Starting phenix.real_space_refine on Thu Mar 14 19:30:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itf_35705/03_2024/8itf_35705_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itf_35705/03_2024/8itf_35705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itf_35705/03_2024/8itf_35705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itf_35705/03_2024/8itf_35705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itf_35705/03_2024/8itf_35705_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8itf_35705/03_2024/8itf_35705_neut_updated.pdb" } resolution = 3.46 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= 0.005 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 57 5.16 5 C 6131 2.51 5 N 1638 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 253": "OE1" <-> "OE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9551 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2431 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 372 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2283 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "S" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1712 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 938 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'8IA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.76, per 1000 atoms: 0.60 Number of scatterers: 9551 At special positions: 0 Unit cell: (121.55, 91.8, 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 57 16.00 O 1725 8.00 N 1638 7.00 C 6131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " 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: 3.63 Conformation dependent library (CDL) restraints added in 1.9 seconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 14 sheets defined 28.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.765A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 38 No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.803A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) 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 350 removed outlier: 4.070A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 30 through 43 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 helix chain 'R' and resid 34 through 59 removed outlier: 4.479A pdb=" N LEU R 39 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU R 41 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY R 42 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE R 48 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY R 49 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN R 50 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU R 51 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU R 52 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS R 59 " --> pdb=" O ALA R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 83 removed outlier: 4.081A pdb=" N VAL R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY R 82 " --> pdb=" O ASP R 78 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 92 removed outlier: 4.003A pdb=" N ARG R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 88 through 92' Processing helix chain 'R' and resid 102 through 112 removed outlier: 4.084A pdb=" N LYS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR R 109 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 135 Processing helix chain 'R' and resid 140 through 143 No H-bonds generated for 'chain 'R' and resid 140 through 143' Processing helix chain 'R' and resid 146 through 167 removed outlier: 3.515A pdb=" N GLY R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER R 156 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP R 157 " --> pdb=" O ILE R 153 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE R 167 " --> pdb=" O TYR R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 231 removed outlier: 4.109A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE R 206 " --> pdb=" O CYS R 202 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 3.637A pdb=" N ARG R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS R 230 " --> pdb=" O TYR R 226 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 269 removed outlier: 3.867A pdb=" N ILE R 262 " --> pdb=" O LYS R 258 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA R 263 " --> pdb=" O THR R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 281 Processing helix chain 'R' and resid 290 through 310 removed outlier: 4.102A pdb=" N GLU R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR R 302 " --> pdb=" O TRP R 298 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 316 through 326 removed outlier: 3.671A pdb=" N ILE R 325 " --> pdb=" O ALA R 321 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL R 326 " --> pdb=" O ILE R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 331 No H-bonds generated for 'chain 'R' and resid 329 through 331' 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 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' 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 sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.509A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.031A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.114A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.858A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.110A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.851A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.877A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.928A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.934A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= L, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.926A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.612A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.875A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 969 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: 2.47 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1478 1.28 - 1.42: 2710 1.42 - 1.55: 5500 1.55 - 1.68: 1 1.68 - 1.82: 80 Bond restraints: 9769 Sorted by residual: bond pdb=" C VAL R 300 " pdb=" O VAL R 300 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.17e-02 7.31e+03 5.41e+01 bond pdb=" CA CYS R 116 " pdb=" C CYS R 116 " ideal model delta sigma weight residual 1.525 1.439 0.086 1.25e-02 6.40e+03 4.78e+01 bond pdb=" CA ALA R 305 " pdb=" C ALA R 305 " ideal model delta sigma weight residual 1.519 1.446 0.074 1.32e-02 5.74e+03 3.12e+01 bond pdb=" CA VAL R 300 " pdb=" CB VAL R 300 " ideal model delta sigma weight residual 1.540 1.475 0.065 1.25e-02 6.40e+03 2.71e+01 bond pdb=" CA SER R 114 " pdb=" C SER R 114 " ideal model delta sigma weight residual 1.525 1.460 0.065 1.29e-02 6.01e+03 2.55e+01 ... (remaining 9764 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 242 107.16 - 113.87: 5435 113.87 - 120.58: 3703 120.58 - 127.29: 3815 127.29 - 134.00: 104 Bond angle restraints: 13299 Sorted by residual: angle pdb=" N SER R 304 " pdb=" CA SER R 304 " pdb=" C SER R 304 " ideal model delta sigma weight residual 113.02 104.63 8.39 1.20e+00 6.94e-01 4.89e+01 angle pdb=" N ALA R 305 " pdb=" CA ALA R 305 " pdb=" C ALA R 305 " ideal model delta sigma weight residual 113.88 106.04 7.84 1.23e+00 6.61e-01 4.06e+01 angle pdb=" N PHE R 115 " pdb=" CA PHE R 115 " pdb=" C PHE R 115 " ideal model delta sigma weight residual 111.71 117.49 -5.78 1.15e+00 7.56e-01 2.52e+01 angle pdb=" N VAL R 300 " pdb=" CA VAL R 300 " pdb=" C VAL R 300 " ideal model delta sigma weight residual 110.62 115.51 -4.89 1.02e+00 9.61e-01 2.30e+01 angle pdb=" N ALA R 290 " pdb=" CA ALA R 290 " pdb=" C ALA R 290 " ideal model delta sigma weight residual 113.17 107.38 5.79 1.26e+00 6.30e-01 2.11e+01 ... (remaining 13294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5151 17.87 - 35.73: 435 35.73 - 53.60: 94 53.60 - 71.46: 7 71.46 - 89.33: 10 Dihedral angle restraints: 5697 sinusoidal: 1988 harmonic: 3709 Sorted by residual: dihedral pdb=" CA GLY R 328 " pdb=" C GLY R 328 " pdb=" N LYS R 329 " pdb=" CA LYS R 329 " ideal model delta harmonic sigma weight residual -180.00 -152.36 -27.64 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.34 32.66 1 1.00e+01 1.00e-02 1.52e+01 dihedral pdb=" CA PRO R 31 " pdb=" C PRO R 31 " pdb=" N ARG R 32 " pdb=" CA ARG R 32 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1479 0.105 - 0.209: 55 0.209 - 0.314: 3 0.314 - 0.419: 1 0.419 - 0.523: 1 Chirality restraints: 1539 Sorted by residual: chirality pdb=" CA PHE R 115 " pdb=" N PHE R 115 " pdb=" C PHE R 115 " pdb=" CB PHE R 115 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CA CYS R 116 " pdb=" N CYS R 116 " pdb=" C CYS R 116 " pdb=" CB CYS R 116 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL R 300 " pdb=" N VAL R 300 " pdb=" C VAL R 300 " pdb=" CB VAL R 300 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1536 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 327 " 0.016 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER R 327 " -0.059 2.00e-02 2.50e+03 pdb=" O SER R 327 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY R 328 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP R 30 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO R 31 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 28 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO R 29 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 29 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 29 " 0.031 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2109 2.78 - 3.31: 8431 3.31 - 3.84: 14245 3.84 - 4.37: 16053 4.37 - 4.90: 29119 Nonbonded interactions: 69957 Sorted by model distance: nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.250 2.520 nonbonded pdb=" OG SER S 204 " pdb=" OG1 THR S 215 " model vdw 2.260 2.440 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.293 2.520 nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 301 " model vdw 2.306 2.440 nonbonded pdb=" O PRO A 332 " pdb=" OG1 THR A 335 " model vdw 2.333 2.440 ... (remaining 69952 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: 0.370 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: 2.220 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.900 Find NCS groups from input model: 0.310 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 0.086 9769 Z= 0.306 Angle : 0.643 9.345 13299 Z= 0.383 Chirality : 0.048 0.523 1539 Planarity : 0.005 0.074 1672 Dihedral : 14.169 89.327 3300 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.95 % Allowed : 6.62 % Favored : 92.43 % 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 (0.24), residues: 1255 helix: 0.86 (0.30), residues: 366 sheet: 0.57 (0.29), residues: 306 loop : -1.36 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 317 HIS 0.009 0.001 HIS S 167 PHE 0.014 0.001 PHE R 314 TYR 0.013 0.001 TYR R 226 ARG 0.006 0.000 ARG R 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 288 time to evaluate : 1.008 Fit side-chains REVERT: A 60 MET cc_start: 0.7841 (mmm) cc_final: 0.7261 (tpp) REVERT: B 120 ILE cc_start: 0.8175 (mt) cc_final: 0.7932 (mt) REVERT: B 212 ASP cc_start: 0.7398 (t0) cc_final: 0.7027 (t0) REVERT: R 302 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7654 (t80) REVERT: S 32 PHE cc_start: 0.8204 (m-80) cc_final: 0.7836 (m-80) REVERT: S 71 SER cc_start: 0.7561 (m) cc_final: 0.7204 (p) REVERT: S 76 LYS cc_start: 0.8311 (mttp) cc_final: 0.8081 (mttp) REVERT: S 115 THR cc_start: 0.8052 (m) cc_final: 0.7581 (p) REVERT: N 50 ASP cc_start: 0.7805 (p0) cc_final: 0.7561 (p0) outliers start: 9 outliers final: 7 residues processed: 292 average time/residue: 0.2487 time to fit residues: 96.1781 Evaluate side-chains 275 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 267 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 298 TRP Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 156 GLN R 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9769 Z= 0.138 Angle : 0.507 9.224 13299 Z= 0.259 Chirality : 0.041 0.135 1539 Planarity : 0.004 0.058 1672 Dihedral : 4.727 56.252 1406 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.58 % Allowed : 15.25 % Favored : 83.18 % 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: -0.10 (0.24), residues: 1255 helix: 1.18 (0.29), residues: 367 sheet: 0.69 (0.28), residues: 302 loop : -1.32 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 47 HIS 0.005 0.001 HIS A 220 PHE 0.023 0.001 PHE S 29 TYR 0.011 0.001 TYR S 235 ARG 0.005 0.000 ARG R 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 265 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7797 (mmm) cc_final: 0.7207 (tpp) REVERT: A 221 MET cc_start: 0.7849 (ttm) cc_final: 0.7613 (ttp) REVERT: A 233 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8254 (mmtp) REVERT: B 120 ILE cc_start: 0.8151 (mt) cc_final: 0.7937 (mt) REVERT: B 212 ASP cc_start: 0.7388 (t0) cc_final: 0.7048 (t0) REVERT: R 73 SER cc_start: 0.8420 (t) cc_final: 0.8156 (t) REVERT: R 91 VAL cc_start: 0.8624 (t) cc_final: 0.8415 (m) REVERT: R 158 PHE cc_start: 0.8025 (t80) cc_final: 0.7821 (t80) REVERT: S 32 PHE cc_start: 0.8210 (m-80) cc_final: 0.7820 (m-80) REVERT: S 71 SER cc_start: 0.7641 (m) cc_final: 0.7177 (p) REVERT: S 76 LYS cc_start: 0.8309 (mttp) cc_final: 0.8087 (mttp) REVERT: S 230 MET cc_start: 0.7249 (mmm) cc_final: 0.6890 (mmm) outliers start: 15 outliers final: 10 residues processed: 272 average time/residue: 0.2422 time to fit residues: 87.8597 Evaluate side-chains 269 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 259 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 298 TRP Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 0.2980 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9769 Z= 0.128 Angle : 0.480 8.524 13299 Z= 0.246 Chirality : 0.040 0.141 1539 Planarity : 0.004 0.059 1672 Dihedral : 4.070 55.554 1396 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.31 % Allowed : 17.46 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.24), residues: 1255 helix: 1.35 (0.29), residues: 366 sheet: 0.78 (0.28), residues: 303 loop : -1.27 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.001 PHE S 239 TYR 0.010 0.001 TYR S 235 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 269 time to evaluate : 1.140 Fit side-chains REVERT: A 60 MET cc_start: 0.7692 (mmm) cc_final: 0.7139 (tpp) REVERT: A 221 MET cc_start: 0.7871 (ttm) cc_final: 0.7657 (ttp) REVERT: B 120 ILE cc_start: 0.8138 (mt) cc_final: 0.7934 (mt) REVERT: B 212 ASP cc_start: 0.7343 (t0) cc_final: 0.6982 (t0) REVERT: B 247 ASP cc_start: 0.7631 (p0) cc_final: 0.7361 (p0) REVERT: R 52 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7802 (mt) REVERT: R 73 SER cc_start: 0.8389 (t) cc_final: 0.8134 (t) REVERT: R 158 PHE cc_start: 0.7980 (t80) cc_final: 0.7764 (t80) REVERT: S 32 PHE cc_start: 0.8227 (m-80) cc_final: 0.7827 (m-80) REVERT: S 76 LYS cc_start: 0.8310 (mttp) cc_final: 0.8081 (mttp) REVERT: N 98 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7939 (ttt-90) outliers start: 22 outliers final: 18 residues processed: 274 average time/residue: 0.2260 time to fit residues: 83.0831 Evaluate side-chains 280 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 261 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9769 Z= 0.151 Angle : 0.487 8.595 13299 Z= 0.249 Chirality : 0.040 0.138 1539 Planarity : 0.004 0.060 1672 Dihedral : 3.794 55.149 1394 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.47 % Allowed : 18.61 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1255 helix: 1.39 (0.29), residues: 368 sheet: 0.83 (0.28), residues: 303 loop : -1.32 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS R 108 PHE 0.012 0.001 PHE S 239 TYR 0.010 0.001 TYR S 235 ARG 0.004 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 260 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7672 (mmm) cc_final: 0.7228 (tpp) REVERT: A 221 MET cc_start: 0.7865 (ttm) cc_final: 0.7660 (ttp) REVERT: B 212 ASP cc_start: 0.7351 (t0) cc_final: 0.7007 (t0) REVERT: B 247 ASP cc_start: 0.7621 (p0) cc_final: 0.7363 (p0) REVERT: R 52 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7768 (mt) REVERT: R 73 SER cc_start: 0.8412 (t) cc_final: 0.8170 (t) REVERT: R 158 PHE cc_start: 0.7953 (t80) cc_final: 0.7740 (t80) REVERT: S 32 PHE cc_start: 0.8254 (m-80) cc_final: 0.7822 (m-80) REVERT: S 71 SER cc_start: 0.7774 (m) cc_final: 0.7282 (p) REVERT: S 76 LYS cc_start: 0.8301 (mttp) cc_final: 0.8086 (mttp) REVERT: N 98 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7996 (ttt-90) outliers start: 33 outliers final: 25 residues processed: 273 average time/residue: 0.2431 time to fit residues: 88.9275 Evaluate side-chains 282 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 256 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 40.0000 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 156 GLN R 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9769 Z= 0.230 Angle : 0.539 8.668 13299 Z= 0.280 Chirality : 0.042 0.181 1539 Planarity : 0.004 0.061 1672 Dihedral : 4.109 54.178 1394 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.42 % Allowed : 17.88 % Favored : 77.71 % 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: -0.06 (0.24), residues: 1255 helix: 1.22 (0.29), residues: 372 sheet: 0.75 (0.28), residues: 310 loop : -1.38 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS S 35 PHE 0.019 0.002 PHE N 108 TYR 0.015 0.001 TYR S 235 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 269 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.7635 (mmm) cc_final: 0.7339 (tpp) REVERT: B 72 SER cc_start: 0.8171 (t) cc_final: 0.7700 (p) REVERT: R 73 SER cc_start: 0.8452 (t) cc_final: 0.8204 (t) REVERT: R 313 PHE cc_start: 0.8794 (m-80) cc_final: 0.8585 (m-10) REVERT: S 71 SER cc_start: 0.7914 (m) cc_final: 0.7497 (p) REVERT: S 76 LYS cc_start: 0.8315 (mttp) cc_final: 0.8072 (mttp) REVERT: S 168 SER cc_start: 0.8107 (p) cc_final: 0.7900 (m) REVERT: S 228 TYR cc_start: 0.8141 (m-80) cc_final: 0.7885 (m-80) outliers start: 42 outliers final: 33 residues processed: 287 average time/residue: 0.2313 time to fit residues: 89.2153 Evaluate side-chains 300 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 267 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN R 59 HIS R 108 HIS R 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9769 Z= 0.267 Angle : 0.568 9.015 13299 Z= 0.295 Chirality : 0.043 0.189 1539 Planarity : 0.004 0.060 1672 Dihedral : 4.295 53.388 1394 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.42 % Allowed : 20.29 % Favored : 75.29 % 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: -0.20 (0.24), residues: 1255 helix: 1.10 (0.29), residues: 371 sheet: 0.60 (0.28), residues: 318 loop : -1.43 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.006 0.001 HIS S 35 PHE 0.021 0.002 PHE N 108 TYR 0.016 0.002 TYR S 235 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 269 time to evaluate : 1.006 Fit side-chains REVERT: B 72 SER cc_start: 0.8189 (t) cc_final: 0.7691 (p) REVERT: B 283 ARG cc_start: 0.8126 (tpt-90) cc_final: 0.7783 (tpt90) REVERT: R 73 SER cc_start: 0.8414 (t) cc_final: 0.8155 (t) REVERT: R 81 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8484 (t) REVERT: S 71 SER cc_start: 0.7898 (m) cc_final: 0.7494 (p) REVERT: S 76 LYS cc_start: 0.8320 (mttp) cc_final: 0.8080 (mttp) REVERT: S 228 TYR cc_start: 0.8150 (m-80) cc_final: 0.7919 (m-80) outliers start: 42 outliers final: 37 residues processed: 288 average time/residue: 0.2371 time to fit residues: 91.1529 Evaluate side-chains 300 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 262 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 288 THR Chi-restraints excluded: chain R residue 299 CYS Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 100 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 156 GLN S 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9769 Z= 0.141 Angle : 0.508 8.513 13299 Z= 0.259 Chirality : 0.041 0.177 1539 Planarity : 0.004 0.060 1672 Dihedral : 3.916 54.071 1394 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.79 % Allowed : 21.45 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1255 helix: 1.34 (0.29), residues: 370 sheet: 0.83 (0.28), residues: 314 loop : -1.34 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 47 HIS 0.011 0.001 HIS S 167 PHE 0.018 0.001 PHE R 267 TYR 0.027 0.001 TYR R 226 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 271 time to evaluate : 1.089 Fit side-chains REVERT: B 241 PHE cc_start: 0.8385 (p90) cc_final: 0.8131 (p90) REVERT: B 283 ARG cc_start: 0.8101 (tpt-90) cc_final: 0.7730 (tpt90) REVERT: R 73 SER cc_start: 0.8438 (t) cc_final: 0.8193 (t) REVERT: S 71 SER cc_start: 0.7789 (m) cc_final: 0.7267 (p) REVERT: S 76 LYS cc_start: 0.8303 (mttp) cc_final: 0.8065 (mttp) REVERT: S 140 MET cc_start: 0.8128 (mtm) cc_final: 0.7477 (mtm) REVERT: S 228 TYR cc_start: 0.8069 (m-80) cc_final: 0.7864 (m-80) outliers start: 36 outliers final: 29 residues processed: 287 average time/residue: 0.2291 time to fit residues: 88.5530 Evaluate side-chains 288 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 259 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 0.0170 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9769 Z= 0.139 Angle : 0.507 8.310 13299 Z= 0.258 Chirality : 0.040 0.182 1539 Planarity : 0.004 0.060 1672 Dihedral : 3.805 53.904 1394 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.58 % Allowed : 20.72 % Favored : 75.71 % 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: 0.14 (0.24), residues: 1255 helix: 1.51 (0.29), residues: 366 sheet: 0.85 (0.28), residues: 309 loop : -1.31 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 47 HIS 0.008 0.001 HIS S 167 PHE 0.010 0.001 PHE A 212 TYR 0.021 0.001 TYR R 226 ARG 0.005 0.000 ARG R 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 264 time to evaluate : 1.064 Fit side-chains REVERT: B 283 ARG cc_start: 0.8102 (tpt-90) cc_final: 0.7664 (tpt90) REVERT: R 52 LEU cc_start: 0.7784 (mp) cc_final: 0.7512 (mp) REVERT: R 73 SER cc_start: 0.8456 (t) cc_final: 0.8206 (t) REVERT: S 71 SER cc_start: 0.7863 (m) cc_final: 0.7321 (p) REVERT: S 76 LYS cc_start: 0.8306 (mttp) cc_final: 0.8070 (mttp) REVERT: S 140 MET cc_start: 0.8124 (mtm) cc_final: 0.7488 (mtm) REVERT: S 228 TYR cc_start: 0.8095 (m-80) cc_final: 0.7875 (m-80) outliers start: 34 outliers final: 30 residues processed: 278 average time/residue: 0.2324 time to fit residues: 86.5635 Evaluate side-chains 293 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 156 GLN R 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9769 Z= 0.173 Angle : 0.524 8.469 13299 Z= 0.268 Chirality : 0.041 0.186 1539 Planarity : 0.004 0.060 1672 Dihedral : 3.893 52.991 1394 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.68 % Allowed : 20.72 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.24), residues: 1255 helix: 1.48 (0.29), residues: 366 sheet: 0.85 (0.28), residues: 316 loop : -1.30 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.007 0.001 HIS S 167 PHE 0.021 0.001 PHE R 267 TYR 0.020 0.001 TYR R 226 ARG 0.005 0.000 ARG R 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 1.136 Fit side-chains REVERT: A 291 LEU cc_start: 0.7841 (mm) cc_final: 0.7386 (mt) REVERT: B 283 ARG cc_start: 0.8130 (tpt-90) cc_final: 0.7817 (tpt90) REVERT: R 52 LEU cc_start: 0.7877 (mp) cc_final: 0.7571 (mp) REVERT: R 73 SER cc_start: 0.8452 (t) cc_final: 0.8199 (t) REVERT: S 71 SER cc_start: 0.7862 (m) cc_final: 0.7399 (p) REVERT: S 76 LYS cc_start: 0.8332 (mttp) cc_final: 0.8094 (mttp) REVERT: S 228 TYR cc_start: 0.8123 (m-80) cc_final: 0.7904 (m-80) outliers start: 35 outliers final: 33 residues processed: 277 average time/residue: 0.2321 time to fit residues: 86.4193 Evaluate side-chains 295 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 262 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.0020 chunk 123 optimal weight: 0.0370 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 60 optimal weight: 0.0010 chunk 78 optimal weight: 0.9980 overall best weight: 0.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN B 156 GLN R 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9769 Z= 0.125 Angle : 0.493 8.361 13299 Z= 0.247 Chirality : 0.040 0.186 1539 Planarity : 0.004 0.061 1672 Dihedral : 3.569 54.916 1394 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.84 % Allowed : 21.77 % Favored : 75.39 % 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 (0.24), residues: 1255 helix: 1.57 (0.29), residues: 366 sheet: 0.80 (0.28), residues: 315 loop : -1.22 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.007 0.001 HIS S 167 PHE 0.023 0.001 PHE R 267 TYR 0.019 0.001 TYR R 226 ARG 0.009 0.000 ARG R 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 256 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.7907 (t0) cc_final: 0.7658 (t0) REVERT: B 61 MET cc_start: 0.7165 (ppp) cc_final: 0.6824 (ppp) REVERT: B 241 PHE cc_start: 0.8393 (p90) cc_final: 0.8099 (p90) REVERT: B 283 ARG cc_start: 0.8085 (tpt-90) cc_final: 0.7661 (tpt-90) REVERT: R 73 SER cc_start: 0.8513 (t) cc_final: 0.8253 (t) REVERT: S 76 LYS cc_start: 0.8294 (mttp) cc_final: 0.8093 (mttp) REVERT: S 140 MET cc_start: 0.8030 (mtm) cc_final: 0.7428 (mtm) REVERT: S 228 TYR cc_start: 0.8033 (m-80) cc_final: 0.7822 (m-80) outliers start: 27 outliers final: 22 residues processed: 267 average time/residue: 0.2422 time to fit residues: 85.8196 Evaluate side-chains 278 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 256 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 76 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 253 GLU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.0040 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN R 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094940 restraints weight = 15173.421| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.98 r_work: 0.2958 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9769 Z= 0.286 Angle : 0.598 10.093 13299 Z= 0.306 Chirality : 0.043 0.182 1539 Planarity : 0.004 0.062 1672 Dihedral : 4.118 51.375 1394 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.84 % Allowed : 22.92 % Favored : 74.24 % 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: 0.03 (0.24), residues: 1255 helix: 1.33 (0.29), residues: 368 sheet: 0.78 (0.28), residues: 319 loop : -1.35 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.006 0.002 HIS R 108 PHE 0.037 0.002 PHE S 239 TYR 0.020 0.002 TYR R 226 ARG 0.011 0.001 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.58 seconds wall clock time: 47 minutes 11.38 seconds (2831.38 seconds total)