Starting phenix.real_space_refine on Mon Jun 23 19:02:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbt_38228/06_2025/8xbt_38228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbt_38228/06_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_38228/06_2025/8xbt_38228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbt_38228/06_2025/8xbt_38228.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbt_38228/06_2025/8xbt_38228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbt_38228/06_2025/8xbt_38228.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.52, per 1000 atoms: 0.67 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: 7.68 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 12.81 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: 13.28 Time building geometry restraints manager: 8.84 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: 9.970 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: 0.060 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 79.780 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.220 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:3.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (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 HIS 0.016 0.004 HIS R 244 PHE 0.106 0.013 PHE N 126 TYR 0.118 0.014 TYR N 228 ARG 0.010 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.15126 ( 1579) hydrogen bonds : angle 6.85001 ( 4209) covalent geometry : bond 0.01113 (28823) covalent geometry : angle 1.49869 (40204) 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 : 2.862 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: 0.9103 (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: 0.8967 (ttp80) REVERT: C 38 ASN cc_start: 0.9139 (m-40) cc_final: 0.8625 (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: 0.8638 (tp30) REVERT: D 80 LEU cc_start: 0.9729 (mt) cc_final: 0.9522 (tp) REVERT: D 99 ARG cc_start: 0.9240 (mtt90) cc_final: 0.8954 (ttm110) REVERT: E 53 ARG cc_start: 0.9469 (ttt180) cc_final: 0.9137 (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: 0.9194 (p) REVERT: E 106 ASP cc_start: 0.9285 (m-30) cc_final: 0.8572 (p0) REVERT: E 120 MET cc_start: 0.8717 (mtt) cc_final: 0.8217 (mtp) REVERT: F 44 LYS cc_start: 0.9089 (tttt) cc_final: 0.8768 (ttmt) 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: 0.1188 (mmm) REVERT: K 251 MET cc_start: 0.6914 (mtp) cc_final: 0.6354 (mmm) REVERT: M 196 ASN cc_start: 0.7574 (p0) cc_final: 0.7306 (t0) REVERT: N 210 MET cc_start: 0.1465 (tmm) cc_final: 0.1139 (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: 0.1916 (ttt) REVERT: P 210 MET cc_start: 0.0524 (tmm) cc_final: 0.0214 (tmm) REVERT: Q 210 MET cc_start: -0.1192 (tmm) cc_final: -0.1683 (tmm) REVERT: Q 235 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7706 (tpm170) REVERT: R 125 MET cc_start: 0.5649 (pmm) cc_final: 0.5398 (ptt) REVERT: R 233 SER cc_start: -0.1615 (OUTLIER) cc_final: -0.1917 (t) REVERT: R 243 MET cc_start: 0.5393 (mmt) cc_final: 0.5157 (ptt) outliers start: 46 outliers final: 15 residues processed: 312 average time/residue: 0.4627 time to fit residues: 217.1002 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 : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 175 optimal weight: 40.0000 chunk 273 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 GLN O 114 GLN P 206 GLN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 206 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 GLN R 244 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.067137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.042030 restraints weight = 254752.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.043424 restraints weight = 108309.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.044101 restraints weight = 63784.042| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 28827 Z= 0.297 Angle : 0.724 17.121 40204 Z= 0.404 Chirality : 0.042 0.177 4597 Planarity : 0.007 0.217 4092 Dihedral : 26.631 90.532 6442 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 2714 helix: 0.69 (0.13), residues: 1437 sheet: -0.15 (0.28), residues: 344 loop : -0.61 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS E 113 PHE 0.026 0.003 PHE M 126 TYR 0.020 0.002 TYR M 301 ARG 0.016 0.001 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.06655 ( 1579) hydrogen bonds : angle 5.25501 ( 4209) covalent geometry : bond 0.00640 (28823) covalent geometry : angle 0.72395 (40204) Misc. bond : bond 0.00301 ( 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 152 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9310 (pt) cc_final: 0.9098 (pt) REVERT: A 120 MET cc_start: 0.9131 (mmm) cc_final: 0.8911 (mmm) REVERT: B 88 TYR cc_start: 0.8599 (m-10) cc_final: 0.8251 (m-10) REVERT: C 64 GLU cc_start: 0.8416 (tp30) cc_final: 0.8042 (tp30) REVERT: E 106 ASP cc_start: 0.8569 (m-30) cc_final: 0.7870 (m-30) REVERT: E 120 MET cc_start: 0.8429 (mtt) cc_final: 0.8160 (mtp) REVERT: G 56 GLU cc_start: 0.8831 (tt0) cc_final: 0.8532 (mt-10) REVERT: K 125 MET cc_start: 0.5970 (pmm) cc_final: 0.5428 (pmm) REVERT: M 251 MET cc_start: -0.5671 (ttt) cc_final: -0.6542 (mmp) REVERT: P 210 MET cc_start: 0.0967 (tmm) cc_final: 0.0667 (tmm) REVERT: Q 235 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7096 (tpt170) REVERT: Q 326 MET cc_start: 0.6803 (tpp) cc_final: 0.6361 (pmm) REVERT: R 125 MET cc_start: 0.5486 (pmm) cc_final: 0.5129 (ptt) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.4169 time to fit residues: 99.2022 Evaluate side-chains 106 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 3 optimal weight: 0.9990 chunk 256 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 281 optimal weight: 50.0000 chunk 165 optimal weight: 50.0000 chunk 236 optimal weight: 8.9990 chunk 274 optimal weight: 10.0000 chunk 298 optimal weight: 30.0000 chunk 157 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** K 62 ASN ** 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 244 HIS P 196 ASN P 206 GLN P 244 HIS ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.066959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.041876 restraints weight = 256063.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.043230 restraints weight = 107816.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.043966 restraints weight = 62953.033| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28827 Z= 0.233 Angle : 0.634 15.360 40204 Z= 0.356 Chirality : 0.039 0.148 4597 Planarity : 0.005 0.117 4092 Dihedral : 26.401 90.643 6442 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2714 helix: 0.89 (0.13), residues: 1448 sheet: -0.31 (0.27), residues: 360 loop : -0.47 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 75 PHE 0.017 0.002 PHE K 327 TYR 0.021 0.002 TYR P 216 ARG 0.011 0.001 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.05405 ( 1579) hydrogen bonds : angle 4.83058 ( 4209) covalent geometry : bond 0.00503 (28823) covalent geometry : angle 0.63381 (40204) Misc. bond : bond 0.00182 ( 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 133 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9364 (pt) cc_final: 0.9082 (pt) REVERT: A 120 MET cc_start: 0.9030 (mmm) cc_final: 0.8808 (mmm) REVERT: B 88 TYR cc_start: 0.8505 (m-10) cc_final: 0.8242 (m-10) REVERT: E 50 GLU cc_start: 0.8432 (tp30) cc_final: 0.8121 (tp30) REVERT: E 105 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8518 (tm-30) REVERT: E 120 MET cc_start: 0.8311 (mtt) cc_final: 0.7894 (mtt) REVERT: M 251 MET cc_start: -0.5710 (ttt) cc_final: -0.6578 (mmp) REVERT: N 210 MET cc_start: 0.1007 (tmm) cc_final: 0.0704 (ttp) REVERT: N 211 MET cc_start: 0.0432 (ttm) cc_final: 0.0156 (mtt) REVERT: O 125 MET cc_start: 0.5513 (ptt) cc_final: 0.5147 (ttp) REVERT: O 210 MET cc_start: -0.0875 (ptt) cc_final: -0.1118 (ptt) REVERT: Q 235 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6642 (tpt170) REVERT: Q 326 MET cc_start: 0.6719 (tpp) cc_final: 0.6201 (pmm) REVERT: R 125 MET cc_start: 0.5919 (pmm) cc_final: 0.5544 (ptt) REVERT: R 211 MET cc_start: 0.3421 (ttm) cc_final: 0.2403 (ttm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4012 time to fit residues: 87.5771 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 : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 128 optimal weight: 30.0000 chunk 170 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 HIS ** 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** O 47 HIS Q 101 GLN R 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.066046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.041395 restraints weight = 259689.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.042691 restraints weight = 110010.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.043427 restraints weight = 64791.718| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 28827 Z= 0.263 Angle : 0.656 18.126 40204 Z= 0.366 Chirality : 0.040 0.144 4597 Planarity : 0.005 0.094 4092 Dihedral : 26.454 93.407 6442 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2714 helix: 0.80 (0.13), residues: 1456 sheet: -0.55 (0.27), residues: 376 loop : -0.50 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS F 75 PHE 0.024 0.002 PHE M 126 TYR 0.017 0.002 TYR K 228 ARG 0.009 0.001 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.06049 ( 1579) hydrogen bonds : angle 4.86336 ( 4209) covalent geometry : bond 0.00567 (28823) covalent geometry : angle 0.65571 (40204) Misc. bond : bond 0.00149 ( 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 122 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9403 (pt) cc_final: 0.9081 (pt) REVERT: A 120 MET cc_start: 0.9131 (mmm) cc_final: 0.8846 (mmm) REVERT: E 50 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8706 (mm-30) REVERT: E 105 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8766 (tm-30) REVERT: E 120 MET cc_start: 0.8478 (mtt) cc_final: 0.7986 (mtt) REVERT: F 84 MET cc_start: 0.9157 (mmp) cc_final: 0.8860 (mmm) REVERT: H 61 ILE cc_start: 0.9754 (OUTLIER) cc_final: 0.9491 (tp) REVERT: L 326 MET cc_start: 0.3927 (tpt) cc_final: 0.3644 (tpp) REVERT: M 211 MET cc_start: 0.2227 (ttt) cc_final: 0.1332 (tpp) REVERT: M 251 MET cc_start: -0.5768 (ttt) cc_final: -0.6609 (mmp) REVERT: O 125 MET cc_start: 0.5446 (ptt) cc_final: 0.5070 (ttp) REVERT: O 243 MET cc_start: 0.7994 (mmp) cc_final: 0.7772 (mmm) REVERT: Q 235 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6207 (tpt170) REVERT: Q 326 MET cc_start: 0.6682 (tpp) cc_final: 0.6011 (pmm) REVERT: R 125 MET cc_start: 0.5932 (pmm) cc_final: 0.5701 (ptt) REVERT: R 211 MET cc_start: 0.3525 (ttm) cc_final: 0.2815 (ttm) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.3848 time to fit residues: 76.6308 Evaluate side-chains 98 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 251 optimal weight: 50.0000 chunk 190 optimal weight: 40.0000 chunk 113 optimal weight: 50.0000 chunk 52 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 222 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 P 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.066581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.041852 restraints weight = 258414.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.043158 restraints weight = 109555.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.043880 restraints weight = 64351.684| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 28827 Z= 0.221 Angle : 0.609 16.146 40204 Z= 0.343 Chirality : 0.039 0.145 4597 Planarity : 0.006 0.249 4092 Dihedral : 26.446 92.954 6442 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2714 helix: 0.99 (0.13), residues: 1457 sheet: -0.56 (0.28), residues: 353 loop : -0.60 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 75 PHE 0.017 0.002 PHE M 126 TYR 0.038 0.001 TYR B 88 ARG 0.006 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 1579) hydrogen bonds : angle 4.67074 ( 4209) covalent geometry : bond 0.00474 (28823) covalent geometry : angle 0.60936 (40204) Misc. bond : bond 0.00239 ( 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 125 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9136 (mmm) cc_final: 0.8921 (mmm) REVERT: E 56 LYS cc_start: 0.9428 (tppp) cc_final: 0.9155 (tppp) REVERT: E 120 MET cc_start: 0.8384 (mtt) cc_final: 0.8178 (mtp) REVERT: F 84 MET cc_start: 0.8965 (mmp) cc_final: 0.8690 (mmm) REVERT: L 326 MET cc_start: 0.4017 (tpt) cc_final: 0.3737 (tpp) REVERT: M 211 MET cc_start: 0.2208 (ttt) cc_final: 0.1414 (tpp) REVERT: M 251 MET cc_start: -0.5798 (ttt) cc_final: -0.6618 (mmp) REVERT: N 211 MET cc_start: -0.0619 (tpp) cc_final: -0.1040 (mmt) REVERT: O 158 MET cc_start: -0.0661 (mtm) cc_final: -0.0988 (mtm) REVERT: P 243 MET cc_start: 0.5610 (mmp) cc_final: 0.5304 (tmm) REVERT: Q 235 ARG cc_start: 0.6904 (mtt180) cc_final: 0.5717 (tpt170) REVERT: Q 326 MET cc_start: 0.6722 (tpp) cc_final: 0.5994 (pmm) REVERT: R 125 MET cc_start: 0.6153 (pmm) cc_final: 0.5934 (ptt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3742 time to fit residues: 78.3692 Evaluate side-chains 100 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 121 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 chunk 169 optimal weight: 50.0000 chunk 265 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 240 optimal weight: 6.9990 chunk 191 optimal weight: 0.4980 chunk 269 optimal weight: 6.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 199 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.066871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.042566 restraints weight = 258632.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.043887 restraints weight = 109897.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.044582 restraints weight = 64813.461| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28827 Z= 0.200 Angle : 0.591 15.516 40204 Z= 0.333 Chirality : 0.038 0.141 4597 Planarity : 0.005 0.162 4092 Dihedral : 26.343 93.749 6442 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.04 % Allowed : 1.12 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2714 helix: 1.13 (0.14), residues: 1460 sheet: -0.55 (0.27), residues: 359 loop : -0.62 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 75 PHE 0.015 0.002 PHE K 327 TYR 0.041 0.001 TYR B 88 ARG 0.007 0.000 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.04865 ( 1579) hydrogen bonds : angle 4.55634 ( 4209) covalent geometry : bond 0.00429 (28823) covalent geometry : angle 0.59070 (40204) Misc. bond : bond 0.00185 ( 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 126 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9085 (mmm) cc_final: 0.8812 (mmm) REVERT: E 56 LYS cc_start: 0.9380 (tppp) cc_final: 0.9119 (tppp) REVERT: E 120 MET cc_start: 0.8343 (mtt) cc_final: 0.8114 (mtp) REVERT: F 84 MET cc_start: 0.8836 (mmp) cc_final: 0.8610 (mmm) REVERT: L 326 MET cc_start: 0.4087 (tpt) cc_final: 0.3765 (tpp) REVERT: M 251 MET cc_start: -0.6047 (ttt) cc_final: -0.6773 (mmp) REVERT: N 211 MET cc_start: -0.0075 (tpp) cc_final: -0.0335 (mmm) REVERT: O 125 MET cc_start: 0.5655 (ptt) cc_final: 0.5397 (ttp) REVERT: O 158 MET cc_start: -0.0744 (mtm) cc_final: -0.1123 (mtm) REVERT: P 243 MET cc_start: 0.5514 (mmp) cc_final: 0.5235 (tmm) REVERT: Q 235 ARG cc_start: 0.6788 (mtt180) cc_final: 0.5468 (tpt170) REVERT: Q 243 MET cc_start: 0.0268 (mmt) cc_final: -0.0349 (ttt) REVERT: Q 326 MET cc_start: 0.6648 (tpp) cc_final: 0.5876 (pmm) REVERT: R 125 MET cc_start: 0.6177 (pmm) cc_final: 0.5880 (ptt) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.3744 time to fit residues: 77.6944 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 : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 285 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 177 optimal weight: 50.0000 chunk 109 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 148 optimal weight: 40.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3855 r_free = 0.3855 target = 0.065950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.041327 restraints weight = 257729.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.042614 restraints weight = 111338.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.043335 restraints weight = 66044.979| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28827 Z= 0.235 Angle : 0.622 15.726 40204 Z= 0.347 Chirality : 0.039 0.195 4597 Planarity : 0.005 0.131 4092 Dihedral : 26.381 95.340 6442 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2714 helix: 1.13 (0.14), residues: 1446 sheet: -0.57 (0.28), residues: 356 loop : -0.64 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS B 75 PHE 0.016 0.002 PHE K 327 TYR 0.016 0.001 TYR B 88 ARG 0.007 0.000 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.05395 ( 1579) hydrogen bonds : angle 4.69059 ( 4209) covalent geometry : bond 0.00507 (28823) covalent geometry : angle 0.62156 (40204) Misc. bond : bond 0.00156 ( 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 126 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9206 (mmm) cc_final: 0.8826 (mmm) REVERT: B 98 TYR cc_start: 0.8659 (m-80) cc_final: 0.8413 (m-80) REVERT: E 50 GLU cc_start: 0.8972 (tp30) cc_final: 0.8576 (tp30) REVERT: E 56 LYS cc_start: 0.9461 (tppp) cc_final: 0.9226 (tppp) REVERT: E 120 MET cc_start: 0.8468 (mtt) cc_final: 0.8221 (mtp) REVERT: F 84 MET cc_start: 0.9171 (mmp) cc_final: 0.8855 (mmm) REVERT: L 326 MET cc_start: 0.4102 (tpt) cc_final: 0.3781 (tpp) REVERT: M 251 MET cc_start: -0.5996 (ttt) cc_final: -0.6700 (mmp) REVERT: N 211 MET cc_start: 0.0633 (tpp) cc_final: 0.0262 (mmp) REVERT: O 125 MET cc_start: 0.5369 (ptt) cc_final: 0.5047 (ttp) REVERT: Q 125 MET cc_start: 0.8232 (ptt) cc_final: 0.7914 (pmm) REVERT: Q 211 MET cc_start: -0.5364 (ttt) cc_final: -0.5714 (mtt) REVERT: Q 235 ARG cc_start: 0.6787 (mtt180) cc_final: 0.5549 (tpt170) REVERT: Q 243 MET cc_start: 0.0257 (mmt) cc_final: -0.0298 (ttt) REVERT: R 125 MET cc_start: 0.6600 (pmm) cc_final: 0.6288 (ptt) REVERT: R 211 MET cc_start: 0.3049 (tpp) cc_final: 0.2635 (tpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3721 time to fit residues: 78.1877 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 : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 262 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 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 = 0.3895 r_free = 0.3895 target = 0.067503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.042601 restraints weight = 252832.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.043937 restraints weight = 109837.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.044699 restraints weight = 65405.811| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5072 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= 0.135 Angle : 0.561 12.055 40204 Z= 0.316 Chirality : 0.037 0.150 4597 Planarity : 0.004 0.112 4092 Dihedral : 26.213 92.706 6442 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2714 helix: 1.40 (0.14), residues: 1462 sheet: -0.53 (0.28), residues: 360 loop : -0.64 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.016 0.001 PHE Q 327 TYR 0.044 0.001 TYR B 88 ARG 0.008 0.000 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 1579) hydrogen bonds : angle 4.29114 ( 4209) covalent geometry : bond 0.00285 (28823) covalent geometry : angle 0.56057 (40204) Misc. bond : bond 0.00142 ( 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 143 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9202 (mmm) cc_final: 0.8848 (mmm) REVERT: B 98 TYR cc_start: 0.8606 (m-80) cc_final: 0.8375 (m-80) REVERT: E 56 LYS cc_start: 0.9419 (tppp) cc_final: 0.9155 (tppp) REVERT: F 84 MET cc_start: 0.9065 (mmp) cc_final: 0.8842 (tpp) REVERT: F 88 TYR cc_start: 0.9038 (m-10) cc_final: 0.8821 (m-80) REVERT: L 326 MET cc_start: 0.4091 (tpt) cc_final: 0.3803 (tpp) REVERT: M 251 MET cc_start: -0.6259 (ttt) cc_final: -0.6885 (mmp) REVERT: N 211 MET cc_start: 0.2330 (mmt) cc_final: 0.2099 (mmp) REVERT: O 125 MET cc_start: 0.5392 (ptt) cc_final: 0.5145 (ttp) REVERT: Q 125 MET cc_start: 0.8163 (ptt) cc_final: 0.7851 (pmm) REVERT: Q 211 MET cc_start: -0.5585 (ttt) cc_final: -0.5869 (mtt) REVERT: Q 235 ARG cc_start: 0.6723 (mtt180) cc_final: 0.5435 (tpt170) REVERT: Q 243 MET cc_start: 0.0333 (mmt) cc_final: -0.0158 (ttt) REVERT: Q 326 MET cc_start: 0.6746 (tpt) cc_final: 0.6024 (pmm) REVERT: R 125 MET cc_start: 0.6681 (pmm) cc_final: 0.6367 (ptt) REVERT: R 211 MET cc_start: 0.2656 (tpp) cc_final: 0.2265 (tpp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.4085 time to fit residues: 98.1618 Evaluate side-chains 106 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 213 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 134 optimal weight: 40.0000 chunk 138 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 279 optimal weight: 50.0000 chunk 19 optimal weight: 0.0670 chunk 166 optimal weight: 20.0000 overall best weight: 4.3724 ------------------------------------------------------------------------------- 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 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 = 0.3870 r_free = 0.3870 target = 0.066278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.041591 restraints weight = 256580.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.042867 restraints weight = 110657.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.043595 restraints weight = 66021.099| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28827 Z= 0.195 Angle : 0.589 14.509 40204 Z= 0.330 Chirality : 0.038 0.147 4597 Planarity : 0.004 0.110 4092 Dihedral : 26.179 95.003 6442 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2714 helix: 1.40 (0.14), residues: 1445 sheet: -0.52 (0.28), residues: 357 loop : -0.62 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS B 75 PHE 0.015 0.002 PHE K 327 TYR 0.015 0.001 TYR B 88 ARG 0.008 0.000 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 1579) hydrogen bonds : angle 4.44939 ( 4209) covalent geometry : bond 0.00420 (28823) covalent geometry : angle 0.58896 (40204) Misc. bond : bond 0.00141 ( 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 131 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9213 (mmm) cc_final: 0.8856 (mmm) REVERT: B 98 TYR cc_start: 0.8595 (m-80) cc_final: 0.8349 (m-80) REVERT: E 50 GLU cc_start: 0.8981 (tp30) cc_final: 0.8605 (tp30) REVERT: E 56 LYS cc_start: 0.9442 (tppp) cc_final: 0.9179 (tppp) REVERT: E 120 MET cc_start: 0.8336 (mtp) cc_final: 0.7661 (mtt) REVERT: F 84 MET cc_start: 0.9158 (mmp) cc_final: 0.8664 (mmm) REVERT: L 326 MET cc_start: 0.4124 (tpt) cc_final: 0.3905 (tpp) REVERT: M 251 MET cc_start: -0.6238 (ttt) cc_final: -0.6819 (mmp) REVERT: N 158 MET cc_start: -0.1235 (ptm) cc_final: -0.1626 (ptp) REVERT: O 125 MET cc_start: 0.5458 (ptt) cc_final: 0.5232 (ttp) REVERT: O 210 MET cc_start: -0.0486 (ptt) cc_final: -0.0999 (ptt) REVERT: Q 211 MET cc_start: -0.5560 (ttt) cc_final: -0.5847 (mtt) REVERT: Q 235 ARG cc_start: 0.6668 (mtt180) cc_final: 0.5306 (tpt170) REVERT: Q 243 MET cc_start: 0.0450 (mmt) cc_final: -0.0039 (ttt) REVERT: Q 326 MET cc_start: 0.6755 (tpt) cc_final: 0.5968 (pmm) REVERT: R 125 MET cc_start: 0.6828 (pmm) cc_final: 0.6496 (ptt) REVERT: R 211 MET cc_start: 0.2567 (tpp) cc_final: 0.2251 (tpp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3657 time to fit residues: 80.0022 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 : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 64 optimal weight: 0.8980 chunk 180 optimal weight: 30.0000 chunk 44 optimal weight: 0.0070 chunk 287 optimal weight: 5.9990 chunk 137 optimal weight: 40.0000 chunk 18 optimal weight: 1.9990 chunk 111 optimal weight: 40.0000 chunk 290 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 chunk 182 optimal weight: 40.0000 chunk 110 optimal weight: 20.0000 overall best weight: 1.3940 ------------------------------------------------------------------------------- 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 38 ASN ** F 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.067875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.042971 restraints weight = 252904.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.044280 restraints weight = 109416.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.045012 restraints weight = 64990.136| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28827 Z= 0.130 Angle : 0.558 11.572 40204 Z= 0.313 Chirality : 0.037 0.196 4597 Planarity : 0.004 0.081 4092 Dihedral : 25.977 92.551 6442 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.16), residues: 2714 helix: 1.60 (0.14), residues: 1447 sheet: -0.46 (0.28), residues: 358 loop : -0.52 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.014 0.001 PHE K 327 TYR 0.011 0.001 TYR N 315 ARG 0.017 0.000 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 1579) hydrogen bonds : angle 4.17037 ( 4209) covalent geometry : bond 0.00277 (28823) covalent geometry : angle 0.55831 (40204) Misc. bond : bond 0.00206 ( 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 139 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9203 (mmm) cc_final: 0.8878 (mmm) REVERT: B 98 TYR cc_start: 0.8512 (m-80) cc_final: 0.8289 (m-80) REVERT: E 50 GLU cc_start: 0.8934 (tp30) cc_final: 0.8522 (tp30) REVERT: E 56 LYS cc_start: 0.9392 (tppp) cc_final: 0.9129 (tppp) REVERT: E 105 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8838 (tm-30) REVERT: E 120 MET cc_start: 0.8213 (mtp) cc_final: 0.7456 (mtt) REVERT: F 68 ASP cc_start: 0.9088 (m-30) cc_final: 0.8885 (m-30) REVERT: F 84 MET cc_start: 0.9066 (mmp) cc_final: 0.8837 (mmm) REVERT: F 88 TYR cc_start: 0.8956 (m-10) cc_final: 0.8584 (m-80) REVERT: L 158 MET cc_start: -0.0783 (mmm) cc_final: -0.1365 (mmt) REVERT: L 326 MET cc_start: 0.4147 (tpt) cc_final: 0.3937 (tpp) REVERT: M 251 MET cc_start: -0.6296 (ttt) cc_final: -0.6872 (mmp) REVERT: N 158 MET cc_start: -0.2287 (ptm) cc_final: -0.2599 (ptp) REVERT: N 210 MET cc_start: -0.0067 (ptm) cc_final: -0.0324 (tmm) REVERT: N 211 MET cc_start: -0.1245 (tpp) cc_final: -0.1508 (tpp) REVERT: N 326 MET cc_start: 0.8870 (pmm) cc_final: 0.8512 (ttm) REVERT: O 125 MET cc_start: 0.5409 (ptt) cc_final: 0.5200 (ttp) REVERT: Q 211 MET cc_start: -0.5575 (ttt) cc_final: -0.5792 (mtt) REVERT: Q 235 ARG cc_start: 0.6784 (mtt180) cc_final: 0.5407 (tpt170) REVERT: Q 243 MET cc_start: 0.0648 (mmt) cc_final: 0.0189 (ttt) REVERT: Q 326 MET cc_start: 0.6773 (tpt) cc_final: 0.6061 (pmm) REVERT: R 125 MET cc_start: 0.6762 (pmm) cc_final: 0.6407 (ptt) REVERT: R 211 MET cc_start: 0.2769 (tpp) cc_final: 0.2346 (tpp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.4705 time to fit residues: 110.1441 Evaluate side-chains 111 residues out of total 2239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 203 optimal weight: 40.0000 chunk 283 optimal weight: 8.9990 chunk 281 optimal weight: 50.0000 chunk 135 optimal weight: 5.9990 chunk 201 optimal weight: 50.0000 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 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** ** M 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 188 ASN ** 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 = 0.3859 r_free = 0.3859 target = 0.066453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.040648 restraints weight = 255606.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.042141 restraints weight = 105124.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.042928 restraints weight = 60859.794| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28827 Z= 0.176 Angle : 0.578 14.093 40204 Z= 0.323 Chirality : 0.038 0.186 4597 Planarity : 0.004 0.087 4092 Dihedral : 26.024 94.357 6442 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2714 helix: 1.55 (0.14), residues: 1445 sheet: -0.48 (0.28), residues: 353 loop : -0.58 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.015 0.002 PHE K 327 TYR 0.019 0.001 TYR B 88 ARG 0.012 0.000 ARG O 310 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 1579) hydrogen bonds : angle 4.30435 ( 4209) covalent geometry : bond 0.00381 (28823) covalent geometry : angle 0.57780 (40204) Misc. bond : bond 0.00190 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13547.02 seconds wall clock time: 239 minutes 6.52 seconds (14346.52 seconds total)