 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 125 TYR Chi-restraints excluded: chain 1 residue 136 ASP Chi-restraints excluded: chain 1 residue 191 LEU Chi-restraints excluded: chain 1 residue 212 GLU Chi-restraints excluded: chain 1 residue 241 ASP Chi-restraints excluded: chain 2 residue 190 LYS Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain H residue 63 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain L residue 193 ASP Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain O residue 134 MET Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain P residue 240 SER Chi-restraints excluded: chain Q residue 32 CYS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 61 LYS Chi-restraints excluded: chain T residue 113 CYS Chi-restraints excluded: chain T residue 199 GLN Chi-restraints excluded: chain U residue 151 GLU Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain V residue 59 LYS Chi-restraints excluded: chain V residue 74 ILE Chi-restraints excluded: chain W residue 119 TYR Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 131 GLU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 114 GLU Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Z residue 175 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 406 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 469 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 555 optimal weight: 0.0470 chunk 347 optimal weight: 0.1980 chunk 338 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN F 52 ASN F 60 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN L 164 GLN M 99 ASN Q 235 GLN Z 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 46545 Z= 0.193 Angle : 0.481 6.306 62903 Z= 0.261 Chirality : 0.043 0.168 7158 Planarity : 0.004 0.052 8041 Dihedral : 4.629 21.912 6339 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.39 % Allowed : 10.85 % Favored : 87.76 % 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: 1.33 (0.11), residues: 5705 helix: 2.46 (0.11), residues: 2150 sheet: 0.03 (0.13), residues: 1423 loop : -0.08 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 133 HIS 0.004 0.001 HIS O 209 PHE 0.016 0.001 PHE F 179 TYR 0.018 0.001 TYR G 102 ARG 0.004 0.000 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 427 time to evaluate : 5.635 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: symmetry clash revert: symmetry clash REVERT: 1 125 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.5995 (m-80) REVERT: 2 190 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7581 (mtmt) REVERT: C 52 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7600 (mt) REVERT: C 231 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: D 143 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: F 113 CYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7454 (t) REVERT: H 79 GLN cc_start: 0.8073 (tt0) cc_final: 0.7787 (tt0) REVERT: J 31 GLN cc_start: 0.8441 (mt0) cc_final: 0.8067 (mt0) REVERT: K 64 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: K 154 GLU cc_start: 0.7657 (mp0) cc_final: 0.7107 (mp0) REVERT: K 158 ASP cc_start: 0.7592 (m-30) cc_final: 0.7260 (m-30) REVERT: N 214 MET cc_start: 0.8559 (mmt) cc_final: 0.7264 (mmt) REVERT: P 78 MET cc_start: 0.8579 (mtm) cc_final: 0.8296 (mtm) REVERT: P 116 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8075 (ttmm) REVERT: P 143 ASN cc_start: 0.7700 (m-40) cc_final: 0.7435 (t0) REVERT: Q 52 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6904 (mt) REVERT: Q 119 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6999 (mtp-110) REVERT: R 17 ILE cc_start: 0.4856 (mm) cc_final: 0.4586 (mt) REVERT: R 235 GLN cc_start: 0.6657 (tm-30) cc_final: 0.6388 (tm-30) REVERT: S 20 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.5386 (ptt90) REVERT: T 113 CYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7410 (t) REVERT: T 199 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6578 (mp10) REVERT: U 19 ARG cc_start: 0.8396 (ptm-80) cc_final: 0.8113 (ptm160) REVERT: U 61 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6609 (tm-30) REVERT: U 151 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: W 227 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: X 131 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6162 (tm-30) REVERT: Y 158 ASP cc_start: 0.7645 (m-30) cc_final: 0.7313 (m-30) outliers start: 69 outliers final: 34 residues processed: 468 average time/residue: 2.7033 time to fit residues: 1609.9515 Evaluate side-chains 458 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 409 time to evaluate : 5.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 125 TYR Chi-restraints excluded: chain 1 residue 136 ASP Chi-restraints excluded: chain 1 residue 212 GLU Chi-restraints excluded: chain 1 residue 241 ASP Chi-restraints excluded: chain 2 residue 190 LYS Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 63 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 32 CYS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 113 CYS Chi-restraints excluded: chain T residue 199 GLN Chi-restraints excluded: chain U residue 151 GLU Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain V residue 74 ILE Chi-restraints excluded: chain W residue 119 TYR Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 227 GLU Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 131 GLU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 126 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 0.0370 chunk 221 optimal weight: 2.9990 chunk 331 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 352 optimal weight: 5.9990 chunk 378 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 436 optimal weight: 7.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 123 GLN F 52 ASN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 GLN L 164 GLN M 99 ASN O 175 GLN Q 209 ASN Q 235 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46545 Z= 0.215 Angle : 0.481 6.131 62903 Z= 0.261 Chirality : 0.043 0.166 7158 Planarity : 0.004 0.052 8041 Dihedral : 4.567 22.190 6339 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.35 % Allowed : 11.31 % Favored : 87.34 % 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: 1.38 (0.11), residues: 5705 helix: 2.52 (0.11), residues: 2154 sheet: 0.03 (0.13), residues: 1447 loop : -0.05 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 133 HIS 0.004 0.001 HIS O 209 PHE 0.019 0.001 PHE T 179 TYR 0.024 0.001 TYR G 102 ARG 0.004 0.000 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 414 time to evaluate : 5.641 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: symmetry clash revert: symmetry clash REVERT: 1 71 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7537 (ttt) REVERT: 1 125 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.6010 (m-80) REVERT: C 52 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7612 (mt) REVERT: C 119 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6954 (mtp-110) REVERT: C 231 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: D 17 ILE cc_start: 0.4891 (mm) cc_final: 0.4676 (mt) REVERT: D 143 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: F 113 CYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7459 (t) REVERT: H 79 GLN cc_start: 0.8072 (tt0) cc_final: 0.7784 (tt0) REVERT: J 31 GLN cc_start: 0.8447 (mt0) cc_final: 0.8088 (mt0) REVERT: K 64 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: K 158 ASP cc_start: 0.7600 (m-30) cc_final: 0.7279 (m-30) REVERT: N 214 MET cc_start: 0.8508 (mmt) cc_final: 0.7247 (mmt) REVERT: P 78 MET cc_start: 0.8606 (mtm) cc_final: 0.8325 (mtm) REVERT: P 116 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8080 (ttmm) REVERT: P 143 ASN cc_start: 0.7700 (m-40) cc_final: 0.7430 (t0) REVERT: Q 119 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7021 (mtp-110) REVERT: R 17 ILE cc_start: 0.4875 (mm) cc_final: 0.4606 (mt) REVERT: R 235 GLN cc_start: 0.6704 (tm-30) cc_final: 0.6486 (tm-30) REVERT: S 20 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5398 (ptt90) REVERT: T 113 CYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7586 (t) REVERT: U 19 ARG cc_start: 0.8404 (ptm-80) cc_final: 0.8137 (ptm160) REVERT: U 61 GLN cc_start: 0.6935 (tm-30) cc_final: 0.6645 (tm-30) REVERT: U 151 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: X 131 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: Y 114 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: Y 158 ASP cc_start: 0.7654 (m-30) cc_final: 0.7323 (m-30) REVERT: Z 175 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7619 (mtp) outliers start: 67 outliers final: 39 residues processed: 453 average time/residue: 2.6408 time to fit residues: 1525.9140 Evaluate side-chains 462 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 408 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 1 residue 125 TYR Chi-restraints excluded: chain 1 residue 136 ASP Chi-restraints excluded: chain 1 residue 212 GLU Chi-restraints excluded: chain 1 residue 241 ASP Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 63 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 32 CYS Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 113 CYS Chi-restraints excluded: chain U residue 151 GLU Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain V residue 63 CYS Chi-restraints excluded: chain V residue 74 ILE Chi-restraints excluded: chain W residue 119 TYR Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 131 GLU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 114 GLU Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Z residue 158 LEU Chi-restraints excluded: chain Z residue 175 MET Chi-restraints excluded: chain Z residue 193 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 2.9990 chunk 531 optimal weight: 3.9990 chunk 485 optimal weight: 1.9990 chunk 517 optimal weight: 0.9990 chunk 311 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 406 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 467 optimal weight: 1.9990 chunk 489 optimal weight: 4.9990 chunk 515 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN F 52 ASN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN M 99 ASN Q 235 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46545 Z= 0.214 Angle : 0.478 6.133 62903 Z= 0.259 Chirality : 0.042 0.165 7158 Planarity : 0.004 0.051 8041 Dihedral : 4.529 21.189 6339 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.27 % Allowed : 11.54 % Favored : 87.20 % 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: 1.43 (0.11), residues: 5705 helix: 2.56 (0.11), residues: 2154 sheet: 0.09 (0.13), residues: 1433 loop : -0.05 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 130 HIS 0.004 0.001 HIS O 209 PHE 0.019 0.001 PHE T 179 TYR 0.029 0.001 TYR G 102 ARG 0.005 0.000 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 424 time to evaluate : 5.810 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 71 MET cc_start: 0.8057 (ttm) cc_final: 0.7525 (ttt) REVERT: 1 125 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.6024 (m-80) REVERT: C 52 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7654 (mt) REVERT: C 119 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6975 (mtp-110) REVERT: C 231 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: D 17 ILE cc_start: 0.4904 (mm) cc_final: 0.4690 (mt) REVERT: H 79 GLN cc_start: 0.8054 (tt0) cc_final: 0.7779 (tt0) REVERT: J 31 GLN cc_start: 0.8443 (mt0) cc_final: 0.8124 (mt0) REVERT: J 131 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: K 154 GLU cc_start: 0.7690 (mp0) cc_final: 0.7158 (mp0) REVERT: K 158 ASP cc_start: 0.7602 (m-30) cc_final: 0.7279 (m-30) REVERT: P 78 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8315 (mtm) REVERT: P 116 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8033 (ttmm) REVERT: P 143 ASN cc_start: 0.7697 (m-40) cc_final: 0.7434 (t0) REVERT: Q 52 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6937 (mt) REVERT: Q 119 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7062 (mtp-110) REVERT: R 17 ILE cc_start: 0.5032 (mm) cc_final: 0.4756 (mt) REVERT: S 20 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5403 (ptt90) REVERT: T 113 CYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7428 (t) REVERT: U 19 ARG cc_start: 0.8402 (ptm-80) cc_final: 0.8164 (ptm160) REVERT: U 61 GLN cc_start: 0.6879 (tm-30) cc_final: 0.6656 (tm-30) REVERT: U 151 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: Y 114 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: Y 158 ASP cc_start: 0.7655 (m-30) cc_final: 0.7318 (m-30) outliers start: 63 outliers final: 37 residues processed: 460 average time/residue: 2.6780 time to fit residues: 1571.5107 Evaluate side-chains 452 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 403 time to evaluate : 5.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 125 TYR Chi-restraints excluded: chain 1 residue 136 ASP Chi-restraints excluded: chain 1 residue 212 GLU Chi-restraints excluded: chain 1 residue 241 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 63 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 32 CYS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 113 CYS Chi-restraints excluded: chain U residue 151 GLU Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain V residue 74 ILE Chi-restraints excluded: chain W residue 119 TYR Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 114 GLU Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Z residue 158 LEU Chi-restraints excluded: chain Z residue 193 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 0.5980 chunk 547 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 573 optimal weight: 3.9990 chunk 528 optimal weight: 0.9980 chunk 456 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN M 99 ASN ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 235 GLN S 114 GLN T 60 GLN W 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46545 Z= 0.209 Angle : 0.477 6.113 62903 Z= 0.259 Chirality : 0.042 0.164 7158 Planarity : 0.004 0.051 8041 Dihedral : 4.495 22.433 6339 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.11 % Allowed : 11.96 % Favored : 86.93 % 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: 1.47 (0.11), residues: 5705 helix: 2.63 (0.11), residues: 2148 sheet: 0.07 (0.13), residues: 1433 loop : -0.04 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 130 HIS 0.004 0.001 HIS A 209 PHE 0.018 0.001 PHE T 179 TYR 0.045 0.001 TYR G 102 ARG 0.004 0.000 ARG M 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11410 Ramachandran restraints generated. 5705 Oldfield, 0 Emsley, 5705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 427 time to evaluate : 5.734 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 71 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7516 (ttt) REVERT: 2 98 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6794 (mpp-170) REVERT: C 52 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7715 (mt) REVERT: C 119 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6974 (mtp-110) REVERT: C 231 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: D 17 ILE cc_start: 0.4908 (mm) cc_final: 0.4697 (mt) REVERT: D 181 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6705 (mmm160) REVERT: D 183 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6663 (pp20) REVERT: F 113 CYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7588 (t) REVERT: H 79 GLN cc_start: 0.8054 (tt0) cc_final: 0.7777 (tt0) REVERT: J 31 GLN cc_start: 0.8423 (mt0) cc_final: 0.8135 (mt0) REVERT: J 131 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6398 (tm-30) REVERT: K 158 ASP cc_start: 0.7600 (m-30) cc_final: 0.7277 (m-30) REVERT: P 78 MET cc_start: 0.8601 (mtm) cc_final: 0.8317 (mtm) REVERT: P 116 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8030 (ttmm) REVERT: P 143 ASN cc_start: 0.7673 (m-40) cc_final: 0.7413 (t0) REVERT: Q 52 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6982 (mt) REVERT: Q 119 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7069 (mtp-110) REVERT: R 56 ASP cc_start: 0.6950 (t0) cc_final: 0.6707 (t0) REVERT: S 20 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.5362 (ptt90) REVERT: T 113 CYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7425 (t) REVERT: U 19 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.8153 (ptm160) REVERT: U 61 GLN cc_start: 0.6876 (tm-30) cc_final: 0.6657 (tm-30) REVERT: U 151 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: Y 114 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: Y 158 ASP cc_start: 0.7651 (m-30) cc_final: 0.7314 (m-30) outliers start: 55 outliers final: 38 residues processed: 462 average time/residue: 2.7842 time to fit residues: 1645.1050 Evaluate side-chains 461 residues out of total 4967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 411 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 1 residue 136 ASP Chi-restraints excluded: chain 1 residue 193 TYR Chi-restraints excluded: chain 1 residue 212 GLU Chi-restraints excluded: chain 1 residue 241 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 63 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain I residue 119 TYR Chi-restraints excluded: chain I residue 245 SER Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain M residue 38 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 32 CYS Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 107 GLU Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain S residue 20 ARG Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain T residue 113 CYS Chi-restraints excluded: chain U residue 151 GLU Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain V residue 74 ILE Chi-restraints excluded: chain W residue 119 TYR Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 114 GLU Chi-restraints excluded: chain Y residue 126 GLU Chi-restraints excluded: chain Z residue 158 LEU Chi-restraints excluded: chain Z residue 193 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 0.8980 chunk 486 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 421 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 457 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 469 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 123 GLN L 164 GLN M 99 ASN ** N 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 235 GLN S 114 GLN T 60 GLN U 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107008 restraints weight = 168500.391| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.83 r_work: 0.3142 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 46545 Z= 0.161 Angle : 0.458 6.039 62903 Z= 0.248 Chirality : 0.042 0.159 7158 Planarity : 0.004 0.051 8041 Dihedral : 4.379 20.627 6339 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.03 % Allowed : 12.16 % Favored : 86.81 % 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: 1.57 (0.11), residues: 5705 helix: 2.74 (0.11), residues: 2150 sheet: 0.08 (0.13), residues: 1397 loop : 0.03 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 133 HIS 0.004 0.001 HIS A 209 PHE 0.019 0.001 PHE T 179 TYR 0.021 0.001 TYR G 102 ARG 0.005 0.000 ARG M 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26554.01 seconds wall clock time: 458 minutes 29.95 seconds (27509.95 seconds total)