Starting phenix.real_space_refine on Wed Feb 14 17:52:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh0_22872/02_2024/7kh0_22872_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh0_22872/02_2024/7kh0_22872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh0_22872/02_2024/7kh0_22872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh0_22872/02_2024/7kh0_22872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh0_22872/02_2024/7kh0_22872_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh0_22872/02_2024/7kh0_22872_updated.pdb" } resolution = 2.8 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= 0.003 sd= 0.051 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 68 5.16 5 C 6270 2.51 5 N 1728 2.21 5 O 1832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ASP 191": "OD1" <-> "OD2" Residue "R GLU 231": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "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: 9898 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2117 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1869 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "G" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 462 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "S" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1807 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 5.93, per 1000 atoms: 0.60 Number of scatterers: 9898 At special positions: 0 Unit cell: (83.3, 126.65, 133.45, 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 68 16.00 O 1832 8.00 N 1728 7.00 C 6270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.91 Conformation dependent library (CDL) restraints added in 1.9 seconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 15 sheets defined 31.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'R' and resid 34 through 68 Processing helix chain 'R' and resid 73 through 102 removed outlier: 3.998A pdb=" N LEU R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 109 through 142 removed outlier: 3.614A pdb=" N ARG R 113 " --> pdb=" O ASP R 109 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER R 127 " --> pdb=" O MET R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 177 removed outlier: 3.811A pdb=" N LEU R 172 " --> pdb=" O LEU R 168 " (cutoff:3.500A) Proline residue: R 173 - end of helix removed outlier: 4.418A pdb=" N PHE R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 238 removed outlier: 3.583A pdb=" N TYR R 205 " --> pdb=" O GLY R 201 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL R 206 " --> pdb=" O ARG R 202 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR R 207 " --> pdb=" O ARG R 203 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA R 216 " --> pdb=" O MET R 212 " (cutoff:3.500A) Proline residue: R 217 - end of helix removed outlier: 3.779A pdb=" N VAL R 237 " --> pdb=" O HIS R 233 " (cutoff:3.500A) Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 265 through 296 removed outlier: 3.624A pdb=" N VAL R 275 " --> pdb=" O ARG R 271 " (cutoff:3.500A) Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 305 through 312 removed outlier: 3.836A pdb=" N LEU R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 319 No H-bonds generated for 'chain 'R' and resid 317 through 319' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 331 through 339 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.715A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.521A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.928A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.953A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 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 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.896A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.782A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.758A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.940A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.632A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.466A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.708A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.965A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.501A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.541A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 149 removed outlier: 6.885A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL S 149 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLU S 246 " --> pdb=" O VAL S 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.588A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 225 through 231 removed outlier: 3.638A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= O, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.538A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1191 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: 2.68 Time building geometry restraints manager: 4.19 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: 2276 1.33 - 1.45: 2355 1.45 - 1.58: 5380 1.58 - 1.70: 0 1.70 - 1.83: 97 Bond restraints: 10108 Sorted by residual: bond pdb=" N GLU R 231 " pdb=" CA GLU R 231 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.28e-02 6.10e+03 1.15e+01 bond pdb=" N LEU R 172 " pdb=" CA LEU R 172 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.24e+00 bond pdb=" N CYS R 195 " pdb=" CA CYS R 195 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.48e+00 bond pdb=" N TRP R 164 " pdb=" CA TRP R 164 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.43e+00 bond pdb=" N TRP R 293 " pdb=" CA TRP R 293 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.21e-02 6.83e+03 7.63e+00 ... (remaining 10103 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.69: 277 106.69 - 113.58: 5503 113.58 - 120.48: 3958 120.48 - 127.38: 3852 127.38 - 134.27: 115 Bond angle restraints: 13705 Sorted by residual: angle pdb=" N GLU R 303 " pdb=" CA GLU R 303 " pdb=" C GLU R 303 " ideal model delta sigma weight residual 112.88 99.90 12.98 1.29e+00 6.01e-01 1.01e+02 angle pdb=" C LEU A 388 " pdb=" N ARG A 389 " pdb=" CA ARG A 389 " ideal model delta sigma weight residual 121.66 111.68 9.98 1.76e+00 3.23e-01 3.22e+01 angle pdb=" C PHE R 178 " pdb=" CA PHE R 178 " pdb=" CB PHE R 178 " ideal model delta sigma weight residual 111.41 120.44 -9.03 1.65e+00 3.67e-01 3.00e+01 angle pdb=" N TYR L 2 " pdb=" CA TYR L 2 " pdb=" C TYR L 2 " ideal model delta sigma weight residual 112.90 105.83 7.07 1.31e+00 5.83e-01 2.92e+01 angle pdb=" O ILE A 383 " pdb=" C ILE A 383 " pdb=" N GLN A 384 " ideal model delta sigma weight residual 121.80 116.00 5.80 1.13e+00 7.83e-01 2.64e+01 ... (remaining 13700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5491 17.77 - 35.54: 425 35.54 - 53.31: 73 53.31 - 71.08: 12 71.08 - 88.85: 13 Dihedral angle restraints: 6014 sinusoidal: 2336 harmonic: 3678 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 192 " pdb=" CB CYS R 192 " ideal model delta sinusoidal sigma weight residual -86.00 -150.93 64.93 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -21.13 -64.87 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 50.36 42.64 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 6011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1289 0.066 - 0.131: 225 0.131 - 0.196: 17 0.196 - 0.262: 6 0.262 - 0.327: 2 Chirality restraints: 1539 Sorted by residual: chirality pdb=" CA CYS L 1 " pdb=" N CYS L 1 " pdb=" C CYS L 1 " pdb=" CB CYS L 1 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA PHE R 178 " pdb=" N PHE R 178 " pdb=" C PHE R 178 " pdb=" CB PHE R 178 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ARG R 181 " pdb=" N ARG R 181 " pdb=" C ARG R 181 " pdb=" CB ARG R 181 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1536 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 383 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C ILE A 383 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE A 383 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 384 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 178 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C PHE R 178 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE R 178 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA R 179 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 291 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLN R 291 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN R 291 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU R 292 " 0.012 2.00e-02 2.50e+03 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 426 2.72 - 3.26: 9605 3.26 - 3.81: 15524 3.81 - 4.35: 18976 4.35 - 4.90: 33706 Nonbonded interactions: 78237 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.171 2.440 nonbonded pdb=" NH2 ARG B 8 " pdb=" OE1 GLN N 120 " model vdw 2.177 2.520 nonbonded pdb=" NH2 ARG S 202 " pdb=" OE2 GLU S 220 " model vdw 2.196 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.217 2.440 nonbonded pdb=" OE2 GLU A 344 " pdb=" NH1 ARG A 347 " model vdw 2.239 2.520 ... (remaining 78232 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=0.00 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: 0.950 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: 4.030 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.420 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.005 0.043 10108 Z= 0.320 Angle : 0.759 12.977 13705 Z= 0.477 Chirality : 0.050 0.327 1539 Planarity : 0.004 0.049 1749 Dihedral : 13.348 88.851 3622 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.57 % Allowed : 0.85 % Favored : 98.59 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.13 % 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: 0.17 (0.23), residues: 1245 helix: 1.42 (0.27), residues: 380 sheet: 0.24 (0.28), residues: 338 loop : -0.91 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 332 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 77 TYR 0.016 0.001 TYR S 190 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8250 (t70) cc_final: 0.7964 (t70) REVERT: R 136 ASP cc_start: 0.8720 (t0) cc_final: 0.8470 (t0) REVERT: R 323 TRP cc_start: 0.7914 (m100) cc_final: 0.7620 (m-10) REVERT: B 8 ARG cc_start: 0.8565 (mtt180) cc_final: 0.7986 (mmt180) REVERT: B 10 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8723 (mm-30) REVERT: B 312 ASP cc_start: 0.8287 (t0) cc_final: 0.8060 (t0) REVERT: L 7 PRO cc_start: 0.8921 (Cg_exo) cc_final: 0.8700 (Cg_endo) REVERT: S 73 ASP cc_start: 0.8577 (t70) cc_final: 0.7979 (t0) REVERT: S 244 LYS cc_start: 0.8716 (tttt) cc_final: 0.8293 (ttpt) REVERT: S 246 GLU cc_start: 0.7611 (mp0) cc_final: 0.7067 (mp0) REVERT: N 73 ASP cc_start: 0.8589 (t70) cc_final: 0.7984 (t0) outliers start: 6 outliers final: 0 residues processed: 198 average time/residue: 1.4399 time to fit residues: 302.0979 Evaluate side-chains 141 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 174 GLN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10108 Z= 0.249 Angle : 0.586 7.598 13705 Z= 0.305 Chirality : 0.044 0.174 1539 Planarity : 0.004 0.044 1749 Dihedral : 4.385 37.196 1387 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.70 % Allowed : 10.84 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.44 (0.23), residues: 1245 helix: 1.66 (0.26), residues: 384 sheet: 0.45 (0.28), residues: 341 loop : -0.85 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 193 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE R 77 TYR 0.015 0.001 TYR S 190 ARG 0.009 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8358 (t70) cc_final: 0.8070 (t70) REVERT: R 136 ASP cc_start: 0.8719 (t0) cc_final: 0.8413 (OUTLIER) REVERT: B 10 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8679 (mm-30) REVERT: B 15 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8754 (tptt) REVERT: B 312 ASP cc_start: 0.8319 (t0) cc_final: 0.8056 (t0) REVERT: A 392 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: G 20 LYS cc_start: 0.9262 (tppp) cc_final: 0.8569 (mtmp) REVERT: G 22 GLU cc_start: 0.9025 (tt0) cc_final: 0.8753 (tt0) REVERT: S 73 ASP cc_start: 0.8396 (t70) cc_final: 0.7911 (t0) REVERT: S 244 LYS cc_start: 0.8705 (tttt) cc_final: 0.8276 (ttpt) REVERT: S 246 GLU cc_start: 0.7608 (mp0) cc_final: 0.7063 (mp0) REVERT: N 73 ASP cc_start: 0.7877 (t70) cc_final: 0.7289 (t0) REVERT: N 83 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8841 (mtp) outliers start: 18 outliers final: 10 residues processed: 166 average time/residue: 1.3269 time to fit residues: 234.9281 Evaluate side-chains 151 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.0980 chunk 121 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN G 24 ASN S 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10108 Z= 0.208 Angle : 0.547 7.072 13705 Z= 0.280 Chirality : 0.042 0.148 1539 Planarity : 0.004 0.044 1749 Dihedral : 4.164 32.882 1387 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.60 % Allowed : 12.82 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.62 (0.23), residues: 1245 helix: 1.87 (0.26), residues: 384 sheet: 0.57 (0.28), residues: 338 loop : -0.79 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 193 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE S 203 TYR 0.013 0.001 TYR S 190 ARG 0.009 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8269 (t70) cc_final: 0.7953 (t70) REVERT: R 129 MET cc_start: 0.8723 (tpp) cc_final: 0.8504 (tpt) REVERT: R 136 ASP cc_start: 0.8743 (t0) cc_final: 0.8433 (OUTLIER) REVERT: B 10 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8685 (mm-30) REVERT: B 15 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8776 (tptt) REVERT: B 25 CYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8108 (p) REVERT: B 59 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: B 214 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8267 (mmm-85) REVERT: B 217 MET cc_start: 0.7748 (ptm) cc_final: 0.7443 (ppp) REVERT: B 312 ASP cc_start: 0.8332 (t0) cc_final: 0.8089 (t0) REVERT: A 392 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: G 14 LYS cc_start: 0.9246 (mmpt) cc_final: 0.9011 (mmmm) REVERT: G 17 GLU cc_start: 0.9169 (tp30) cc_final: 0.8889 (tp30) REVERT: G 20 LYS cc_start: 0.9241 (tppp) cc_final: 0.8761 (mtmp) REVERT: S 73 ASP cc_start: 0.8399 (t70) cc_final: 0.7827 (t0) REVERT: S 76 LYS cc_start: 0.8874 (ptpp) cc_final: 0.8633 (ptpp) REVERT: S 244 LYS cc_start: 0.8716 (tttt) cc_final: 0.8498 (ttpp) REVERT: N 73 ASP cc_start: 0.7903 (t70) cc_final: 0.7284 (t0) REVERT: N 83 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8857 (mtp) outliers start: 17 outliers final: 9 residues processed: 160 average time/residue: 1.3674 time to fit residues: 233.0375 Evaluate side-chains 153 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10108 Z= 0.293 Angle : 0.564 7.747 13705 Z= 0.290 Chirality : 0.043 0.142 1539 Planarity : 0.004 0.043 1749 Dihedral : 4.188 31.971 1387 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.70 % Allowed : 14.51 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.23), residues: 1245 helix: 1.92 (0.27), residues: 384 sheet: 0.58 (0.27), residues: 338 loop : -0.76 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 193 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE S 203 TYR 0.013 0.001 TYR S 190 ARG 0.008 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8283 (t70) cc_final: 0.7979 (t70) REVERT: R 136 ASP cc_start: 0.8756 (t0) cc_final: 0.8449 (OUTLIER) REVERT: B 10 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8749 (mm-30) REVERT: B 15 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8815 (tptt) REVERT: B 59 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: B 217 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7534 (ppp) REVERT: B 312 ASP cc_start: 0.8333 (t0) cc_final: 0.8069 (t0) REVERT: A 392 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: G 17 GLU cc_start: 0.9217 (tp30) cc_final: 0.9002 (tp30) REVERT: G 20 LYS cc_start: 0.9252 (tppp) cc_final: 0.8863 (mtmp) REVERT: S 43 LYS cc_start: 0.9245 (mmtm) cc_final: 0.9001 (mmpt) REVERT: S 73 ASP cc_start: 0.8413 (t70) cc_final: 0.7807 (t0) REVERT: S 244 LYS cc_start: 0.8691 (tttt) cc_final: 0.8370 (ttpt) REVERT: S 246 GLU cc_start: 0.7769 (mp0) cc_final: 0.7334 (mp0) REVERT: N 73 ASP cc_start: 0.7936 (t70) cc_final: 0.7383 (t0) REVERT: N 83 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8832 (mtp) outliers start: 18 outliers final: 8 residues processed: 155 average time/residue: 1.3814 time to fit residues: 227.8430 Evaluate side-chains 151 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 10108 Z= 0.371 Angle : 0.594 8.356 13705 Z= 0.306 Chirality : 0.044 0.146 1539 Planarity : 0.004 0.044 1749 Dihedral : 4.277 32.380 1387 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.73 % Allowed : 15.17 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.58 (0.23), residues: 1245 helix: 1.80 (0.26), residues: 391 sheet: 0.48 (0.27), residues: 341 loop : -0.76 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 193 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE S 203 TYR 0.013 0.001 TYR S 190 ARG 0.009 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8337 (t70) cc_final: 0.8035 (t70) REVERT: R 129 MET cc_start: 0.8741 (tpp) cc_final: 0.8500 (tpt) REVERT: R 136 ASP cc_start: 0.8771 (t0) cc_final: 0.8462 (OUTLIER) REVERT: B 10 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8779 (mm-30) REVERT: B 25 CYS cc_start: 0.8432 (m) cc_final: 0.8088 (p) REVERT: B 59 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8305 (m-80) REVERT: B 214 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.8291 (mmm-85) REVERT: B 217 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7640 (ppp) REVERT: B 312 ASP cc_start: 0.8338 (t0) cc_final: 0.8054 (t0) REVERT: A 392 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: G 14 LYS cc_start: 0.9237 (mmpt) cc_final: 0.9012 (mmmm) REVERT: G 17 GLU cc_start: 0.9227 (tp30) cc_final: 0.9024 (tp30) REVERT: G 20 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8892 (mtmp) REVERT: S 73 ASP cc_start: 0.8416 (t70) cc_final: 0.7815 (t0) REVERT: S 244 LYS cc_start: 0.8663 (tttt) cc_final: 0.8305 (ttpt) REVERT: S 246 GLU cc_start: 0.7738 (mp0) cc_final: 0.7293 (mp0) REVERT: N 73 ASP cc_start: 0.7946 (t70) cc_final: 0.7378 (t0) REVERT: N 83 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8890 (mtp) outliers start: 29 outliers final: 12 residues processed: 160 average time/residue: 1.3762 time to fit residues: 234.2469 Evaluate side-chains 155 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10108 Z= 0.172 Angle : 0.542 8.576 13705 Z= 0.275 Chirality : 0.042 0.253 1539 Planarity : 0.004 0.042 1749 Dihedral : 3.962 26.247 1387 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.45 % Allowed : 16.49 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.23), residues: 1245 helix: 2.02 (0.26), residues: 389 sheet: 0.64 (0.27), residues: 333 loop : -0.64 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 193 HIS 0.002 0.000 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.016 0.001 TYR L 2 ARG 0.011 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8254 (t70) cc_final: 0.7945 (t70) REVERT: R 100 LYS cc_start: 0.8702 (tppt) cc_final: 0.8203 (mttm) REVERT: R 136 ASP cc_start: 0.8721 (t0) cc_final: 0.8444 (OUTLIER) REVERT: R 323 TRP cc_start: 0.8019 (m100) cc_final: 0.7621 (m-10) REVERT: B 10 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8761 (mm-30) REVERT: B 59 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: B 214 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8333 (mmm-85) REVERT: B 217 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7601 (ppp) REVERT: B 312 ASP cc_start: 0.8320 (t0) cc_final: 0.8103 (t0) REVERT: A 392 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: G 17 GLU cc_start: 0.9237 (tp30) cc_final: 0.9033 (tp30) REVERT: G 20 LYS cc_start: 0.9212 (tppp) cc_final: 0.8891 (mtmm) REVERT: S 43 LYS cc_start: 0.9249 (mmtm) cc_final: 0.9022 (mmpt) REVERT: S 65 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8949 (tptm) REVERT: S 73 ASP cc_start: 0.8396 (t70) cc_final: 0.7757 (t0) REVERT: S 246 GLU cc_start: 0.7739 (mp0) cc_final: 0.7510 (mp0) REVERT: N 83 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8796 (mtp) outliers start: 26 outliers final: 16 residues processed: 167 average time/residue: 1.3119 time to fit residues: 233.8526 Evaluate side-chains 163 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10108 Z= 0.172 Angle : 0.542 8.559 13705 Z= 0.276 Chirality : 0.042 0.203 1539 Planarity : 0.004 0.049 1749 Dihedral : 3.790 22.811 1387 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.17 % Allowed : 16.87 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.93 (0.23), residues: 1245 helix: 2.10 (0.26), residues: 390 sheet: 0.68 (0.27), residues: 336 loop : -0.56 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 193 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR S 190 ARG 0.013 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8147 (t70) cc_final: 0.7833 (t70) REVERT: R 100 LYS cc_start: 0.8709 (tppt) cc_final: 0.8194 (mttm) REVERT: R 136 ASP cc_start: 0.8715 (t0) cc_final: 0.8507 (t0) REVERT: R 323 TRP cc_start: 0.8041 (m100) cc_final: 0.7635 (m-10) REVERT: B 10 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8746 (mm-30) REVERT: B 59 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: B 217 MET cc_start: 0.7900 (ptm) cc_final: 0.7503 (ppp) REVERT: B 312 ASP cc_start: 0.8341 (t0) cc_final: 0.8126 (t0) REVERT: A 365 CYS cc_start: 0.8118 (m) cc_final: 0.7257 (p) REVERT: A 392 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: G 14 LYS cc_start: 0.9223 (mmpt) cc_final: 0.8943 (mmmm) REVERT: G 17 GLU cc_start: 0.9245 (tp30) cc_final: 0.9020 (tp30) REVERT: G 20 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8913 (mtmm) REVERT: S 43 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8944 (mmpt) REVERT: S 73 ASP cc_start: 0.8341 (t70) cc_final: 0.7787 (t0) REVERT: S 246 GLU cc_start: 0.7709 (mp0) cc_final: 0.7450 (mp0) outliers start: 23 outliers final: 11 residues processed: 163 average time/residue: 1.3434 time to fit residues: 233.4283 Evaluate side-chains 157 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10108 Z= 0.178 Angle : 0.559 8.962 13705 Z= 0.283 Chirality : 0.041 0.178 1539 Planarity : 0.004 0.054 1749 Dihedral : 3.740 21.662 1387 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.60 % Allowed : 17.81 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.98 (0.24), residues: 1245 helix: 2.13 (0.26), residues: 389 sheet: 0.77 (0.28), residues: 335 loop : -0.57 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 193 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR S 190 ARG 0.014 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8110 (t70) cc_final: 0.7797 (t70) REVERT: R 100 LYS cc_start: 0.8717 (tppt) cc_final: 0.8195 (mttm) REVERT: R 323 TRP cc_start: 0.8081 (m100) cc_final: 0.7692 (m-10) REVERT: B 10 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8744 (mm-30) REVERT: B 59 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: B 217 MET cc_start: 0.7963 (ptm) cc_final: 0.7552 (ppp) REVERT: B 262 MET cc_start: 0.8483 (ttm) cc_final: 0.8217 (ttm) REVERT: B 312 ASP cc_start: 0.8347 (t0) cc_final: 0.8131 (t0) REVERT: A 211 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8630 (mtpp) REVERT: A 365 CYS cc_start: 0.8091 (m) cc_final: 0.7248 (p) REVERT: A 392 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: G 14 LYS cc_start: 0.9227 (mmpt) cc_final: 0.8946 (mmmm) REVERT: G 17 GLU cc_start: 0.9248 (tp30) cc_final: 0.9019 (tp30) REVERT: S 43 LYS cc_start: 0.9170 (mmtm) cc_final: 0.8930 (mmpt) REVERT: S 73 ASP cc_start: 0.8311 (t70) cc_final: 0.7760 (t0) outliers start: 17 outliers final: 11 residues processed: 164 average time/residue: 1.4288 time to fit residues: 249.3793 Evaluate side-chains 159 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10108 Z= 0.184 Angle : 0.576 9.346 13705 Z= 0.289 Chirality : 0.042 0.167 1539 Planarity : 0.004 0.057 1749 Dihedral : 3.742 21.263 1387 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.70 % Allowed : 18.66 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.99 (0.24), residues: 1245 helix: 2.08 (0.26), residues: 390 sheet: 0.77 (0.27), residues: 341 loop : -0.51 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 323 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE S 203 TYR 0.010 0.001 TYR S 190 ARG 0.014 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.8011 (t70) cc_final: 0.7691 (t70) REVERT: R 100 LYS cc_start: 0.8637 (tppt) cc_final: 0.8130 (mttm) REVERT: R 323 TRP cc_start: 0.8095 (m100) cc_final: 0.7697 (m-10) REVERT: B 10 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8800 (mm-30) REVERT: B 59 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: B 217 MET cc_start: 0.8031 (ptm) cc_final: 0.7751 (pmt) REVERT: B 262 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8271 (ttm) REVERT: B 312 ASP cc_start: 0.8352 (t0) cc_final: 0.8129 (t0) REVERT: A 365 CYS cc_start: 0.8084 (m) cc_final: 0.7216 (p) REVERT: A 392 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: G 14 LYS cc_start: 0.9221 (mmpt) cc_final: 0.8932 (mmmm) REVERT: G 20 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8545 (mtmm) REVERT: S 43 LYS cc_start: 0.9152 (mmtm) cc_final: 0.8944 (mmpt) REVERT: S 73 ASP cc_start: 0.8306 (t70) cc_final: 0.7770 (t0) outliers start: 18 outliers final: 12 residues processed: 158 average time/residue: 1.3822 time to fit residues: 232.5571 Evaluate side-chains 158 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 0.0010 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 96 GLN ** L 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10108 Z= 0.169 Angle : 0.588 9.557 13705 Z= 0.294 Chirality : 0.041 0.156 1539 Planarity : 0.004 0.060 1749 Dihedral : 3.646 20.220 1387 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.32 % Allowed : 19.23 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.98 (0.24), residues: 1245 helix: 2.04 (0.26), residues: 391 sheet: 0.71 (0.27), residues: 347 loop : -0.46 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 323 HIS 0.007 0.001 HIS A 220 PHE 0.017 0.001 PHE A 212 TYR 0.010 0.001 TYR S 190 ARG 0.015 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: R 85 ASP cc_start: 0.7971 (t70) cc_final: 0.7638 (t70) REVERT: R 100 LYS cc_start: 0.8611 (tppt) cc_final: 0.8065 (mttm) REVERT: B 10 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8809 (mm-30) REVERT: B 59 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: B 217 MET cc_start: 0.8021 (ptm) cc_final: 0.7699 (pmt) REVERT: B 262 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8260 (ttm) REVERT: B 312 ASP cc_start: 0.8349 (t0) cc_final: 0.8142 (t0) REVERT: A 317 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8074 (ptp90) REVERT: A 365 CYS cc_start: 0.8102 (m) cc_final: 0.7222 (p) REVERT: A 392 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: G 14 LYS cc_start: 0.9217 (mmpt) cc_final: 0.8970 (mmmm) REVERT: G 20 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8568 (mtmm) REVERT: S 73 ASP cc_start: 0.8302 (t70) cc_final: 0.7778 (t0) outliers start: 14 outliers final: 10 residues processed: 157 average time/residue: 1.4320 time to fit residues: 238.6054 Evaluate side-chains 154 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 80 HIS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.0020 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.055548 restraints weight = 22552.358| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.35 r_work: 0.2602 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10108 Z= 0.230 Angle : 0.611 10.437 13705 Z= 0.307 Chirality : 0.042 0.146 1539 Planarity : 0.004 0.059 1749 Dihedral : 3.779 22.213 1387 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.32 % Allowed : 19.98 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.96 (0.23), residues: 1245 helix: 2.08 (0.26), residues: 389 sheet: 0.68 (0.27), residues: 349 loop : -0.50 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 323 HIS 0.007 0.001 HIS A 220 PHE 0.014 0.001 PHE L 3 TYR 0.011 0.001 TYR S 190 ARG 0.015 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.00 seconds wall clock time: 78 minutes 27.33 seconds (4707.33 seconds total)