Starting phenix.real_space_refine on Wed Feb 14 03:21:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihj_35446/02_2024/8ihj_35446_updated.pdb" } resolution = 3.07 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= 0.004 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5450 2.51 5 N 1435 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 109": "OD1" <-> "OD2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "C GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8509 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1702 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1701 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2480 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.58 Number of scatterers: 8509 At special positions: 0 Unit cell: (93.6, 116.22, 132.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1571 8.00 N 1435 7.00 C 5450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.8 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 15 sheets defined 33.8% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'R' and resid 24 through 27 No H-bonds generated for 'chain 'R' and resid 24 through 27' Processing helix chain 'R' and resid 30 through 54 removed outlier: 3.513A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 77 Processing helix chain 'R' and resid 80 through 88 removed outlier: 3.682A pdb=" N TYR R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 128 removed outlier: 3.651A pdb=" N ALA R 108 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 137 No H-bonds generated for 'chain 'R' and resid 135 through 137' Processing helix chain 'R' and resid 141 through 158 removed outlier: 3.835A pdb=" N VAL R 156 " --> pdb=" O TRP R 152 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY R 157 " --> pdb=" O GLY R 153 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 164 removed outlier: 3.529A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 217 removed outlier: 3.910A pdb=" N PHE R 193 " --> pdb=" O HIS R 189 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.600A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 259 removed outlier: 4.239A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.590A pdb=" N VAL R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 293 removed outlier: 3.686A pdb=" N SER R 271 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 272 " --> pdb=" O TYR R 269 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP R 273 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU R 274 " --> pdb=" O SER R 271 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU R 289 " --> pdb=" O ASN R 286 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP R 290 " --> pdb=" O SER R 287 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.753A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.171A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.590A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.766A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.769A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.823A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.727A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.690A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.542A pdb=" N ILE R 169 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 174 " --> pdb=" O ASN R 171 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 269 removed outlier: 4.016A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 18 through 23 Processing sheet with id= D, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= E, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= F, first strand: chain 'S' and resid 92 through 94 removed outlier: 3.502A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.500A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 226 through 231 removed outlier: 6.306A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.889A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.776A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.891A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.008A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.977A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.377A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.516A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2734 1.34 - 1.46: 2178 1.46 - 1.58: 3720 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8703 Sorted by residual: bond pdb=" C1 P9X R 501 " pdb=" C6 P9X R 501 " ideal model delta sigma weight residual 1.402 1.525 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C1 P9X R 501 " pdb=" O1 P9X R 501 " ideal model delta sigma weight residual 1.578 1.463 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C3 P9X R 501 " pdb=" C4 P9X R 501 " ideal model delta sigma weight residual 1.414 1.362 0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C4 P9X R 501 " pdb=" O1 P9X R 501 " ideal model delta sigma weight residual 1.413 1.362 0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" C5 P9X R 501 " pdb=" O2 P9X R 501 " ideal model delta sigma weight residual 1.259 1.306 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 8698 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.56: 175 106.56 - 113.43: 4743 113.43 - 120.29: 3009 120.29 - 127.16: 3814 127.16 - 134.03: 96 Bond angle restraints: 11837 Sorted by residual: angle pdb=" C3 P9X R 501 " pdb=" C4 P9X R 501 " pdb=" C5 P9X R 501 " ideal model delta sigma weight residual 120.00 133.09 -13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CA GLN A 333 " pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 107.55 4.45 1.40e+00 5.10e-01 1.01e+01 angle pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " pdb=" CD GLN A 333 " ideal model delta sigma weight residual 112.60 117.41 -4.81 1.70e+00 3.46e-01 8.00e+00 angle pdb=" C5 P9X R 501 " pdb=" C4 P9X R 501 " pdb=" O1 P9X R 501 " ideal model delta sigma weight residual 120.00 112.16 7.84 3.00e+00 1.11e-01 6.84e+00 ... (remaining 11832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4392 18.01 - 36.02: 528 36.02 - 54.04: 116 54.04 - 72.05: 20 72.05 - 90.06: 9 Dihedral angle restraints: 5065 sinusoidal: 1813 harmonic: 3252 Sorted by residual: dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " pdb=" OD1 ASP B 195 " ideal model delta sinusoidal sigma weight residual -30.00 -90.12 60.12 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual -86.00 -114.57 28.57 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 5062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 905 0.031 - 0.063: 308 0.063 - 0.094: 88 0.094 - 0.126: 53 0.126 - 0.157: 4 Chirality restraints: 1358 Sorted by residual: chirality pdb=" C1 P9X R 501 " pdb=" C2 P9X R 501 " pdb=" C6 P9X R 501 " pdb=" O1 P9X R 501 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE R 178 " pdb=" N ILE R 178 " pdb=" C ILE R 178 " pdb=" CB ILE R 178 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1355 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO S 75 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 98 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO R 99 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 99 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 99 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO S 236 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.027 5.00e-02 4.00e+02 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 254 2.70 - 3.25: 8114 3.25 - 3.80: 12776 3.80 - 4.35: 16755 4.35 - 4.90: 28916 Nonbonded interactions: 66815 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.193 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.217 2.440 nonbonded pdb=" O ILE S 138 " pdb=" OG1 THR S 238 " model vdw 2.285 2.440 nonbonded pdb=" OD1 ASN R 68 " pdb=" OG SER R 148 " model vdw 2.289 2.440 ... (remaining 66810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.630 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.400 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.003 0.123 8703 Z= 0.198 Angle : 0.494 13.087 11837 Z= 0.253 Chirality : 0.039 0.157 1358 Planarity : 0.005 0.112 1499 Dihedral : 16.515 90.058 2954 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.11 % Allowed : 27.10 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1106 helix: -0.25 (0.28), residues: 350 sheet: -0.09 (0.33), residues: 263 loop : -1.04 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS R 133 PHE 0.018 0.001 PHE R 107 TYR 0.020 0.001 TYR S 235 ARG 0.009 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.871 Fit side-chains REVERT: A 271 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7979 (ptmm) REVERT: A 313 ARG cc_start: 0.6520 (mtp180) cc_final: 0.5855 (ptp-170) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.2239 time to fit residues: 36.8864 Evaluate side-chains 117 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8703 Z= 0.353 Angle : 0.564 6.664 11837 Z= 0.302 Chirality : 0.044 0.193 1358 Planarity : 0.005 0.070 1499 Dihedral : 4.436 41.452 1202 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.59 % Allowed : 24.23 % Favored : 71.18 % 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 (0.25), residues: 1106 helix: 0.36 (0.27), residues: 358 sheet: -0.03 (0.32), residues: 264 loop : -1.24 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.001 PHE S 27 TYR 0.024 0.002 TYR S 235 ARG 0.005 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 0.955 Fit side-chains REVERT: R 109 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7802 (tpp) REVERT: A 229 ASP cc_start: 0.7629 (p0) cc_final: 0.7401 (p0) REVERT: A 272 ASP cc_start: 0.7968 (m-30) cc_final: 0.7720 (m-30) REVERT: S 235 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.7028 (t80) REVERT: B 234 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8694 (t80) outliers start: 40 outliers final: 23 residues processed: 157 average time/residue: 0.2107 time to fit residues: 45.4021 Evaluate side-chains 145 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8703 Z= 0.156 Angle : 0.465 6.907 11837 Z= 0.247 Chirality : 0.040 0.148 1358 Planarity : 0.004 0.053 1499 Dihedral : 4.106 34.445 1202 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.90 % Allowed : 26.64 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.25), residues: 1106 helix: 0.92 (0.28), residues: 355 sheet: 0.02 (0.32), residues: 264 loop : -1.17 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE S 27 TYR 0.019 0.001 TYR S 235 ARG 0.004 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 0.952 Fit side-chains REVERT: A 272 ASP cc_start: 0.7991 (m-30) cc_final: 0.7751 (m-30) REVERT: A 298 GLU cc_start: 0.7487 (tt0) cc_final: 0.7224 (tt0) REVERT: A 313 ARG cc_start: 0.6654 (mtp180) cc_final: 0.5910 (ptp-170) REVERT: A 318 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6367 (tm-30) REVERT: S 235 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6704 (t80) REVERT: C 37 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8012 (tt) outliers start: 34 outliers final: 17 residues processed: 149 average time/residue: 0.2000 time to fit residues: 41.3424 Evaluate side-chains 135 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8703 Z= 0.144 Angle : 0.453 6.502 11837 Z= 0.238 Chirality : 0.040 0.139 1358 Planarity : 0.004 0.049 1499 Dihedral : 3.938 30.393 1202 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.05 % Allowed : 25.37 % Favored : 69.58 % 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 (0.25), residues: 1106 helix: 1.26 (0.28), residues: 358 sheet: -0.02 (0.32), residues: 266 loop : -1.13 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.020 0.001 PHE R 276 TYR 0.017 0.001 TYR S 235 ARG 0.005 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 0.964 Fit side-chains REVERT: R 192 MET cc_start: 0.6392 (tmm) cc_final: 0.6053 (tpp) REVERT: A 272 ASP cc_start: 0.7989 (m-30) cc_final: 0.7760 (m-30) REVERT: A 298 GLU cc_start: 0.7439 (tt0) cc_final: 0.7174 (tt0) REVERT: A 313 ARG cc_start: 0.6620 (mtp180) cc_final: 0.5911 (ptp-170) REVERT: A 318 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6336 (tm-30) REVERT: S 235 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6608 (t80) REVERT: B 234 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8644 (t80) REVERT: C 37 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7927 (tt) outliers start: 44 outliers final: 29 residues processed: 160 average time/residue: 0.1935 time to fit residues: 43.4594 Evaluate side-chains 151 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0980 chunk 1 optimal weight: 0.0980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8703 Z= 0.118 Angle : 0.432 6.395 11837 Z= 0.229 Chirality : 0.040 0.148 1358 Planarity : 0.004 0.049 1499 Dihedral : 3.734 25.040 1202 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.25 % Allowed : 26.41 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1106 helix: 1.44 (0.28), residues: 359 sheet: 0.03 (0.31), residues: 266 loop : -1.05 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.012 0.001 PHE R 38 TYR 0.015 0.001 TYR S 235 ARG 0.006 0.000 ARG S 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 0.996 Fit side-chains REVERT: R 192 MET cc_start: 0.6393 (tmm) cc_final: 0.6007 (tpp) REVERT: A 298 GLU cc_start: 0.7437 (tt0) cc_final: 0.7226 (tt0) REVERT: A 313 ARG cc_start: 0.6663 (mtp180) cc_final: 0.5879 (ptp-170) REVERT: A 318 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6327 (tm-30) REVERT: S 235 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.6552 (t80) REVERT: B 234 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8609 (t80) REVERT: C 37 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7908 (tt) outliers start: 37 outliers final: 22 residues processed: 158 average time/residue: 0.2031 time to fit residues: 44.6339 Evaluate side-chains 147 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 8703 Z= 0.454 Angle : 0.591 8.096 11837 Z= 0.313 Chirality : 0.045 0.203 1358 Planarity : 0.004 0.053 1499 Dihedral : 4.454 38.359 1202 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.66 % Allowed : 24.80 % Favored : 68.54 % 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: -0.22 (0.25), residues: 1106 helix: 1.19 (0.28), residues: 355 sheet: -0.06 (0.31), residues: 269 loop : -1.19 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.021 0.002 PHE S 27 TYR 0.025 0.002 TYR S 235 ARG 0.006 0.001 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 115 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: R 141 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8101 (m-40) REVERT: A 318 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6263 (tm-30) REVERT: S 235 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6906 (t80) REVERT: S 237 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7690 (pp) REVERT: B 234 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8664 (t80) REVERT: C 37 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8020 (tt) outliers start: 58 outliers final: 41 residues processed: 163 average time/residue: 0.1903 time to fit residues: 43.4839 Evaluate side-chains 160 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 113 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 141 ASN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 161 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 HIS A 255 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8703 Z= 0.125 Angle : 0.456 6.454 11837 Z= 0.240 Chirality : 0.040 0.153 1358 Planarity : 0.004 0.050 1499 Dihedral : 3.922 27.805 1202 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.48 % Allowed : 26.41 % Favored : 69.12 % 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: 0.04 (0.25), residues: 1106 helix: 1.43 (0.28), residues: 362 sheet: 0.02 (0.31), residues: 264 loop : -1.04 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.020 0.001 PHE R 276 TYR 0.016 0.001 TYR S 235 ARG 0.007 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 1.116 Fit side-chains REVERT: R 192 MET cc_start: 0.6126 (tmm) cc_final: 0.5841 (tpp) REVERT: A 298 GLU cc_start: 0.7369 (tt0) cc_final: 0.7123 (tt0) REVERT: A 318 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6291 (tm-30) REVERT: S 235 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.6225 (t80) REVERT: B 234 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8586 (t80) REVERT: C 37 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7942 (tt) outliers start: 39 outliers final: 29 residues processed: 156 average time/residue: 0.1995 time to fit residues: 43.3809 Evaluate side-chains 148 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 20.0000 chunk 31 optimal weight: 0.0170 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 50.0000 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8703 Z= 0.400 Angle : 0.571 7.383 11837 Z= 0.301 Chirality : 0.044 0.199 1358 Planarity : 0.004 0.053 1499 Dihedral : 4.448 37.962 1202 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.74 % Allowed : 25.72 % Favored : 68.54 % 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: -0.24 (0.25), residues: 1106 helix: 1.17 (0.28), residues: 358 sheet: -0.06 (0.31), residues: 268 loop : -1.21 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.002 PHE S 27 TYR 0.024 0.002 TYR S 235 ARG 0.009 0.001 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 118 time to evaluate : 1.051 Fit side-chains REVERT: R 192 MET cc_start: 0.6253 (tmm) cc_final: 0.5959 (tpp) REVERT: A 298 GLU cc_start: 0.7337 (tt0) cc_final: 0.7019 (tt0) REVERT: A 318 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6255 (tm-30) REVERT: S 235 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6864 (t80) REVERT: S 237 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7826 (pp) REVERT: B 82 TRP cc_start: 0.9291 (OUTLIER) cc_final: 0.8985 (m100) REVERT: B 234 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8651 (t80) REVERT: C 37 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7993 (tt) outliers start: 50 outliers final: 38 residues processed: 160 average time/residue: 0.2020 time to fit residues: 45.0622 Evaluate side-chains 158 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 114 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8703 Z= 0.213 Angle : 0.491 6.896 11837 Z= 0.259 Chirality : 0.041 0.168 1358 Planarity : 0.004 0.052 1499 Dihedral : 4.194 34.185 1202 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.94 % Allowed : 26.29 % Favored : 68.77 % 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: -0.12 (0.25), residues: 1106 helix: 1.35 (0.28), residues: 358 sheet: -0.10 (0.31), residues: 264 loop : -1.15 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE S 27 TYR 0.021 0.001 TYR S 235 ARG 0.009 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 117 time to evaluate : 0.857 Fit side-chains REVERT: R 102 LEU cc_start: 0.7318 (tt) cc_final: 0.7103 (tp) REVERT: R 192 MET cc_start: 0.6202 (tmm) cc_final: 0.5872 (tpp) REVERT: A 298 GLU cc_start: 0.7323 (tt0) cc_final: 0.7071 (tt0) REVERT: A 318 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: S 235 TYR cc_start: 0.6834 (OUTLIER) cc_final: 0.6397 (t80) REVERT: S 237 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7510 (pp) REVERT: B 234 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8662 (t80) REVERT: C 37 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7984 (tt) outliers start: 43 outliers final: 37 residues processed: 154 average time/residue: 0.1992 time to fit residues: 42.8935 Evaluate side-chains 157 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 50.0000 chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 0.3980 chunk 53 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8703 Z= 0.133 Angle : 0.452 6.534 11837 Z= 0.238 Chirality : 0.040 0.147 1358 Planarity : 0.004 0.051 1499 Dihedral : 3.868 26.530 1202 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.71 % Allowed : 26.52 % Favored : 68.77 % 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: 0.12 (0.25), residues: 1106 helix: 1.53 (0.29), residues: 363 sheet: 0.01 (0.32), residues: 263 loop : -0.99 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.010 0.001 PHE R 82 TYR 0.016 0.001 TYR S 235 ARG 0.009 0.000 ARG S 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 1.012 Fit side-chains REVERT: R 102 LEU cc_start: 0.7198 (tt) cc_final: 0.6971 (tp) REVERT: R 109 MET cc_start: 0.7969 (ttt) cc_final: 0.7727 (tpt) REVERT: R 192 MET cc_start: 0.6205 (tmm) cc_final: 0.5864 (tpp) REVERT: A 298 GLU cc_start: 0.7312 (tt0) cc_final: 0.7102 (tt0) REVERT: A 318 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6345 (tm-30) REVERT: S 235 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.5999 (t80) REVERT: S 237 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7163 (pt) REVERT: B 61 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8871 (ttp) REVERT: B 82 TRP cc_start: 0.9133 (OUTLIER) cc_final: 0.8791 (m100) REVERT: B 234 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8642 (t80) REVERT: C 37 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7944 (tt) outliers start: 41 outliers final: 31 residues processed: 156 average time/residue: 0.1886 time to fit residues: 41.2362 Evaluate side-chains 153 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 115 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102791 restraints weight = 10990.434| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.81 r_work: 0.3123 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8703 Z= 0.333 Angle : 0.538 7.239 11837 Z= 0.283 Chirality : 0.043 0.186 1358 Planarity : 0.004 0.052 1499 Dihedral : 4.272 32.636 1202 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.71 % Allowed : 26.52 % Favored : 68.77 % 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: -0.16 (0.25), residues: 1106 helix: 1.30 (0.28), residues: 362 sheet: -0.11 (0.31), residues: 263 loop : -1.18 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.001 PHE S 27 TYR 0.023 0.001 TYR S 235 ARG 0.009 0.001 ARG S 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.90 seconds wall clock time: 38 minutes 46.80 seconds (2326.80 seconds total)