Starting phenix.real_space_refine on Mon Aug 25 11:04:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbt_38228/08_2025/8xbt_38228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbt_38228/08_2025/8xbt_38228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbt_38228/08_2025/8xbt_38228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbt_38228/08_2025/8xbt_38228.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbt_38228/08_2025/8xbt_38228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbt_38228/08_2025/8xbt_38228.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 P 309 5.49 5 S 106 5.16 5 C 16431 2.51 5 N 5045 2.21 5 O 5885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 227 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27776 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3189 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3143 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "L" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "M" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "O" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "P" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "Q" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Time building chain proxies: 6.60, per 1000 atoms: 0.24 Number of scatterers: 27776 At special positions: 0 Unit cell: (183.38, 149.46, 131.44, 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 106 16.00 P 309 15.00 O 5885 8.00 N 5045 7.00 C 16431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 18 sheets defined 58.1% alpha, 14.3% beta 150 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.698A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.595A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.579A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.739A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.486A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 24 through 26 No H-bonds generated for 'chain 'K' and resid 24 through 26' Processing helix chain 'K' and resid 27 through 32 Processing helix chain 'K' and resid 34 through 44 Processing helix chain 'K' and resid 49 through 54 Processing helix chain 'K' and resid 56 through 62 removed outlier: 4.287A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 79 Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.521A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 179 Processing helix chain 'K' and resid 181 through 188 removed outlier: 4.003A pdb=" N ASP K 187 " --> pdb=" O SER K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 211 removed outlier: 4.221A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 231 removed outlier: 4.051A pdb=" N LEU K 227 " --> pdb=" O SER K 223 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR K 228 " --> pdb=" O ALA K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 259 removed outlier: 3.687A pdb=" N ARG K 241 " --> pdb=" O GLU K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 296 Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 179 removed outlier: 3.870A pdb=" N LEU L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 213 removed outlier: 4.009A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 232 removed outlier: 4.191A pdb=" N TYR L 228 " --> pdb=" O ALA L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 236 No H-bonds generated for 'chain 'L' and resid 234 through 236' Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 289 through 293 Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 179 removed outlier: 3.572A pdb=" N LEU M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG M 177 " --> pdb=" O ALA M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 211 removed outlier: 4.178A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 232 Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 237 through 260 removed outlier: 4.284A pdb=" N GLN M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET M 243 " --> pdb=" O SER M 239 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS M 244 " --> pdb=" O ALA M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 296 Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 Processing helix chain 'N' and resid 145 through 146 No H-bonds generated for 'chain 'N' and resid 145 through 146' Processing helix chain 'N' and resid 147 through 151 Processing helix chain 'N' and resid 167 through 179 removed outlier: 3.785A pdb=" N ARG N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 211 removed outlier: 3.665A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 232 removed outlier: 3.568A pdb=" N LEU N 227 " --> pdb=" O SER N 223 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 236 No H-bonds generated for 'chain 'N' and resid 234 through 236' Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 291 through 296 removed outlier: 4.639A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 32 removed outlier: 4.197A pdb=" N GLU O 29 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN O 30 " --> pdb=" O ARG O 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS O 31 " --> pdb=" O LEU O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 45 Processing helix chain 'O' and resid 48 through 54 removed outlier: 3.520A pdb=" N VAL O 52 " --> pdb=" O THR O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 62 removed outlier: 3.880A pdb=" N LEU O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 82 Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 Processing helix chain 'O' and resid 145 through 146 No H-bonds generated for 'chain 'O' and resid 145 through 146' Processing helix chain 'O' and resid 147 through 151 Processing helix chain 'O' and resid 167 through 176 Processing helix chain 'O' and resid 177 through 179 No H-bonds generated for 'chain 'O' and resid 177 through 179' Processing helix chain 'O' and resid 181 through 188 removed outlier: 3.589A pdb=" N ASP O 187 " --> pdb=" O SER O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 212 removed outlier: 3.543A pdb=" N MET O 210 " --> pdb=" O GLN O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 232 removed outlier: 4.353A pdb=" N LEU O 227 " --> pdb=" O SER O 223 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR O 228 " --> pdb=" O ALA O 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 234 through 236 No H-bonds generated for 'chain 'O' and resid 234 through 236' Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 291 through 295 removed outlier: 4.869A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 291 through 295' Processing helix chain 'P' and resid 24 through 31 Processing helix chain 'P' and resid 34 through 45 removed outlier: 4.085A pdb=" N LEU P 41 " --> pdb=" O ASP P 37 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU P 42 " --> pdb=" O VAL P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 54 removed outlier: 3.844A pdb=" N VAL P 52 " --> pdb=" O THR P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 63 removed outlier: 3.611A pdb=" N LEU P 60 " --> pdb=" O PRO P 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 82 Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 Processing helix chain 'P' and resid 145 through 146 No H-bonds generated for 'chain 'P' and resid 145 through 146' Processing helix chain 'P' and resid 147 through 151 Processing helix chain 'P' and resid 167 through 178 removed outlier: 3.645A pdb=" N LEU P 171 " --> pdb=" O ARG P 167 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG P 177 " --> pdb=" O ALA P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 188 removed outlier: 3.791A pdb=" N ASP P 187 " --> pdb=" O SER P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 211 removed outlier: 3.748A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 232 Processing helix chain 'P' and resid 234 through 236 No H-bonds generated for 'chain 'P' and resid 234 through 236' Processing helix chain 'P' and resid 237 through 260 Processing helix chain 'P' and resid 290 through 296 removed outlier: 4.039A pdb=" N HIS P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'Q' and resid 132 through 144 Processing helix chain 'Q' and resid 145 through 146 No H-bonds generated for 'chain 'Q' and resid 145 through 146' Processing helix chain 'Q' and resid 147 through 151 Processing helix chain 'Q' and resid 167 through 178 removed outlier: 3.728A pdb=" N ARG Q 177 " --> pdb=" O ALA Q 173 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR Q 178 " --> pdb=" O VAL Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 188 Processing helix chain 'Q' and resid 196 through 211 removed outlier: 3.573A pdb=" N ALA Q 209 " --> pdb=" O TYR Q 205 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 223 through 232 removed outlier: 3.897A pdb=" N LEU Q 227 " --> pdb=" O SER Q 223 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR Q 228 " --> pdb=" O ALA Q 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 260 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 3.915A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 32 removed outlier: 3.578A pdb=" N ARG R 27 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU R 29 " --> pdb=" O SER R 26 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN R 30 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 45 Processing helix chain 'R' and resid 48 through 52 Processing helix chain 'R' and resid 56 through 62 removed outlier: 3.794A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 82 Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.511A pdb=" N ILE R 136 " --> pdb=" O GLY R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 146 No H-bonds generated for 'chain 'R' and resid 145 through 146' Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 167 through 179 removed outlier: 3.590A pdb=" N LEU R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG R 177 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR R 178 " --> pdb=" O VAL R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 188 Processing helix chain 'R' and resid 196 through 211 Processing helix chain 'R' and resid 225 through 232 Processing helix chain 'R' and resid 234 through 236 No H-bonds generated for 'chain 'R' and resid 234 through 236' Processing helix chain 'R' and resid 237 through 260 Processing helix chain 'R' and resid 291 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.076A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.826A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.244A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.824A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 189 through 193 removed outlier: 3.671A pdb=" N ALA K 192 " --> pdb=" O TYR K 159 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP K 316 " --> pdb=" O ARG K 299 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR K 301 " --> pdb=" O ILE K 314 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE K 314 " --> pdb=" O TYR K 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 323 " --> pdb=" O ILE K 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 189 through 193 removed outlier: 3.854A pdb=" N ALA L 192 " --> pdb=" O TYR L 159 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP L 161 " --> pdb=" O ALA L 192 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS L 156 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE L 220 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N MET L 158 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASP L 222 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE L 160 " --> pdb=" O ASP L 222 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER L 121 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE L 265 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR L 123 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASN L 267 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET L 125 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE L 311 " --> pdb=" O ARG L 303 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY L 333 " --> pdb=" O ASN L 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 189 through 193 removed outlier: 5.139A pdb=" N LYS M 156 " --> pdb=" O TYR M 216 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER M 121 " --> pdb=" O VAL M 263 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE M 265 " --> pdb=" O SER M 121 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR M 123 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN M 267 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET M 125 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR M 298 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE M 327 " --> pdb=" O ARG M 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.522A pdb=" N LYS N 156 " --> pdb=" O TYR N 216 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR N 315 " --> pdb=" O ARG N 299 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY N 333 " --> pdb=" O ASN N 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 189 through 193 removed outlier: 3.640A pdb=" N ALA O 192 " --> pdb=" O TYR O 159 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER O 121 " --> pdb=" O VAL O 263 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE O 265 " --> pdb=" O SER O 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR O 123 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN O 267 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET O 125 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE O 122 " --> pdb=" O SER O 296 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR O 298 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG O 299 " --> pdb=" O TYR O 315 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE O 311 " --> pdb=" O ARG O 303 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 189 through 193 removed outlier: 6.992A pdb=" N ALA P 157 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ALA P 192 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR P 159 " --> pdb=" O ALA P 192 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR P 298 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR P 301 " --> pdb=" O ILE P 314 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE P 314 " --> pdb=" O TYR P 301 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG P 303 " --> pdb=" O CYS P 312 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N CYS P 312 " --> pdb=" O ARG P 303 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 189 through 193 removed outlier: 5.231A pdb=" N LYS Q 156 " --> pdb=" O TYR Q 216 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR Q 298 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Q 124 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP Q 316 " --> pdb=" O ARG Q 299 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR Q 301 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE Q 314 " --> pdb=" O TYR Q 301 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG Q 303 " --> pdb=" O CYS Q 312 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N CYS Q 312 " --> pdb=" O ARG Q 303 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA Q 323 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 189 through 193 removed outlier: 5.407A pdb=" N LYS R 156 " --> pdb=" O TYR R 216 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLN R 268 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG R 299 " --> pdb=" O TYR R 315 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE R 311 " --> pdb=" O ARG R 303 " (cutoff:3.500A) 1199 hydrogen bonds defined for protein. 3453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5468 1.33 - 1.45: 7911 1.45 - 1.57: 14656 1.57 - 1.70: 616 1.70 - 1.82: 172 Bond restraints: 28823 Sorted by residual: bond pdb=" N ARG N 150 " pdb=" CA ARG N 150 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.10e-02 8.26e+03 1.17e+01 bond pdb=" N TYR P 178 " pdb=" CA TYR P 178 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" N GLU N 322 " pdb=" CA GLU N 322 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" N GLY M 305 " pdb=" CA GLY M 305 " ideal model delta sigma weight residual 1.442 1.467 -0.026 7.70e-03 1.69e+04 1.10e+01 bond pdb=" CZ ARG L 150 " pdb=" NH1 ARG L 150 " ideal model delta sigma weight residual 1.323 1.277 0.046 1.40e-02 5.10e+03 1.10e+01 ... (remaining 28818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 37725 3.05 - 6.10: 2391 6.10 - 9.15: 82 9.15 - 12.20: 5 12.20 - 15.25: 1 Bond angle restraints: 40204 Sorted by residual: angle pdb=" CA PHE Q 195 " pdb=" CB PHE Q 195 " pdb=" CG PHE Q 195 " ideal model delta sigma weight residual 113.80 121.20 -7.40 1.00e+00 1.00e+00 5.47e+01 angle pdb=" CA PHE R 129 " pdb=" CB PHE R 129 " pdb=" CG PHE R 129 " ideal model delta sigma weight residual 113.80 120.92 -7.12 1.00e+00 1.00e+00 5.07e+01 angle pdb=" C ASN Q 196 " pdb=" N THR Q 197 " pdb=" CA THR Q 197 " ideal model delta sigma weight residual 120.28 129.09 -8.81 1.34e+00 5.57e-01 4.33e+01 angle pdb=" CA PHE K 46 " pdb=" CB PHE K 46 " pdb=" CG PHE K 46 " ideal model delta sigma weight residual 113.80 120.26 -6.46 1.00e+00 1.00e+00 4.18e+01 angle pdb=" CA PHE O 129 " pdb=" CB PHE O 129 " pdb=" CG PHE O 129 " ideal model delta sigma weight residual 113.80 119.96 -6.16 1.00e+00 1.00e+00 3.80e+01 ... (remaining 40199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.41: 13386 20.41 - 40.82: 1780 40.82 - 61.24: 1351 61.24 - 81.65: 91 81.65 - 102.06: 12 Dihedral angle restraints: 16620 sinusoidal: 8702 harmonic: 7918 Sorted by residual: dihedral pdb=" CD ARG Q 310 " pdb=" NE ARG Q 310 " pdb=" CZ ARG Q 310 " pdb=" NH1 ARG Q 310 " ideal model delta sinusoidal sigma weight residual 0.00 -90.30 90.30 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CD ARG R 310 " pdb=" NE ARG R 310 " pdb=" CZ ARG R 310 " pdb=" NH1 ARG R 310 " ideal model delta sinusoidal sigma weight residual 0.00 86.20 -86.20 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CD ARG K 254 " pdb=" NE ARG K 254 " pdb=" CZ ARG K 254 " pdb=" NH1 ARG K 254 " ideal model delta sinusoidal sigma weight residual 0.00 85.48 -85.48 1 1.00e+01 1.00e-02 8.84e+01 ... (remaining 16617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 4193 0.135 - 0.269: 357 0.269 - 0.404: 33 0.404 - 0.538: 4 0.538 - 0.673: 10 Chirality restraints: 4597 Sorted by residual: chirality pdb=" CA SER P 317 " pdb=" N SER P 317 " pdb=" C SER P 317 " pdb=" CB SER P 317 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" P DC J 4 " pdb=" OP1 DC J 4 " pdb=" OP2 DC J 4 " pdb=" O5' DC J 4 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DC I 151 " pdb=" OP1 DC I 151 " pdb=" OP2 DC I 151 " pdb=" O5' DC I 151 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 4594 not shown) Planarity restraints: 4092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 254 " -1.097 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG K 254 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG K 254 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 254 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG K 254 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 310 " -1.092 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG Q 310 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG Q 310 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 310 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 310 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 310 " -1.090 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG R 310 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG R 310 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG R 310 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG R 310 " -0.016 2.00e-02 2.50e+03 ... (remaining 4089 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 11 1.83 - 2.60: 216 2.60 - 3.37: 35953 3.37 - 4.13: 76884 4.13 - 4.90: 125378 Nonbonded interactions: 238442 Sorted by model distance: nonbonded pdb=" O GLY O 305 " pdb=" NH1 ARG O 310 " model vdw 1.066 3.120 nonbonded pdb=" O THR R 165 " pdb=" NH1 ARG R 170 " model vdw 1.281 3.120 nonbonded pdb=" OP1 DA I 153 " pdb=" CB ARG P 235 " model vdw 1.336 3.440 nonbonded pdb=" O THR R 165 " pdb=" CZ ARG R 170 " model vdw 1.424 3.270 nonbonded pdb=" ND1 HIS M 138 " pdb=" NH2 ARG M 170 " model vdw 1.427 3.200 ... (remaining 238437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.440 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.100 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 : 0.012 0.444 28827 Z= 0.766 Angle : 1.499 15.251 40204 Z= 0.979 Chirality : 0.083 0.673 4597 Planarity : 0.037 0.492 4092 Dihedral : 23.156 102.062 11550 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.05 % Allowed : 4.51 % Favored : 93.43 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.14), residues: 2714 helix: -0.67 (0.12), residues: 1396 sheet: 0.03 (0.31), residues: 269 loop : -1.09 (0.17), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 52 TYR 0.118 0.014 TYR N 228 PHE 0.106 0.013 PHE N 126 HIS 0.016 0.004 HIS R 244 Details of bonding type rmsd covalent geometry : bond 0.01113 (28823) covalent geometry : angle 1.49869 (40204) hydrogen bonds : bond 0.15126 ( 1579) hydrogen bonds : angle 6.85001 ( 4209) Misc. bond : bond 0.33273 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.9652 (mt) cc_final: 0.9418 (mm) REVERT: A 105 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9116 (mm-30) REVERT: A 119 ILE cc_start: 0.9407 (pt) cc_final: 0.9102 (pt) REVERT: B 88 TYR cc_start: 0.9147 (m-10) cc_final: 0.8817 (m-80) REVERT: B 92 ARG cc_start: 0.9374 (ptm-80) cc_final: 0.8966 (ttp80) REVERT: C 38 ASN cc_start: 0.9139 (m-40) cc_final: 0.8626 (m-40) REVERT: C 56 GLU cc_start: 0.9324 (tt0) cc_final: 0.8446 (tt0) REVERT: C 64 GLU cc_start: 0.9192 (tp30) cc_final: 0.8637 (tp30) REVERT: D 80 LEU cc_start: 0.9729 (mt) cc_final: 0.9523 (tp) REVERT: D 99 ARG cc_start: 0.9240 (mtt90) cc_final: 0.8939 (ttm110) REVERT: E 53 ARG cc_start: 0.9469 (ttt180) cc_final: 0.9141 (ttp80) REVERT: E 94 GLU cc_start: 0.9687 (mm-30) cc_final: 0.8980 (mm-30) REVERT: E 96 CYS cc_start: 0.9400 (m) cc_final: 0.9195 (p) REVERT: E 106 ASP cc_start: 0.9285 (m-30) cc_final: 0.8571 (p0) REVERT: E 120 MET cc_start: 0.8717 (mtt) cc_final: 0.8216 (mtp) REVERT: F 44 LYS cc_start: 0.9089 (tttt) cc_final: 0.8696 (ttmm) REVERT: F 59 LYS cc_start: 0.9695 (tttm) cc_final: 0.9226 (tppp) REVERT: F 63 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9066 (mt-10) REVERT: F 84 MET cc_start: 0.9186 (mmm) cc_final: 0.8843 (mmm) REVERT: G 25 PHE cc_start: 0.8825 (m-80) cc_final: 0.8543 (m-10) REVERT: G 56 GLU cc_start: 0.9314 (tt0) cc_final: 0.8907 (tt0) REVERT: K 243 MET cc_start: 0.1410 (mmt) cc_final: 0.1189 (mmm) REVERT: K 251 MET cc_start: 0.6914 (mtp) cc_final: 0.6358 (mmm) REVERT: M 196 ASN cc_start: 0.7574 (p0) cc_final: 0.7305 (t0) REVERT: N 210 MET cc_start: 0.1465 (tmm) cc_final: 0.1138 (tmm) REVERT: N 243 MET cc_start: 0.0676 (mmt) cc_final: 0.0445 (mmt) REVERT: P 125 MET cc_start: 0.5208 (pmm) cc_final: 0.4898 (pmm) REVERT: P 158 MET cc_start: 0.2224 (mmm) cc_final: 0.1915 (ttt) REVERT: P 210 MET cc_start: 0.0524 (tmm) cc_final: 0.0213 (tmm) REVERT: Q 210 MET cc_start: -0.1192 (tmm) cc_final: -0.1685 (tmm) REVERT: Q 235 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7705 (tpm170) REVERT: R 125 MET cc_start: 0.5649 (pmm) cc_final: 0.5397 (ptt) REVERT: R 233 SER cc_start: -0.1615 (OUTLIER) cc_final: -0.1916 (t) REVERT: R 243 MET cc_start: 0.5393 (mmt) cc_final: 0.5158 (ptt) outliers start: 46 outliers final: 15 residues processed: 312 average time/residue: 0.1959 time to fit residues: 92.0639 Evaluate side-chains 151 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 84 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN K 62 ASN K 135 GLN ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN P 206 GLN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 206 GLN R 114 GLN R 244 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.067764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.042722 restraints weight = 254132.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.044089 restraints weight = 107730.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.044837 restraints weight = 63223.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.045268 restraints weight = 45928.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.045493 restraints weight = 38323.933| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28827 Z= 0.255 Angle : 0.686 15.810 40204 Z= 0.386 Chirality : 0.041 0.174 4597 Planarity : 0.007 0.206 4092 Dihedral : 26.565 89.597 6442 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 2714 helix: 0.79 (0.13), residues: 1434 sheet: -0.20 (0.27), residues: 359 loop : -0.51 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG O 310 TYR 0.018 0.002 TYR M 301 PHE 0.025 0.002 PHE M 126 HIS 0.012 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00547 (28823) covalent geometry : angle 0.68597 (40204) hydrogen bonds : bond 0.06066 ( 1579) hydrogen bonds : angle 5.10377 ( 4209) Misc. bond : bond 0.00249 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9275 (pt) cc_final: 0.9070 (pt) REVERT: B 44 LYS cc_start: 0.9249 (tttt) cc_final: 0.8985 (ttmm) REVERT: B 88 TYR cc_start: 0.8560 (m-10) cc_final: 0.8223 (m-10) REVERT: C 56 GLU cc_start: 0.8761 (tt0) cc_final: 0.8438 (mt-10) REVERT: C 64 GLU cc_start: 0.8186 (tp30) cc_final: 0.7834 (tp30) REVERT: E 106 ASP cc_start: 0.8519 (m-30) cc_final: 0.7763 (m-30) REVERT: E 120 MET cc_start: 0.8225 (mtt) cc_final: 0.7952 (mtp) REVERT: F 59 LYS cc_start: 0.9555 (tttm) cc_final: 0.8855 (tppp) REVERT: F 84 MET cc_start: 0.8901 (mmm) cc_final: 0.8652 (tpt) REVERT: K 125 MET cc_start: 0.5940 (pmm) cc_final: 0.5377 (pmm) REVERT: M 251 MET cc_start: -0.5703 (ttt) cc_final: -0.6574 (mmp) REVERT: N 211 MET cc_start: -0.0857 (ttm) cc_final: -0.1224 (mtt) REVERT: P 210 MET cc_start: 0.0984 (tmm) cc_final: 0.0717 (tmm) REVERT: Q 235 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7001 (tpt170) REVERT: Q 251 MET cc_start: 0.3827 (tpp) cc_final: 0.2458 (mtt) REVERT: Q 326 MET cc_start: 0.6759 (tpp) cc_final: 0.6316 (pmm) REVERT: R 125 MET cc_start: 0.5411 (pmm) cc_final: 0.5046 (ptt) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.1895 time to fit residues: 46.5218 Evaluate side-chains 107 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 264 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 261 optimal weight: 50.0000 chunk 174 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 178 optimal weight: 50.0000 chunk 17 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 196 ASN P 206 GLN P 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.068658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.043670 restraints weight = 255146.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.045057 restraints weight = 106277.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.045818 restraints weight = 61548.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.046211 restraints weight = 44043.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.046450 restraints weight = 36631.738| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28827 Z= 0.154 Angle : 0.575 13.391 40204 Z= 0.326 Chirality : 0.037 0.146 4597 Planarity : 0.004 0.111 4092 Dihedral : 26.093 89.977 6442 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2714 helix: 1.20 (0.14), residues: 1450 sheet: -0.24 (0.28), residues: 349 loop : -0.35 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 310 TYR 0.022 0.001 TYR P 216 PHE 0.021 0.002 PHE E 104 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00327 (28823) covalent geometry : angle 0.57507 (40204) hydrogen bonds : bond 0.04302 ( 1579) hydrogen bonds : angle 4.43649 ( 4209) Misc. bond : bond 0.00171 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8168 (mm-30) REVERT: B 88 TYR cc_start: 0.8447 (m-10) cc_final: 0.8158 (m-80) REVERT: B 98 TYR cc_start: 0.8525 (m-80) cc_final: 0.8323 (m-80) REVERT: C 38 ASN cc_start: 0.8790 (m-40) cc_final: 0.8535 (m-40) REVERT: D 71 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8580 (mm-30) REVERT: E 90 MET cc_start: 0.8883 (mmm) cc_final: 0.8594 (mmm) REVERT: F 84 MET cc_start: 0.8447 (mmm) cc_final: 0.7888 (tpp) REVERT: K 211 MET cc_start: -0.4205 (mtp) cc_final: -0.4505 (mtp) REVERT: M 211 MET cc_start: 0.2662 (tpp) cc_final: 0.2438 (tpp) REVERT: M 251 MET cc_start: -0.5745 (ttt) cc_final: -0.6635 (mmp) REVERT: N 210 MET cc_start: 0.0513 (tmm) cc_final: 0.0101 (ttp) REVERT: O 125 MET cc_start: 0.5516 (ptt) cc_final: 0.5117 (ttp) REVERT: Q 235 ARG cc_start: 0.7416 (mtt180) cc_final: 0.6828 (tpt170) REVERT: Q 251 MET cc_start: 0.4512 (tpp) cc_final: 0.3356 (mtt) REVERT: Q 326 MET cc_start: 0.6673 (tpp) cc_final: 0.6226 (pmm) REVERT: R 125 MET cc_start: 0.5561 (pmm) cc_final: 0.5104 (ptt) REVERT: R 210 MET cc_start: 0.6045 (ptm) cc_final: 0.5821 (ppp) REVERT: R 211 MET cc_start: 0.3682 (tpp) cc_final: 0.3327 (tpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1590 time to fit residues: 42.0420 Evaluate side-chains 110 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 243 optimal weight: 30.0000 chunk 145 optimal weight: 40.0000 chunk 264 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 239 optimal weight: 8.9990 chunk 283 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS R 34 ASN R 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.068021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.043302 restraints weight = 256100.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.044658 restraints weight = 107695.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.045403 restraints weight = 62655.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.045803 restraints weight = 44932.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.046043 restraints weight = 37289.308| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28827 Z= 0.168 Angle : 0.559 14.352 40204 Z= 0.318 Chirality : 0.037 0.168 4597 Planarity : 0.004 0.077 4092 Dihedral : 25.997 90.857 6442 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.16), residues: 2714 helix: 1.30 (0.14), residues: 1449 sheet: -0.34 (0.27), residues: 363 loop : -0.26 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 310 TYR 0.014 0.001 TYR K 228 PHE 0.021 0.002 PHE M 126 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00359 (28823) covalent geometry : angle 0.55898 (40204) hydrogen bonds : bond 0.04433 ( 1579) hydrogen bonds : angle 4.29289 ( 4209) Misc. bond : bond 0.00140 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8351 (mm-30) REVERT: A 120 MET cc_start: 0.9247 (mmp) cc_final: 0.8972 (mmm) REVERT: B 66 ILE cc_start: 0.9633 (mm) cc_final: 0.9416 (pt) REVERT: B 88 TYR cc_start: 0.8544 (m-10) cc_final: 0.8336 (m-10) REVERT: B 98 TYR cc_start: 0.8587 (m-80) cc_final: 0.8363 (m-80) REVERT: C 38 ASN cc_start: 0.8910 (m-40) cc_final: 0.8500 (m110) REVERT: D 71 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8710 (mm-30) REVERT: E 73 GLU cc_start: 0.8770 (tt0) cc_final: 0.8434 (tm-30) REVERT: E 120 MET cc_start: 0.8049 (mtp) cc_final: 0.7558 (mtt) REVERT: F 84 MET cc_start: 0.8497 (mmm) cc_final: 0.8204 (tpp) REVERT: K 125 MET cc_start: 0.5760 (pmm) cc_final: 0.5322 (pmm) REVERT: M 251 MET cc_start: -0.5771 (ttt) cc_final: -0.6571 (mmp) REVERT: N 210 MET cc_start: 0.0541 (tmm) cc_final: -0.0093 (ptm) REVERT: O 210 MET cc_start: -0.0956 (ptt) cc_final: -0.1299 (ptt) REVERT: O 243 MET cc_start: 0.8090 (mmp) cc_final: 0.7888 (mmm) REVERT: P 243 MET cc_start: 0.5591 (mmp) cc_final: 0.5301 (tmm) REVERT: Q 235 ARG cc_start: 0.7312 (mtt180) cc_final: 0.6499 (tpt170) REVERT: Q 243 MET cc_start: 0.0496 (mmt) cc_final: -0.0067 (ttt) REVERT: Q 251 MET cc_start: 0.4456 (tpp) cc_final: 0.3329 (mtt) REVERT: Q 326 MET cc_start: 0.6726 (tpp) cc_final: 0.6272 (pmm) REVERT: R 125 MET cc_start: 0.5493 (pmm) cc_final: 0.5286 (ptt) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1422 time to fit residues: 34.1305 Evaluate side-chains 103 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 141 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 chunk 183 optimal weight: 50.0000 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 299 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 HIS O 244 HIS Q 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.066944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.042188 restraints weight = 256608.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.043586 restraints weight = 110539.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.044284 restraints weight = 64987.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.044672 restraints weight = 47002.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.044874 restraints weight = 39135.684| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28827 Z= 0.219 Angle : 0.596 16.272 40204 Z= 0.338 Chirality : 0.039 0.197 4597 Planarity : 0.006 0.290 4092 Dihedral : 26.068 91.866 6442 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.16), residues: 2714 helix: 1.19 (0.14), residues: 1460 sheet: -0.49 (0.27), residues: 358 loop : -0.37 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 310 TYR 0.015 0.001 TYR K 228 PHE 0.016 0.002 PHE M 126 HIS 0.013 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00473 (28823) covalent geometry : angle 0.59624 (40204) hydrogen bonds : bond 0.05231 ( 1579) hydrogen bonds : angle 4.46050 ( 4209) Misc. bond : bond 0.00313 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9251 (mmp) cc_final: 0.8818 (mmm) REVERT: E 50 GLU cc_start: 0.8516 (tp30) cc_final: 0.8096 (tp30) REVERT: E 120 MET cc_start: 0.8246 (mtp) cc_final: 0.7925 (mtp) REVERT: F 84 MET cc_start: 0.8573 (mmm) cc_final: 0.8084 (tpp) REVERT: M 251 MET cc_start: -0.5870 (ttt) cc_final: -0.6621 (mmp) REVERT: P 243 MET cc_start: 0.5625 (mmp) cc_final: 0.5335 (tmm) REVERT: Q 235 ARG cc_start: 0.7187 (mtt180) cc_final: 0.6258 (tpt170) REVERT: Q 243 MET cc_start: 0.0388 (mmt) cc_final: -0.0163 (ttt) REVERT: Q 251 MET cc_start: 0.4117 (tpp) cc_final: 0.2902 (mtt) REVERT: Q 326 MET cc_start: 0.6646 (tpp) cc_final: 0.6040 (pmm) REVERT: R 125 MET cc_start: 0.5563 (pmm) cc_final: 0.5269 (ptt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1407 time to fit residues: 28.6045 Evaluate side-chains 96 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 76 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 178 optimal weight: 50.0000 chunk 234 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 190 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 263 optimal weight: 50.0000 chunk 187 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.066725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.041732 restraints weight = 256183.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.043166 restraints weight = 104708.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.043929 restraints weight = 60584.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.044374 restraints weight = 43692.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.044581 restraints weight = 36164.399| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28827 Z= 0.196 Angle : 0.582 14.121 40204 Z= 0.328 Chirality : 0.038 0.141 4597 Planarity : 0.005 0.175 4092 Dihedral : 26.012 92.676 6442 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2714 helix: 1.29 (0.14), residues: 1454 sheet: -0.51 (0.27), residues: 370 loop : -0.39 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 310 TYR 0.029 0.001 TYR B 88 PHE 0.015 0.002 PHE L 248 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00422 (28823) covalent geometry : angle 0.58210 (40204) hydrogen bonds : bond 0.04613 ( 1579) hydrogen bonds : angle 4.36597 ( 4209) Misc. bond : bond 0.00216 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.619 Fit side-chains REVERT: A 120 MET cc_start: 0.9312 (mmp) cc_final: 0.8764 (mmm) REVERT: B 98 TYR cc_start: 0.8634 (m-80) cc_final: 0.8296 (m-80) REVERT: E 50 GLU cc_start: 0.8943 (tp30) cc_final: 0.8575 (tp30) REVERT: E 56 LYS cc_start: 0.9466 (tppp) cc_final: 0.9222 (tppp) REVERT: E 120 MET cc_start: 0.8225 (mtp) cc_final: 0.7844 (mtp) REVERT: F 84 MET cc_start: 0.8679 (mmm) cc_final: 0.8342 (tpp) REVERT: M 251 MET cc_start: -0.5871 (ttt) cc_final: -0.6574 (mmp) REVERT: O 125 MET cc_start: 0.5399 (ptt) cc_final: 0.5046 (ttp) REVERT: O 210 MET cc_start: -0.1224 (ptt) cc_final: -0.1860 (ptt) REVERT: O 211 MET cc_start: -0.3835 (ttt) cc_final: -0.4203 (tpp) REVERT: O 243 MET cc_start: 0.7989 (mmp) cc_final: 0.7769 (mmm) REVERT: P 243 MET cc_start: 0.5697 (mmp) cc_final: 0.5439 (tmm) REVERT: Q 235 ARG cc_start: 0.7098 (mtt180) cc_final: 0.5980 (tpt170) REVERT: Q 243 MET cc_start: 0.0278 (mmt) cc_final: -0.0229 (ttt) REVERT: Q 251 MET cc_start: 0.3872 (tpp) cc_final: 0.2647 (mtt) REVERT: Q 326 MET cc_start: 0.6679 (tpp) cc_final: 0.6031 (pmm) REVERT: R 125 MET cc_start: 0.6035 (pmm) cc_final: 0.5740 (ptt) REVERT: R 211 MET cc_start: 0.3202 (tpp) cc_final: 0.2656 (tpp) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.1415 time to fit residues: 29.1926 Evaluate side-chains 99 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 136 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 261 optimal weight: 40.0000 chunk 43 optimal weight: 0.4980 chunk 265 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.068156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.043018 restraints weight = 251863.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.044505 restraints weight = 102511.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.045294 restraints weight = 58969.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.045764 restraints weight = 42565.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.046024 restraints weight = 35250.506| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28827 Z= 0.128 Angle : 0.536 11.934 40204 Z= 0.304 Chirality : 0.037 0.139 4597 Planarity : 0.004 0.135 4092 Dihedral : 25.722 90.967 6442 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.16), residues: 2714 helix: 1.58 (0.14), residues: 1449 sheet: -0.31 (0.28), residues: 364 loop : -0.40 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 310 TYR 0.039 0.001 TYR B 88 PHE 0.013 0.001 PHE Q 248 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00269 (28823) covalent geometry : angle 0.53566 (40204) hydrogen bonds : bond 0.03613 ( 1579) hydrogen bonds : angle 4.05496 ( 4209) Misc. bond : bond 0.00171 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.931 Fit side-chains REVERT: A 120 MET cc_start: 0.9226 (mmp) cc_final: 0.8904 (mmm) REVERT: B 98 TYR cc_start: 0.8586 (m-80) cc_final: 0.8296 (m-80) REVERT: E 50 GLU cc_start: 0.8948 (tp30) cc_final: 0.8588 (tp30) REVERT: E 56 LYS cc_start: 0.9389 (tppp) cc_final: 0.9128 (tppp) REVERT: E 120 MET cc_start: 0.8062 (mtp) cc_final: 0.7561 (mtt) REVERT: M 211 MET cc_start: 0.0594 (ttt) cc_final: -0.0189 (tpp) REVERT: M 251 MET cc_start: -0.5899 (ttt) cc_final: -0.6679 (mmp) REVERT: N 326 MET cc_start: 0.8977 (pmm) cc_final: 0.8597 (ttm) REVERT: O 125 MET cc_start: 0.5362 (ptt) cc_final: 0.5068 (ttp) REVERT: O 210 MET cc_start: -0.1285 (ptt) cc_final: -0.1909 (ptt) REVERT: O 211 MET cc_start: -0.4051 (ttt) cc_final: -0.4335 (tpp) REVERT: Q 125 MET cc_start: 0.8050 (ptt) cc_final: 0.7728 (pmm) REVERT: Q 235 ARG cc_start: 0.6999 (mtt180) cc_final: 0.5816 (tpt170) REVERT: Q 243 MET cc_start: 0.0693 (mmt) cc_final: 0.0238 (ttt) REVERT: Q 251 MET cc_start: 0.4116 (tpp) cc_final: 0.2997 (mtt) REVERT: Q 326 MET cc_start: 0.6581 (tpp) cc_final: 0.6064 (pmm) REVERT: R 125 MET cc_start: 0.6085 (pmm) cc_final: 0.5793 (ptt) REVERT: R 211 MET cc_start: 0.3345 (tpp) cc_final: 0.2795 (tpp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1470 time to fit residues: 34.9137 Evaluate side-chains 101 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 194 optimal weight: 50.0000 chunk 234 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 231 optimal weight: 40.0000 chunk 199 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 179 optimal weight: 40.0000 chunk 141 optimal weight: 20.0000 chunk 196 optimal weight: 40.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.065984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.040796 restraints weight = 259195.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.042172 restraints weight = 111824.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.042886 restraints weight = 66067.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.043288 restraints weight = 48109.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.043362 restraints weight = 40241.832| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28827 Z= 0.248 Angle : 0.624 18.919 40204 Z= 0.348 Chirality : 0.039 0.169 4597 Planarity : 0.004 0.126 4092 Dihedral : 25.992 93.618 6442 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.16), residues: 2714 helix: 1.27 (0.13), residues: 1451 sheet: -0.48 (0.27), residues: 373 loop : -0.45 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 310 TYR 0.029 0.002 TYR B 88 PHE 0.015 0.002 PHE K 327 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00538 (28823) covalent geometry : angle 0.62423 (40204) hydrogen bonds : bond 0.05413 ( 1579) hydrogen bonds : angle 4.48050 ( 4209) Misc. bond : bond 0.00154 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9408 (mmp) cc_final: 0.8839 (mmm) REVERT: E 50 GLU cc_start: 0.9059 (tp30) cc_final: 0.8642 (tp30) REVERT: E 56 LYS cc_start: 0.9500 (tppp) cc_final: 0.9264 (tppp) REVERT: E 120 MET cc_start: 0.8384 (mtp) cc_final: 0.7964 (mtp) REVERT: F 63 GLU cc_start: 0.9041 (pt0) cc_final: 0.8819 (pp20) REVERT: L 158 MET cc_start: -0.1535 (mmp) cc_final: -0.2116 (mmt) REVERT: M 251 MET cc_start: -0.5790 (ttt) cc_final: -0.6543 (mmp) REVERT: O 125 MET cc_start: 0.5421 (ptt) cc_final: 0.5110 (ttp) REVERT: O 211 MET cc_start: -0.3787 (ttt) cc_final: -0.4102 (tpp) REVERT: Q 125 MET cc_start: 0.8213 (ptt) cc_final: 0.7901 (pmm) REVERT: Q 235 ARG cc_start: 0.6373 (mtt180) cc_final: 0.5470 (tpt170) REVERT: Q 243 MET cc_start: 0.0494 (mmt) cc_final: 0.0097 (ttt) REVERT: Q 251 MET cc_start: 0.4444 (tpp) cc_final: 0.3399 (mtm) REVERT: Q 326 MET cc_start: 0.6643 (tpp) cc_final: 0.6072 (pmm) REVERT: R 125 MET cc_start: 0.6586 (pmm) cc_final: 0.6280 (ptt) REVERT: R 211 MET cc_start: 0.3882 (tpp) cc_final: 0.3361 (tpp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1499 time to fit residues: 29.0559 Evaluate side-chains 93 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 149 optimal weight: 0.0020 chunk 6 optimal weight: 0.8980 chunk 219 optimal weight: 50.0000 chunk 60 optimal weight: 0.4980 chunk 218 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 280 optimal weight: 40.0000 chunk 143 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 206 optimal weight: 40.0000 chunk 186 optimal weight: 40.0000 overall best weight: 3.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.067113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.042138 restraints weight = 256292.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.043471 restraints weight = 111690.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.044208 restraints weight = 66707.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.044605 restraints weight = 48744.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.044852 restraints weight = 40955.437| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28827 Z= 0.169 Angle : 0.576 15.633 40204 Z= 0.323 Chirality : 0.038 0.158 4597 Planarity : 0.004 0.119 4092 Dihedral : 25.925 92.622 6442 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.16), residues: 2714 helix: 1.37 (0.14), residues: 1451 sheet: -0.36 (0.28), residues: 360 loop : -0.44 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 310 TYR 0.014 0.001 TYR H 83 PHE 0.014 0.001 PHE K 327 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00366 (28823) covalent geometry : angle 0.57614 (40204) hydrogen bonds : bond 0.04254 ( 1579) hydrogen bonds : angle 4.25020 ( 4209) Misc. bond : bond 0.00143 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9329 (mmp) cc_final: 0.9005 (mmm) REVERT: B 98 TYR cc_start: 0.8540 (m-80) cc_final: 0.8301 (m-80) REVERT: E 50 GLU cc_start: 0.8738 (tp30) cc_final: 0.8419 (tp30) REVERT: E 56 LYS cc_start: 0.9468 (tppp) cc_final: 0.9196 (tppp) REVERT: E 120 MET cc_start: 0.8328 (mtp) cc_final: 0.7812 (mtt) REVERT: F 63 GLU cc_start: 0.9031 (pt0) cc_final: 0.8782 (pp20) REVERT: L 158 MET cc_start: -0.1560 (mmp) cc_final: -0.1835 (mpp) REVERT: M 251 MET cc_start: -0.5801 (ttt) cc_final: -0.6542 (mmp) REVERT: O 125 MET cc_start: 0.5455 (ptt) cc_final: 0.5236 (ttp) REVERT: O 210 MET cc_start: -0.0811 (ptt) cc_final: -0.1552 (ptt) REVERT: O 211 MET cc_start: -0.3937 (ttt) cc_final: -0.4222 (tpp) REVERT: O 243 MET cc_start: 0.7295 (mmm) cc_final: 0.6943 (mmm) REVERT: Q 125 MET cc_start: 0.8160 (ptt) cc_final: 0.7852 (pmm) REVERT: Q 235 ARG cc_start: 0.6434 (mtt180) cc_final: 0.5478 (tpt170) REVERT: Q 243 MET cc_start: 0.0582 (mmt) cc_final: 0.0138 (ttt) REVERT: Q 251 MET cc_start: 0.4337 (tpp) cc_final: 0.3320 (mtm) REVERT: Q 326 MET cc_start: 0.6631 (tpp) cc_final: 0.6088 (pmm) REVERT: R 125 MET cc_start: 0.6579 (pmm) cc_final: 0.6234 (ptt) REVERT: R 211 MET cc_start: 0.3356 (tpp) cc_final: 0.2831 (tpp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1417 time to fit residues: 29.9999 Evaluate side-chains 99 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 91 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 chunk 146 optimal weight: 40.0000 chunk 234 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 231 optimal weight: 50.0000 chunk 104 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.066451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.041712 restraints weight = 256877.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.043022 restraints weight = 112475.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.043755 restraints weight = 67279.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.044181 restraints weight = 49288.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.044395 restraints weight = 41272.825| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28827 Z= 0.202 Angle : 0.597 15.391 40204 Z= 0.335 Chirality : 0.039 0.159 4597 Planarity : 0.004 0.120 4092 Dihedral : 25.977 93.184 6442 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2714 helix: 1.30 (0.13), residues: 1449 sheet: -0.38 (0.28), residues: 353 loop : -0.44 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 310 TYR 0.025 0.001 TYR B 88 PHE 0.018 0.002 PHE E 104 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00437 (28823) covalent geometry : angle 0.59722 (40204) hydrogen bonds : bond 0.04940 ( 1579) hydrogen bonds : angle 4.40085 ( 4209) Misc. bond : bond 0.00139 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.9331 (mmp) cc_final: 0.8994 (mmm) REVERT: B 98 TYR cc_start: 0.8606 (m-80) cc_final: 0.8311 (m-80) REVERT: E 50 GLU cc_start: 0.8740 (tp30) cc_final: 0.8411 (tp30) REVERT: E 56 LYS cc_start: 0.9481 (tppp) cc_final: 0.9194 (tppp) REVERT: E 120 MET cc_start: 0.8398 (mtp) cc_final: 0.7903 (mtt) REVERT: F 63 GLU cc_start: 0.9083 (pt0) cc_final: 0.8856 (pp20) REVERT: L 158 MET cc_start: -0.1427 (mmp) cc_final: -0.1754 (mpp) REVERT: M 251 MET cc_start: -0.5780 (ttt) cc_final: -0.6511 (mmp) REVERT: O 125 MET cc_start: 0.5438 (ptt) cc_final: 0.5214 (ttp) REVERT: Q 125 MET cc_start: 0.8151 (ptt) cc_final: 0.7828 (pmm) REVERT: Q 211 MET cc_start: -0.5266 (ttt) cc_final: -0.6108 (mtt) REVERT: Q 235 ARG cc_start: 0.6456 (mtt180) cc_final: 0.5324 (tpt170) REVERT: Q 243 MET cc_start: 0.0577 (mmt) cc_final: 0.0124 (ttt) REVERT: Q 251 MET cc_start: 0.3459 (tpp) cc_final: 0.2188 (mtt) REVERT: Q 326 MET cc_start: 0.6532 (tpp) cc_final: 0.5952 (pmm) REVERT: R 125 MET cc_start: 0.6767 (pmm) cc_final: 0.6396 (ptt) REVERT: R 211 MET cc_start: 0.3122 (tpp) cc_final: 0.2451 (tpp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1560 time to fit residues: 31.7297 Evaluate side-chains 97 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 123 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.066534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.041379 restraints weight = 256796.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.042685 restraints weight = 110673.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.043399 restraints weight = 65575.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.043788 restraints weight = 47835.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.044038 restraints weight = 40261.480| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28827 Z= 0.189 Angle : 0.593 16.980 40204 Z= 0.331 Chirality : 0.038 0.153 4597 Planarity : 0.004 0.118 4092 Dihedral : 25.990 92.597 6442 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.16), residues: 2714 helix: 1.37 (0.14), residues: 1444 sheet: -0.38 (0.28), residues: 353 loop : -0.45 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 310 TYR 0.054 0.001 TYR B 88 PHE 0.015 0.002 PHE K 327 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00410 (28823) covalent geometry : angle 0.59336 (40204) hydrogen bonds : bond 0.04528 ( 1579) hydrogen bonds : angle 4.35348 ( 4209) Misc. bond : bond 0.00137 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7578.77 seconds wall clock time: 130 minutes 14.20 seconds (7814.20 seconds total)