Starting phenix.real_space_refine on Fri Mar 15 13:07:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/03_2024/7o12_12687_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/03_2024/7o12_12687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/03_2024/7o12_12687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/03_2024/7o12_12687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/03_2024/7o12_12687_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o12_12687/03_2024/7o12_12687_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 36 5.16 5 C 7471 2.51 5 N 2047 2.21 5 O 2128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "E ASP 219": "OD1" <-> "OD2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11691 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3140 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain: "E" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1880 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain breaks: 3 Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 6.79, per 1000 atoms: 0.58 Number of scatterers: 11691 At special positions: 0 Unit cell: (83.106, 168.264, 134.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 3 11.99 O 2128 8.00 N 2047 7.00 C 7471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.97 Conformation dependent library (CDL) restraints added in 2.4 seconds 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 13 sheets defined 42.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.532A pdb=" N MET B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 5.106A pdb=" N GLN B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.707A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.439A pdb=" N ASP B 110 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 111 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 116 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 131 through 142 removed outlier: 4.001A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.530A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 removed outlier: 4.358A pdb=" N GLU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ALA B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 193' Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.776A pdb=" N GLU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.563A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.849A pdb=" N ARG C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLN C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 75' Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.572A pdb=" N LEU C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 116 removed outlier: 4.439A pdb=" N ASP C 110 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU C 111 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 116 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 161 through 176 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'C' and resid 287 through 298 removed outlier: 3.560A pdb=" N MET C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.516A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.503A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 6 No H-bonds generated for 'chain 'E' and resid 3 through 6' Processing helix chain 'E' and resid 8 through 15 Processing helix chain 'E' and resid 19 through 40 removed outlier: 3.527A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 74 removed outlier: 3.817A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.977A pdb=" N THR E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 119 removed outlier: 3.633A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 139 through 142 No H-bonds generated for 'chain 'E' and resid 139 through 142' Processing helix chain 'E' and resid 144 through 167 removed outlier: 3.593A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 187 removed outlier: 3.507A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 209 through 215 removed outlier: 3.535A pdb=" N LEU E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU E 214 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU E 215 " --> pdb=" O TRP E 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 215' Processing helix chain 'E' and resid 217 through 223 Processing helix chain 'E' and resid 249 through 273 removed outlier: 3.526A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 removed outlier: 4.049A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 41 removed outlier: 3.524A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 74 removed outlier: 3.743A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 79 through 82 No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.974A pdb=" N THR D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 128 removed outlier: 3.914A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 166 removed outlier: 3.591A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 187 removed outlier: 3.560A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 199 Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 237 through 243 removed outlier: 4.017A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 273 removed outlier: 3.558A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.815A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 181 through 184 removed outlier: 7.045A pdb=" N ARG B 197 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE B 35 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA B 199 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= D, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.617A pdb=" N GLN C 7 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 197 through 200 removed outlier: 3.839A pdb=" N PHE C 35 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 181 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU C 34 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 183 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 254 through 258 removed outlier: 3.659A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.313A pdb=" N GLN A 63 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU A 47 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG A 65 " --> pdb=" O LEU A 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.550A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.019A pdb=" N THR A 94 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ARG A 124 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 146 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N HIS A 176 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A 198 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 220 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG A 242 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N PHE A 265 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N HIS A 302 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA A 325 " --> pdb=" O PHE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.874A pdb=" N GLN A 119 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN A 141 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG A 171 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N HIS A 193 " --> pdb=" O VAL A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 184 through 187 Processing sheet with id= L, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.417A pdb=" N THR A 237 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR A 260 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 310 through 312 418 hydrogen bonds defined for protein. 1182 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: 3.47 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3661 1.33 - 1.45: 2211 1.45 - 1.57: 5972 1.57 - 1.69: 6 1.69 - 1.81: 62 Bond restraints: 11912 Sorted by residual: bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.529 0.171 2.00e-02 2.50e+03 7.30e+01 bond pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 1.700 1.532 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 1.795 1.679 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.680 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" O5' ANP B 402 " pdb=" PA ANP B 402 " ideal model delta sigma weight residual 1.655 1.557 0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 11907 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.37: 228 105.37 - 112.59: 6135 112.59 - 119.81: 4531 119.81 - 127.03: 5114 127.03 - 134.24: 177 Bond angle restraints: 16185 Sorted by residual: angle pdb=" PB ANP C 402 " pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 126.95 103.57 23.38 3.00e+00 1.11e-01 6.07e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 105.67 21.28 3.00e+00 1.11e-01 5.03e+01 angle pdb=" CG1 VAL B 31 " pdb=" CB VAL B 31 " pdb=" CG2 VAL B 31 " ideal model delta sigma weight residual 110.80 99.06 11.74 2.20e+00 2.07e-01 2.85e+01 angle pdb=" PA ANP B 402 " pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 125.41 109.66 15.75 3.00e+00 1.11e-01 2.75e+01 angle pdb=" PA ANP C 402 " pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 125.41 110.62 14.79 3.00e+00 1.11e-01 2.43e+01 ... (remaining 16180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 6547 22.39 - 44.77: 436 44.77 - 67.15: 64 67.15 - 89.54: 19 89.54 - 111.92: 2 Dihedral angle restraints: 7068 sinusoidal: 2809 harmonic: 4259 Sorted by residual: dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU E 73 " pdb=" C LEU E 73 " pdb=" N ALA E 74 " pdb=" CA ALA E 74 " ideal model delta harmonic sigma weight residual 180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA SER D 240 " pdb=" C SER D 240 " pdb=" N LEU D 241 " pdb=" CA LEU D 241 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1620 0.102 - 0.203: 216 0.203 - 0.305: 22 0.305 - 0.407: 6 0.407 - 0.508: 1 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" CB VAL C 187 " pdb=" CA VAL C 187 " pdb=" CG1 VAL C 187 " pdb=" CG2 VAL C 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE B 255 " pdb=" CA ILE B 255 " pdb=" CG1 ILE B 255 " pdb=" CG2 ILE B 255 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1862 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 187 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C VAL B 187 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL B 187 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 188 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO D 67 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 97 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C GLU A 97 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 97 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP A 98 " 0.017 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 31 2.37 - 3.00: 5901 3.00 - 3.63: 18683 3.63 - 4.27: 28800 4.27 - 4.90: 46792 Nonbonded interactions: 100207 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 1.734 2.170 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 1.944 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G ANP B 402 " model vdw 2.095 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2B ANP B 402 " model vdw 2.106 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G ANP C 402 " model vdw 2.107 2.170 ... (remaining 100202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 132 or resid 136 through \ 228 or resid 245 through 274)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 6.290 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.840 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.171 11912 Z= 0.760 Angle : 1.294 23.378 16185 Z= 0.647 Chirality : 0.073 0.508 1865 Planarity : 0.008 0.076 2060 Dihedral : 15.583 111.922 4352 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.82 % Allowed : 9.50 % Favored : 89.68 % 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: -5.32 (0.15), residues: 1493 helix: -4.25 (0.09), residues: 639 sheet: -3.34 (0.30), residues: 194 loop : -2.63 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 45 HIS 0.010 0.002 HIS A 176 PHE 0.022 0.003 PHE A 56 TYR 0.026 0.003 TYR E 93 ARG 0.012 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8580 (tmm) cc_final: 0.8304 (tmm) REVERT: B 61 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8748 (tppt) REVERT: B 200 ILE cc_start: 0.9798 (mt) cc_final: 0.9536 (tt) REVERT: C 46 MET cc_start: 0.9251 (mtm) cc_final: 0.9048 (mtm) REVERT: C 83 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8827 (p) REVERT: C 295 MET cc_start: 0.8078 (mmm) cc_final: 0.7064 (mmm) REVERT: A 62 MET cc_start: 0.8065 (mmp) cc_final: 0.7818 (mmm) REVERT: A 103 THR cc_start: 0.9281 (p) cc_final: 0.9081 (p) REVERT: A 235 LYS cc_start: 0.9338 (mmtt) cc_final: 0.9002 (tppt) REVERT: A 334 LYS cc_start: 0.9540 (tttt) cc_final: 0.8928 (ttmm) REVERT: E 66 MET cc_start: 0.9390 (mmm) cc_final: 0.9083 (mpp) REVERT: E 138 MET cc_start: 0.8877 (tpt) cc_final: 0.8568 (tpp) REVERT: E 171 LYS cc_start: 0.9204 (tttt) cc_final: 0.8974 (tmmt) REVERT: E 213 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9256 (mm) REVERT: E 255 CYS cc_start: 0.9128 (t) cc_final: 0.8716 (t) REVERT: D 82 ASP cc_start: 0.8899 (t70) cc_final: 0.8611 (t0) REVERT: D 83 GLU cc_start: 0.9154 (pt0) cc_final: 0.8734 (pp20) REVERT: D 138 MET cc_start: 0.8849 (tmm) cc_final: 0.8293 (tmm) REVERT: D 171 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8941 (ttmm) REVERT: D 219 ASP cc_start: 0.9182 (m-30) cc_final: 0.8977 (m-30) outliers start: 10 outliers final: 3 residues processed: 104 average time/residue: 0.2647 time to fit residues: 39.0885 Evaluate side-chains 69 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 131 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 115 GLN B 214 GLN B 283 HIS C 214 GLN C 263 HIS A 30 GLN A 53 GLN A 63 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS A 179 ASN A 190 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 417 HIS D 205 ASN D 225 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11912 Z= 0.197 Angle : 0.609 9.854 16185 Z= 0.305 Chirality : 0.041 0.172 1865 Planarity : 0.005 0.060 2060 Dihedral : 9.687 137.250 1709 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.05 % Allowed : 13.92 % Favored : 84.03 % 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: -3.27 (0.19), residues: 1493 helix: -1.73 (0.17), residues: 659 sheet: -2.85 (0.30), residues: 216 loop : -2.22 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 253 HIS 0.005 0.001 HIS B 263 PHE 0.011 0.001 PHE E 157 TYR 0.008 0.001 TYR A 208 ARG 0.008 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8504 (tmm) cc_final: 0.8268 (tmm) REVERT: B 61 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8714 (tppt) REVERT: B 200 ILE cc_start: 0.9770 (mt) cc_final: 0.9473 (tt) REVERT: C 37 HIS cc_start: 0.8247 (m-70) cc_final: 0.7726 (m90) REVERT: C 112 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9473 (mm) REVERT: C 295 MET cc_start: 0.8107 (mmm) cc_final: 0.7601 (mmm) REVERT: A 125 MET cc_start: 0.8961 (mpp) cc_final: 0.8691 (mpp) REVERT: A 235 LYS cc_start: 0.9314 (mmtt) cc_final: 0.9042 (tppt) REVERT: A 334 LYS cc_start: 0.9502 (tttt) cc_final: 0.8980 (ttmm) REVERT: E 143 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8919 (m-10) REVERT: E 255 CYS cc_start: 0.8740 (t) cc_final: 0.8484 (t) REVERT: D 82 ASP cc_start: 0.8868 (t70) cc_final: 0.8569 (t0) REVERT: D 83 GLU cc_start: 0.9118 (pt0) cc_final: 0.8707 (pp20) REVERT: D 114 LEU cc_start: 0.8954 (tt) cc_final: 0.8554 (mp) REVERT: D 138 MET cc_start: 0.8874 (tmm) cc_final: 0.8295 (tmm) REVERT: D 255 CYS cc_start: 0.9353 (t) cc_final: 0.8897 (t) outliers start: 25 outliers final: 11 residues processed: 104 average time/residue: 0.2250 time to fit residues: 35.0601 Evaluate side-chains 79 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 131 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 0.0010 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11912 Z= 0.192 Angle : 0.571 8.854 16185 Z= 0.282 Chirality : 0.041 0.154 1865 Planarity : 0.004 0.039 2060 Dihedral : 7.994 135.302 1708 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.29 % Allowed : 14.82 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.21), residues: 1493 helix: -0.24 (0.20), residues: 657 sheet: -2.56 (0.32), residues: 216 loop : -1.91 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 253 HIS 0.010 0.001 HIS C 263 PHE 0.011 0.001 PHE E 157 TYR 0.007 0.001 TYR A 208 ARG 0.004 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8471 (tmm) cc_final: 0.8227 (tmm) REVERT: B 61 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8698 (tppt) REVERT: B 200 ILE cc_start: 0.9772 (mt) cc_final: 0.9554 (tt) REVERT: C 37 HIS cc_start: 0.8288 (m-70) cc_final: 0.7635 (m-70) REVERT: C 133 MET cc_start: 0.9343 (mtm) cc_final: 0.9101 (mtm) REVERT: C 268 LEU cc_start: 0.9604 (mt) cc_final: 0.9388 (mt) REVERT: C 295 MET cc_start: 0.8271 (mmm) cc_final: 0.7216 (mmm) REVERT: A 125 MET cc_start: 0.9084 (mpp) cc_final: 0.8540 (mpp) REVERT: A 235 LYS cc_start: 0.9313 (mmtt) cc_final: 0.9028 (tppt) REVERT: A 334 LYS cc_start: 0.9504 (tttt) cc_final: 0.9129 (tttp) REVERT: A 420 MET cc_start: 0.8119 (mmm) cc_final: 0.7911 (mmm) REVERT: E 143 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8932 (m-10) REVERT: E 168 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8898 (p) REVERT: E 212 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8848 (mp) REVERT: E 255 CYS cc_start: 0.8674 (t) cc_final: 0.8294 (t) REVERT: D 82 ASP cc_start: 0.8809 (t70) cc_final: 0.8515 (t0) REVERT: D 83 GLU cc_start: 0.9063 (pt0) cc_final: 0.8680 (pp20) REVERT: D 114 LEU cc_start: 0.8904 (tt) cc_final: 0.8512 (mp) REVERT: D 138 MET cc_start: 0.8891 (tmm) cc_final: 0.8307 (tmm) REVERT: D 219 ASP cc_start: 0.9117 (m-30) cc_final: 0.8892 (m-30) REVERT: D 255 CYS cc_start: 0.9347 (t) cc_final: 0.8942 (t) outliers start: 28 outliers final: 19 residues processed: 95 average time/residue: 0.2009 time to fit residues: 29.7452 Evaluate side-chains 86 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11912 Z= 0.258 Angle : 0.591 9.780 16185 Z= 0.291 Chirality : 0.041 0.152 1865 Planarity : 0.003 0.037 2060 Dihedral : 7.600 133.788 1708 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.70 % Allowed : 16.79 % Favored : 80.51 % 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: -1.33 (0.22), residues: 1493 helix: 0.49 (0.21), residues: 657 sheet: -2.39 (0.33), residues: 216 loop : -1.77 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 20 HIS 0.002 0.001 HIS C 283 PHE 0.013 0.001 PHE E 157 TYR 0.007 0.001 TYR A 208 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 65 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8475 (tmm) cc_final: 0.8192 (tmm) REVERT: B 61 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8739 (tppt) REVERT: B 200 ILE cc_start: 0.9778 (mt) cc_final: 0.9515 (tt) REVERT: C 37 HIS cc_start: 0.8281 (m-70) cc_final: 0.7154 (m-70) REVERT: C 261 ASN cc_start: 0.8373 (t0) cc_final: 0.8151 (t0) REVERT: C 268 LEU cc_start: 0.9601 (mt) cc_final: 0.9388 (mt) REVERT: C 295 MET cc_start: 0.8411 (mmm) cc_final: 0.6862 (mmm) REVERT: A 125 MET cc_start: 0.9044 (mpp) cc_final: 0.8309 (mpp) REVERT: A 209 MET cc_start: 0.9035 (mmm) cc_final: 0.8825 (mmt) REVERT: A 235 LYS cc_start: 0.9328 (mmtt) cc_final: 0.9033 (tppt) REVERT: A 334 LYS cc_start: 0.9509 (tttt) cc_final: 0.9129 (tttp) REVERT: E 143 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8961 (m-10) REVERT: E 252 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8988 (tp) REVERT: E 255 CYS cc_start: 0.8671 (t) cc_final: 0.8306 (t) REVERT: D 82 ASP cc_start: 0.8879 (t70) cc_final: 0.8575 (t0) REVERT: D 83 GLU cc_start: 0.9087 (pt0) cc_final: 0.8723 (pp20) REVERT: D 114 LEU cc_start: 0.8947 (tt) cc_final: 0.8555 (mp) REVERT: D 138 MET cc_start: 0.8968 (tmm) cc_final: 0.8343 (tmm) REVERT: D 219 ASP cc_start: 0.8963 (m-30) cc_final: 0.8709 (m-30) REVERT: D 255 CYS cc_start: 0.9354 (t) cc_final: 0.8975 (t) outliers start: 33 outliers final: 18 residues processed: 97 average time/residue: 0.1914 time to fit residues: 29.5406 Evaluate side-chains 82 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain E residue 143 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11912 Z= 0.217 Angle : 0.563 9.368 16185 Z= 0.277 Chirality : 0.041 0.150 1865 Planarity : 0.003 0.038 2060 Dihedral : 7.471 133.958 1706 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.62 % Allowed : 17.77 % Favored : 79.61 % 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: -0.85 (0.23), residues: 1493 helix: 0.95 (0.21), residues: 647 sheet: -2.26 (0.33), residues: 216 loop : -1.51 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 236 HIS 0.002 0.001 HIS C 283 PHE 0.011 0.001 PHE E 157 TYR 0.007 0.001 TYR A 208 ARG 0.002 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 65 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8457 (tmm) cc_final: 0.8182 (tmm) REVERT: B 31 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 46 MET cc_start: 0.9597 (mmm) cc_final: 0.9392 (mmm) REVERT: B 61 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8726 (tppt) REVERT: B 200 ILE cc_start: 0.9780 (mt) cc_final: 0.9560 (tt) REVERT: B 295 MET cc_start: 0.8667 (mmm) cc_final: 0.8324 (mmm) REVERT: C 112 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9424 (mm) REVERT: C 133 MET cc_start: 0.9322 (mtm) cc_final: 0.8773 (ptm) REVERT: C 268 LEU cc_start: 0.9591 (mt) cc_final: 0.9390 (mt) REVERT: A 125 MET cc_start: 0.9074 (mpp) cc_final: 0.8353 (mpp) REVERT: A 235 LYS cc_start: 0.9318 (mmtt) cc_final: 0.9028 (tppt) REVERT: A 334 LYS cc_start: 0.9496 (tttt) cc_final: 0.9110 (tttp) REVERT: E 252 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8988 (tp) REVERT: E 255 CYS cc_start: 0.8681 (t) cc_final: 0.8315 (t) REVERT: D 11 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8146 (tm-30) REVERT: D 82 ASP cc_start: 0.8886 (t70) cc_final: 0.8586 (t0) REVERT: D 83 GLU cc_start: 0.9072 (pt0) cc_final: 0.8730 (pp20) REVERT: D 114 LEU cc_start: 0.8931 (tt) cc_final: 0.8549 (mp) REVERT: D 138 MET cc_start: 0.9012 (tmm) cc_final: 0.8429 (tmm) REVERT: D 219 ASP cc_start: 0.8941 (m-30) cc_final: 0.8695 (m-30) REVERT: D 255 CYS cc_start: 0.9333 (t) cc_final: 0.8975 (t) outliers start: 32 outliers final: 19 residues processed: 96 average time/residue: 0.1900 time to fit residues: 29.0227 Evaluate side-chains 83 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11912 Z= 0.176 Angle : 0.536 9.073 16185 Z= 0.265 Chirality : 0.040 0.192 1865 Planarity : 0.003 0.039 2060 Dihedral : 7.350 133.870 1704 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.21 % Allowed : 18.02 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1493 helix: 1.22 (0.22), residues: 649 sheet: -2.20 (0.32), residues: 221 loop : -1.34 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.007 0.001 HIS C 37 PHE 0.010 0.001 PHE E 157 TYR 0.010 0.001 TYR A 208 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8446 (tmm) cc_final: 0.8186 (tmm) REVERT: B 31 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 61 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8733 (tppt) REVERT: B 200 ILE cc_start: 0.9767 (mt) cc_final: 0.9563 (tt) REVERT: B 295 MET cc_start: 0.8525 (mmm) cc_final: 0.8245 (mmm) REVERT: C 37 HIS cc_start: 0.8281 (m-70) cc_final: 0.7383 (m90) REVERT: C 112 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9403 (mm) REVERT: C 133 MET cc_start: 0.9346 (mtm) cc_final: 0.8752 (ptp) REVERT: C 295 MET cc_start: 0.8295 (mmm) cc_final: 0.7986 (mmm) REVERT: A 125 MET cc_start: 0.9109 (mpp) cc_final: 0.8381 (mpp) REVERT: A 235 LYS cc_start: 0.9323 (mmtt) cc_final: 0.9049 (tppt) REVERT: A 334 LYS cc_start: 0.9477 (tttt) cc_final: 0.9101 (tttp) REVERT: E 35 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8575 (tt) REVERT: E 252 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8978 (tp) REVERT: E 255 CYS cc_start: 0.8625 (t) cc_final: 0.8295 (t) REVERT: D 11 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8204 (tm-30) REVERT: D 82 ASP cc_start: 0.8857 (t70) cc_final: 0.8593 (t0) REVERT: D 83 GLU cc_start: 0.9063 (pt0) cc_final: 0.8718 (pp20) REVERT: D 114 LEU cc_start: 0.8865 (tt) cc_final: 0.8471 (mt) REVERT: D 138 MET cc_start: 0.8984 (tmm) cc_final: 0.8411 (tmm) REVERT: D 187 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9253 (pt) REVERT: D 219 ASP cc_start: 0.8943 (m-30) cc_final: 0.8651 (m-30) REVERT: D 255 CYS cc_start: 0.9316 (t) cc_final: 0.8964 (t) outliers start: 27 outliers final: 20 residues processed: 90 average time/residue: 0.1934 time to fit residues: 27.7590 Evaluate side-chains 86 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11912 Z= 0.155 Angle : 0.536 9.088 16185 Z= 0.262 Chirality : 0.040 0.151 1865 Planarity : 0.003 0.042 2060 Dihedral : 7.224 133.726 1704 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.46 % Allowed : 17.85 % Favored : 79.69 % 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: -0.40 (0.23), residues: 1493 helix: 1.31 (0.22), residues: 654 sheet: -2.01 (0.32), residues: 228 loop : -1.27 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 236 HIS 0.002 0.000 HIS B 97 PHE 0.010 0.001 PHE E 157 TYR 0.008 0.001 TYR A 208 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8488 (tmm) cc_final: 0.8240 (tmm) REVERT: B 61 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8823 (tppt) REVERT: B 200 ILE cc_start: 0.9759 (mt) cc_final: 0.9547 (tt) REVERT: C 37 HIS cc_start: 0.8220 (m-70) cc_final: 0.7227 (m90) REVERT: C 83 VAL cc_start: 0.9303 (OUTLIER) cc_final: 0.8991 (t) REVERT: C 112 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9425 (mm) REVERT: C 133 MET cc_start: 0.9332 (mtm) cc_final: 0.8738 (ptp) REVERT: C 295 MET cc_start: 0.8383 (mmm) cc_final: 0.7611 (mmm) REVERT: A 125 MET cc_start: 0.9109 (mpp) cc_final: 0.8408 (mpp) REVERT: A 235 LYS cc_start: 0.9329 (mmtt) cc_final: 0.9047 (tppt) REVERT: A 334 LYS cc_start: 0.9453 (tttt) cc_final: 0.9087 (tttp) REVERT: E 35 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8597 (tt) REVERT: E 252 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8981 (tp) REVERT: E 255 CYS cc_start: 0.8557 (t) cc_final: 0.8243 (t) REVERT: D 11 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8244 (mm-30) REVERT: D 82 ASP cc_start: 0.8843 (t70) cc_final: 0.8575 (t0) REVERT: D 83 GLU cc_start: 0.9072 (pt0) cc_final: 0.8726 (pp20) REVERT: D 114 LEU cc_start: 0.8800 (tt) cc_final: 0.8459 (mt) REVERT: D 138 MET cc_start: 0.9011 (tmm) cc_final: 0.8412 (tmm) REVERT: D 187 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9227 (pt) REVERT: D 219 ASP cc_start: 0.8921 (m-30) cc_final: 0.8640 (m-30) REVERT: D 255 CYS cc_start: 0.9319 (t) cc_final: 0.8972 (t) outliers start: 30 outliers final: 20 residues processed: 93 average time/residue: 0.1933 time to fit residues: 28.3437 Evaluate side-chains 84 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 59 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 82 ASN C 283 HIS ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11912 Z= 0.469 Angle : 0.754 10.817 16185 Z= 0.366 Chirality : 0.044 0.183 1865 Planarity : 0.004 0.030 2060 Dihedral : 7.323 132.292 1704 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.78 % Allowed : 19.33 % Favored : 77.89 % 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: -0.60 (0.22), residues: 1493 helix: 1.26 (0.21), residues: 650 sheet: -2.14 (0.33), residues: 217 loop : -1.51 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 211 HIS 0.005 0.001 HIS B 263 PHE 0.018 0.002 PHE B 35 TYR 0.011 0.002 TYR B 293 ARG 0.004 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 61 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8532 (tmm) cc_final: 0.8263 (tmm) REVERT: B 61 LYS cc_start: 0.9077 (mtpt) cc_final: 0.8849 (tppt) REVERT: C 37 HIS cc_start: 0.8184 (m-70) cc_final: 0.7655 (m-70) REVERT: C 295 MET cc_start: 0.8505 (mmm) cc_final: 0.7530 (mmm) REVERT: A 125 MET cc_start: 0.9043 (mpp) cc_final: 0.8364 (mpp) REVERT: A 235 LYS cc_start: 0.9399 (mmtt) cc_final: 0.9112 (tppt) REVERT: A 334 LYS cc_start: 0.9541 (tttt) cc_final: 0.9120 (tttp) REVERT: E 35 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8549 (tt) REVERT: E 81 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8446 (mm-30) REVERT: E 252 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9031 (tp) REVERT: E 255 CYS cc_start: 0.8676 (t) cc_final: 0.8360 (t) REVERT: D 11 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8133 (tm-30) REVERT: D 82 ASP cc_start: 0.9067 (t70) cc_final: 0.8756 (t0) REVERT: D 83 GLU cc_start: 0.9155 (pt0) cc_final: 0.8791 (pp20) REVERT: D 138 MET cc_start: 0.9055 (tmm) cc_final: 0.8469 (tmm) REVERT: D 219 ASP cc_start: 0.8841 (m-30) cc_final: 0.8597 (m-30) REVERT: D 255 CYS cc_start: 0.9329 (t) cc_final: 0.8986 (t) outliers start: 34 outliers final: 23 residues processed: 93 average time/residue: 0.2010 time to fit residues: 30.1410 Evaluate side-chains 85 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11912 Z= 0.154 Angle : 0.575 9.315 16185 Z= 0.278 Chirality : 0.041 0.159 1865 Planarity : 0.003 0.039 2060 Dihedral : 7.247 132.846 1704 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.05 % Allowed : 19.82 % Favored : 78.13 % 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: -0.36 (0.23), residues: 1493 helix: 1.47 (0.21), residues: 651 sheet: -2.05 (0.32), residues: 217 loop : -1.39 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 236 HIS 0.002 0.001 HIS B 97 PHE 0.009 0.001 PHE D 157 TYR 0.010 0.001 TYR B 291 ARG 0.002 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8464 (tmm) cc_final: 0.8190 (tmm) REVERT: B 46 MET cc_start: 0.9506 (mmm) cc_final: 0.9273 (mmm) REVERT: B 61 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8817 (tppt) REVERT: B 200 ILE cc_start: 0.9772 (mt) cc_final: 0.9505 (tt) REVERT: C 37 HIS cc_start: 0.8179 (m-70) cc_final: 0.7667 (m-70) REVERT: C 133 MET cc_start: 0.9280 (mtm) cc_final: 0.8778 (ptp) REVERT: C 295 MET cc_start: 0.8446 (mmm) cc_final: 0.7542 (mmm) REVERT: A 125 MET cc_start: 0.9096 (mpp) cc_final: 0.8430 (mpp) REVERT: A 235 LYS cc_start: 0.9353 (mmtt) cc_final: 0.9070 (tppt) REVERT: A 334 LYS cc_start: 0.9474 (tttt) cc_final: 0.9080 (tttp) REVERT: E 35 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8560 (tt) REVERT: E 252 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8997 (tp) REVERT: E 255 CYS cc_start: 0.8621 (t) cc_final: 0.8309 (t) REVERT: D 11 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8285 (tm-30) REVERT: D 82 ASP cc_start: 0.8871 (t70) cc_final: 0.8613 (t0) REVERT: D 83 GLU cc_start: 0.9003 (pt0) cc_final: 0.8675 (pp20) REVERT: D 114 LEU cc_start: 0.8708 (tt) cc_final: 0.8415 (mt) REVERT: D 138 MET cc_start: 0.9056 (tmm) cc_final: 0.8484 (tmm) REVERT: D 219 ASP cc_start: 0.8843 (m-30) cc_final: 0.8605 (m-30) REVERT: D 255 CYS cc_start: 0.9328 (t) cc_final: 0.8991 (t) outliers start: 25 outliers final: 19 residues processed: 89 average time/residue: 0.1992 time to fit residues: 28.2784 Evaluate side-chains 84 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 90 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11912 Z= 0.162 Angle : 0.565 8.750 16185 Z= 0.274 Chirality : 0.041 0.155 1865 Planarity : 0.003 0.042 2060 Dihedral : 7.025 130.637 1704 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.88 % Allowed : 20.07 % Favored : 78.05 % 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 (0.23), residues: 1493 helix: 1.62 (0.21), residues: 649 sheet: -1.92 (0.33), residues: 217 loop : -1.34 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 236 HIS 0.002 0.000 HIS B 97 PHE 0.009 0.001 PHE D 157 TYR 0.027 0.001 TYR B 291 ARG 0.002 0.000 ARG A 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8460 (tmm) cc_final: 0.8213 (tmm) REVERT: B 83 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8605 (t) REVERT: B 200 ILE cc_start: 0.9747 (mt) cc_final: 0.9546 (tt) REVERT: C 133 MET cc_start: 0.9292 (mtm) cc_final: 0.8753 (ptp) REVERT: A 125 MET cc_start: 0.9093 (mpp) cc_final: 0.8465 (mpp) REVERT: A 235 LYS cc_start: 0.9345 (mmtt) cc_final: 0.9054 (tppt) REVERT: A 334 LYS cc_start: 0.9460 (tttt) cc_final: 0.9088 (tttp) REVERT: E 35 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8602 (tt) REVERT: E 252 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9002 (tp) REVERT: E 255 CYS cc_start: 0.8559 (t) cc_final: 0.8249 (t) REVERT: D 11 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8203 (tm-30) REVERT: D 81 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8355 (mm-30) REVERT: D 82 ASP cc_start: 0.8896 (t70) cc_final: 0.8654 (t0) REVERT: D 83 GLU cc_start: 0.9035 (pt0) cc_final: 0.8722 (pp20) REVERT: D 114 LEU cc_start: 0.8661 (tt) cc_final: 0.8391 (mt) REVERT: D 138 MET cc_start: 0.9054 (tmm) cc_final: 0.8554 (tmm) REVERT: D 219 ASP cc_start: 0.8842 (m-30) cc_final: 0.8591 (m-30) REVERT: D 255 CYS cc_start: 0.9302 (t) cc_final: 0.8999 (t) outliers start: 23 outliers final: 19 residues processed: 88 average time/residue: 0.1942 time to fit residues: 26.9694 Evaluate side-chains 84 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain D residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.036263 restraints weight = 76731.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.037483 restraints weight = 39679.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.038304 restraints weight = 25940.301| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11912 Z= 0.144 Angle : 0.565 9.497 16185 Z= 0.274 Chirality : 0.041 0.153 1865 Planarity : 0.003 0.043 2060 Dihedral : 6.968 128.571 1704 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.88 % Allowed : 20.48 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1493 helix: 1.70 (0.21), residues: 648 sheet: -1.83 (0.34), residues: 219 loop : -1.34 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 236 HIS 0.010 0.001 HIS C 37 PHE 0.009 0.001 PHE D 157 TYR 0.022 0.001 TYR B 291 ARG 0.002 0.000 ARG A 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2040.11 seconds wall clock time: 38 minutes 58.15 seconds (2338.15 seconds total)