Starting phenix.real_space_refine on Thu Sep 26 01:51:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/09_2024/6lfm_0877.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/09_2024/6lfm_0877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/09_2024/6lfm_0877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/09_2024/6lfm_0877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/09_2024/6lfm_0877.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lfm_0877/09_2024/6lfm_0877.cif" } resolution = 3.5 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1821 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6510 2.51 5 N 1744 2.21 5 O 1855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10181 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1805 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "E" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 551 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "R" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2451 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 295} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1750 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.20, per 1000 atoms: 0.61 Number of scatterers: 10181 At special positions: 0 Unit cell: (87.3602, 123.414, 156.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1855 8.00 N 1744 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 34 " distance=2.04 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 50 " distance=2.04 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.04 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 19 sheets defined 35.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.561A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.866A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.107A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.612A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.196A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.228A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.524A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 4.319A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 4.062A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.946A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.510A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.567A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 18 through 22 removed outlier: 4.085A pdb=" N ILE D 22 " --> pdb=" O PRO D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 70 removed outlier: 4.728A pdb=" N GLU D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'R' and resid 46 through 60 removed outlier: 4.255A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 75 removed outlier: 3.513A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET R 70 " --> pdb=" O ASN R 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU R 74 " --> pdb=" O MET R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 98 removed outlier: 4.136A pdb=" N LEU R 87 " --> pdb=" O THR R 83 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 111 removed outlier: 3.649A pdb=" N SER R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 108 " --> pdb=" O TRP R 104 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 136 removed outlier: 4.032A pdb=" N CYS R 119 " --> pdb=" O GLY R 115 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER R 123 " --> pdb=" O CYS R 119 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU R 124 " --> pdb=" O LYS R 120 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR R 131 " --> pdb=" O GLU R 127 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE R 134 " --> pdb=" O PHE R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 147 Processing helix chain 'R' and resid 155 through 161 removed outlier: 4.499A pdb=" N ARG R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 182 removed outlier: 3.639A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 214 removed outlier: 3.644A pdb=" N ILE R 213 " --> pdb=" O MET R 209 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 219 Processing helix chain 'R' and resid 220 through 229 Processing helix chain 'R' and resid 230 through 241 Processing helix chain 'R' and resid 245 through 279 removed outlier: 3.819A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG R 251 " --> pdb=" O HIS R 247 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA R 255 " --> pdb=" O ARG R 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix removed outlier: 3.725A pdb=" N LEU R 272 " --> pdb=" O ASN R 268 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR R 275 " --> pdb=" O LEU R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 315 removed outlier: 3.502A pdb=" N ILE R 301 " --> pdb=" O ASP R 297 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS R 306 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER R 307 " --> pdb=" O GLY R 303 " (cutoff:3.500A) Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 332 removed outlier: 3.623A pdb=" N LEU R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.051A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.614A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.790A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.656A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.730A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.958A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.797A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.753A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.597A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.556A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.864A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.850A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.810A pdb=" N VAL D 41 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS D 42 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU E 24 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 184 through 185 Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 4 Processing sheet with id=AB4, first strand: chain 'S' and resid 17 through 21 removed outlier: 3.673A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 45 through 50 removed outlier: 6.709A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 135 through 136 removed outlier: 4.024A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 144 through 148 Processing sheet with id=AB8, first strand: chain 'S' and resid 162 through 163 Processing sheet with id=AB9, first strand: chain 'S' and resid 165 through 166 Processing sheet with id=AC1, first strand: chain 'S' and resid 177 through 178 removed outlier: 3.630A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3266 1.34 - 1.46: 2534 1.46 - 1.59: 4490 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 10390 Sorted by residual: bond pdb=" C10 CLR R 401 " pdb=" C5 CLR R 401 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C4 CLR R 401 " pdb=" C5 CLR R 401 " ideal model delta sigma weight residual 1.506 1.391 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 1.492 1.388 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.395 -0.063 2.00e-02 2.50e+03 9.83e+00 bond pdb=" CB VAL B 187 " pdb=" CG2 VAL B 187 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.64e+00 ... (remaining 10385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 13610 2.72 - 5.44: 402 5.44 - 8.16: 50 8.16 - 10.88: 12 10.88 - 13.60: 5 Bond angle restraints: 14079 Sorted by residual: angle pdb=" N PRO R 30 " pdb=" CA PRO R 30 " pdb=" C PRO R 30 " ideal model delta sigma weight residual 110.70 116.54 -5.84 1.22e+00 6.72e-01 2.29e+01 angle pdb=" CA MET A 240 " pdb=" CB MET A 240 " pdb=" CG MET A 240 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CA PRO R 30 " pdb=" C PRO R 30 " pdb=" N PRO R 31 " ideal model delta sigma weight residual 117.93 123.42 -5.49 1.20e+00 6.94e-01 2.09e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C SER R 190 " pdb=" N ASN R 191 " pdb=" CA ASN R 191 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 ... (remaining 14074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5506 17.56 - 35.11: 621 35.11 - 52.67: 110 52.67 - 70.22: 20 70.22 - 87.78: 16 Dihedral angle restraints: 6273 sinusoidal: 2489 harmonic: 3784 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 -132.53 -47.47 0 5.00e+00 4.00e-02 9.01e+01 dihedral pdb=" CB CYS E 9 " pdb=" SG CYS E 9 " pdb=" SG CYS E 50 " pdb=" CB CYS E 50 " ideal model delta sinusoidal sigma weight residual -86.00 -168.56 82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CA GLU R 45 " pdb=" C GLU R 45 " pdb=" N ILE R 46 " pdb=" CA ILE R 46 " ideal model delta harmonic sigma weight residual -180.00 -136.73 -43.27 0 5.00e+00 4.00e-02 7.49e+01 ... (remaining 6270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1434 0.100 - 0.200: 173 0.200 - 0.300: 11 0.300 - 0.400: 2 0.400 - 0.500: 1 Chirality restraints: 1621 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.82 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" C10 CLR R 401 " pdb=" C1 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C9 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" C17 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C16 CLR R 401 " pdb=" C20 CLR R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1618 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 30 " -0.067 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO R 31 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.052 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO B 236 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 37 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO R 38 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 38 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 38 " 0.037 5.00e-02 4.00e+02 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2907 2.79 - 3.32: 8972 3.32 - 3.85: 16562 3.85 - 4.37: 18981 4.37 - 4.90: 32787 Nonbonded interactions: 80209 Sorted by model distance: nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 228 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP R 94 " pdb=" OG SER R 307 " model vdw 2.280 3.040 nonbonded pdb=" O SER S 192 " pdb=" OG1 THR S 203 " model vdw 2.289 3.040 nonbonded pdb=" ND1 HIS B 54 " pdb=" OG SER B 74 " model vdw 2.308 3.120 ... (remaining 80204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 6 through 72) 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.270 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 0.117 10390 Z= 0.794 Angle : 1.139 13.598 14079 Z= 0.604 Chirality : 0.067 0.500 1621 Planarity : 0.007 0.098 1768 Dihedral : 15.319 87.776 3801 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.27 % Allowed : 9.39 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -5.60 (0.17), residues: 1284 helix: -4.47 (0.11), residues: 416 sheet: -3.43 (0.26), residues: 278 loop : -3.13 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 112 HIS 0.009 0.002 HIS A 213 PHE 0.027 0.003 PHE R 97 TYR 0.028 0.003 TYR S 178 ARG 0.006 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 345 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8374 (ttmt) REVERT: A 243 MET cc_start: 0.8946 (tpp) cc_final: 0.8484 (tpp) REVERT: A 318 GLU cc_start: 0.6789 (tp30) cc_final: 0.5926 (tp30) REVERT: A 341 ASP cc_start: 0.8144 (t0) cc_final: 0.7720 (t0) REVERT: A 346 ASN cc_start: 0.9324 (m-40) cc_final: 0.8991 (m110) REVERT: A 349 LYS cc_start: 0.9043 (tttm) cc_final: 0.8778 (ttpp) REVERT: B 13 GLN cc_start: 0.8750 (mm110) cc_final: 0.7874 (tm-30) REVERT: B 59 TYR cc_start: 0.9000 (m-80) cc_final: 0.8561 (m-80) REVERT: B 101 MET cc_start: 0.9055 (mtp) cc_final: 0.8838 (mtp) REVERT: B 111 TYR cc_start: 0.8978 (m-80) cc_final: 0.8747 (m-10) REVERT: B 172 GLU cc_start: 0.8215 (mp0) cc_final: 0.7943 (mm-30) REVERT: B 188 MET cc_start: 0.7983 (mmm) cc_final: 0.7496 (mmm) REVERT: B 259 GLN cc_start: 0.8380 (pt0) cc_final: 0.7676 (pt0) REVERT: C 13 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.8073 (ptm160) REVERT: C 18 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8403 (tm-30) REVERT: C 20 LYS cc_start: 0.8792 (mttp) cc_final: 0.8274 (ttmm) REVERT: C 27 ARG cc_start: 0.8270 (mtt90) cc_final: 0.7961 (mpt-90) REVERT: D 4 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 13 TYR cc_start: 0.8083 (t80) cc_final: 0.7794 (t80) REVERT: D 20 LYS cc_start: 0.7231 (pptt) cc_final: 0.6983 (pptt) REVERT: D 25 LEU cc_start: 0.8591 (tp) cc_final: 0.8189 (tp) REVERT: D 29 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7245 (tm-30) REVERT: D 32 PRO cc_start: 0.8772 (Cg_endo) cc_final: 0.8543 (Cg_exo) REVERT: E 47 ARG cc_start: 0.6999 (mtt-85) cc_final: 0.6477 (ttm110) REVERT: E 63 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7732 (mp0) REVERT: E 67 LYS cc_start: 0.7782 (mttm) cc_final: 0.7569 (mptt) REVERT: R 50 PHE cc_start: 0.8251 (m-10) cc_final: 0.7968 (m-10) REVERT: R 55 TYR cc_start: 0.8515 (m-80) cc_final: 0.7479 (m-80) REVERT: R 127 GLU cc_start: 0.8892 (tp30) cc_final: 0.8456 (tp30) REVERT: R 174 LEU cc_start: 0.8792 (mm) cc_final: 0.8420 (mm) REVERT: R 228 LEU cc_start: 0.9161 (mm) cc_final: 0.8680 (mm) REVERT: R 287 GLU cc_start: 0.8674 (mm-30) cc_final: 0.7910 (pp20) REVERT: R 310 ASN cc_start: 0.8669 (t0) cc_final: 0.8430 (t0) REVERT: S 73 ASP cc_start: 0.7453 (t0) cc_final: 0.7234 (t0) REVERT: S 83 MET cc_start: 0.8794 (mtm) cc_final: 0.8304 (ptp) REVERT: S 95 TYR cc_start: 0.8723 (m-10) cc_final: 0.8505 (m-10) REVERT: S 125 ASP cc_start: 0.8998 (p0) cc_final: 0.8492 (p0) REVERT: S 130 GLN cc_start: 0.7710 (mt0) cc_final: 0.7296 (mt0) REVERT: S 210 GLU cc_start: 0.7862 (tp30) cc_final: 0.7507 (mm-30) outliers start: 3 outliers final: 0 residues processed: 348 average time/residue: 0.2665 time to fit residues: 122.7115 Evaluate side-chains 270 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS B 62 HIS B 75 GLN B 175 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 89 ASN R 150 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 ASN R 323 HIS S 171 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10390 Z= 0.279 Angle : 0.698 8.607 14079 Z= 0.368 Chirality : 0.045 0.227 1621 Planarity : 0.006 0.077 1768 Dihedral : 6.360 41.421 1474 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.01 % Allowed : 17.68 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.41 (0.19), residues: 1284 helix: -2.86 (0.19), residues: 430 sheet: -2.94 (0.27), residues: 284 loop : -2.81 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 112 HIS 0.003 0.001 HIS R 247 PHE 0.017 0.002 PHE R 218 TYR 0.025 0.002 TYR A 302 ARG 0.005 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 317 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8876 (t70) cc_final: 0.8510 (t0) REVERT: A 243 MET cc_start: 0.8878 (tpp) cc_final: 0.8317 (tpp) REVERT: A 302 TYR cc_start: 0.8763 (t80) cc_final: 0.8473 (t80) REVERT: A 341 ASP cc_start: 0.8503 (t0) cc_final: 0.8122 (t0) REVERT: A 346 ASN cc_start: 0.9270 (m-40) cc_final: 0.8950 (m110) REVERT: A 349 LYS cc_start: 0.9024 (tttm) cc_final: 0.8758 (ttpp) REVERT: B 59 TYR cc_start: 0.8783 (m-80) cc_final: 0.8263 (m-80) REVERT: B 105 TYR cc_start: 0.9038 (t80) cc_final: 0.8614 (t80) REVERT: B 111 TYR cc_start: 0.8921 (m-80) cc_final: 0.8659 (m-10) REVERT: B 157 ILE cc_start: 0.9034 (tt) cc_final: 0.8744 (tt) REVERT: B 159 THR cc_start: 0.9080 (p) cc_final: 0.8800 (p) REVERT: B 172 GLU cc_start: 0.8080 (mp0) cc_final: 0.7872 (mm-30) REVERT: B 188 MET cc_start: 0.8292 (mmm) cc_final: 0.8007 (mmm) REVERT: B 211 TRP cc_start: 0.9247 (m100) cc_final: 0.8681 (m100) REVERT: B 259 GLN cc_start: 0.8199 (pt0) cc_final: 0.7579 (pt0) REVERT: B 297 TRP cc_start: 0.8900 (m100) cc_final: 0.8686 (m100) REVERT: C 13 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.8034 (ptp-110) REVERT: C 20 LYS cc_start: 0.8854 (mttp) cc_final: 0.8571 (ttmm) REVERT: C 25 ILE cc_start: 0.9036 (mp) cc_final: 0.8617 (mp) REVERT: C 27 ARG cc_start: 0.8398 (mtt90) cc_final: 0.8129 (mtt90) REVERT: C 32 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8719 (ttpp) REVERT: D 4 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7568 (mm-30) REVERT: D 13 TYR cc_start: 0.7985 (t80) cc_final: 0.7733 (t80) REVERT: D 29 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7046 (tm-30) REVERT: D 32 PRO cc_start: 0.8624 (Cg_endo) cc_final: 0.8384 (Cg_exo) REVERT: D 68 ARG cc_start: 0.8338 (mmm160) cc_final: 0.7925 (mmm-85) REVERT: E 47 ARG cc_start: 0.6994 (mtt-85) cc_final: 0.6424 (ttm110) REVERT: E 63 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7750 (mp0) REVERT: R 50 PHE cc_start: 0.8290 (m-10) cc_final: 0.7891 (m-10) REVERT: R 55 TYR cc_start: 0.8076 (m-80) cc_final: 0.7318 (m-80) REVERT: R 126 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8242 (ttmm) REVERT: R 127 GLU cc_start: 0.8820 (tp30) cc_final: 0.7827 (tp30) REVERT: R 163 LYS cc_start: 0.8084 (mppt) cc_final: 0.7479 (mptt) REVERT: R 224 LEU cc_start: 0.8823 (tp) cc_final: 0.8445 (tp) REVERT: R 227 MET cc_start: 0.8011 (mtp) cc_final: 0.7685 (ttm) REVERT: R 228 LEU cc_start: 0.9125 (mm) cc_final: 0.8791 (mm) REVERT: R 287 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8043 (pp20) REVERT: R 306 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7858 (t70) REVERT: R 310 ASN cc_start: 0.8543 (t0) cc_final: 0.8307 (t0) REVERT: R 314 TYR cc_start: 0.8882 (m-80) cc_final: 0.8578 (m-80) REVERT: R 323 HIS cc_start: 0.8206 (m90) cc_final: 0.7949 (m-70) REVERT: S 95 TYR cc_start: 0.8756 (m-10) cc_final: 0.8433 (m-10) REVERT: S 221 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8914 (mt) outliers start: 33 outliers final: 21 residues processed: 334 average time/residue: 0.2401 time to fit residues: 109.4364 Evaluate side-chains 307 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 266 HIS B 295 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 150 HIS S 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10390 Z= 0.167 Angle : 0.618 7.872 14079 Z= 0.318 Chirality : 0.043 0.174 1621 Planarity : 0.004 0.069 1768 Dihedral : 5.560 38.843 1474 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.74 % Allowed : 18.87 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.37 (0.21), residues: 1284 helix: -1.68 (0.23), residues: 430 sheet: -2.57 (0.28), residues: 274 loop : -2.39 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 112 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE R 218 TYR 0.016 0.001 TYR A 302 ARG 0.004 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 319 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8831 (t70) cc_final: 0.8439 (t0) REVERT: A 29 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8376 (ttmt) REVERT: A 243 MET cc_start: 0.8793 (tpp) cc_final: 0.8461 (tpp) REVERT: A 341 ASP cc_start: 0.8529 (t0) cc_final: 0.8181 (t0) REVERT: A 349 LYS cc_start: 0.8946 (tttm) cc_final: 0.8680 (ttpp) REVERT: B 10 GLU cc_start: 0.7973 (tp30) cc_final: 0.7747 (tp30) REVERT: B 82 TRP cc_start: 0.8854 (m100) cc_final: 0.8248 (m100) REVERT: B 105 TYR cc_start: 0.9042 (t80) cc_final: 0.8800 (t80) REVERT: B 172 GLU cc_start: 0.7865 (mp0) cc_final: 0.7632 (mm-30) REVERT: B 188 MET cc_start: 0.8251 (mmm) cc_final: 0.8029 (mmm) REVERT: B 211 TRP cc_start: 0.8986 (m100) cc_final: 0.8058 (m100) REVERT: B 220 GLN cc_start: 0.8543 (mp-120) cc_final: 0.8122 (mp10) REVERT: B 226 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7365 (mp0) REVERT: B 258 ASP cc_start: 0.7813 (t0) cc_final: 0.7131 (t0) REVERT: B 259 GLN cc_start: 0.8044 (pt0) cc_final: 0.7588 (pt0) REVERT: C 13 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8225 (ptp-110) REVERT: C 20 LYS cc_start: 0.8805 (mttp) cc_final: 0.8585 (ttmm) REVERT: C 25 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8662 (mp) REVERT: C 38 MET cc_start: 0.7660 (ppp) cc_final: 0.7188 (ppp) REVERT: D 6 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.8225 (ptm160) REVERT: D 29 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7269 (tm-30) REVERT: D 68 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7725 (mmm-85) REVERT: E 47 ARG cc_start: 0.6594 (mtt-85) cc_final: 0.6369 (ttm110) REVERT: E 63 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7845 (mt-10) REVERT: R 50 PHE cc_start: 0.8001 (m-10) cc_final: 0.7557 (m-10) REVERT: R 55 TYR cc_start: 0.7970 (m-80) cc_final: 0.7512 (m-80) REVERT: R 61 LEU cc_start: 0.8205 (tp) cc_final: 0.7947 (tp) REVERT: R 126 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8130 (ttmm) REVERT: R 163 LYS cc_start: 0.8081 (mppt) cc_final: 0.7533 (mptt) REVERT: R 184 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7833 (tpp80) REVERT: R 198 GLU cc_start: 0.5600 (OUTLIER) cc_final: 0.5172 (mt-10) REVERT: R 224 LEU cc_start: 0.8716 (tp) cc_final: 0.8329 (tp) REVERT: R 227 MET cc_start: 0.7742 (mtp) cc_final: 0.7474 (ttm) REVERT: R 228 LEU cc_start: 0.9106 (mm) cc_final: 0.8799 (mm) REVERT: R 264 TRP cc_start: 0.8201 (m100) cc_final: 0.7796 (m100) REVERT: R 287 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8069 (pp20) REVERT: R 306 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7772 (t70) REVERT: R 323 HIS cc_start: 0.8297 (m90) cc_final: 0.7783 (m170) REVERT: R 327 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8068 (ptmt) REVERT: S 6 GLU cc_start: 0.7539 (pm20) cc_final: 0.6104 (pm20) REVERT: S 95 TYR cc_start: 0.8578 (m-10) cc_final: 0.8376 (m-10) REVERT: S 109 ASP cc_start: 0.8173 (p0) cc_final: 0.7933 (p0) REVERT: S 128 MET cc_start: 0.8639 (mmm) cc_final: 0.7898 (mmm) REVERT: S 130 GLN cc_start: 0.7416 (mt0) cc_final: 0.7087 (mt0) outliers start: 41 outliers final: 20 residues processed: 339 average time/residue: 0.2383 time to fit residues: 109.7528 Evaluate side-chains 314 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 291 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 150 HIS R 247 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10390 Z= 0.190 Angle : 0.608 8.288 14079 Z= 0.313 Chirality : 0.042 0.156 1621 Planarity : 0.004 0.068 1768 Dihedral : 5.260 38.498 1474 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.65 % Allowed : 21.06 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.88 (0.22), residues: 1284 helix: -1.10 (0.24), residues: 429 sheet: -2.34 (0.28), residues: 291 loop : -2.21 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 112 HIS 0.002 0.001 HIS S 35 PHE 0.023 0.001 PHE S 200 TYR 0.022 0.001 TYR A 302 ARG 0.004 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 296 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8882 (t70) cc_final: 0.8439 (t0) REVERT: A 29 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8371 (ttmt) REVERT: A 46 LYS cc_start: 0.8495 (tttt) cc_final: 0.8282 (tmtt) REVERT: A 243 MET cc_start: 0.8756 (tpp) cc_final: 0.8276 (tpp) REVERT: A 341 ASP cc_start: 0.8548 (t0) cc_final: 0.8259 (t0) REVERT: A 349 LYS cc_start: 0.8935 (tttm) cc_final: 0.8719 (ttpp) REVERT: B 82 TRP cc_start: 0.8857 (m100) cc_final: 0.8579 (m100) REVERT: B 105 TYR cc_start: 0.9053 (t80) cc_final: 0.8791 (t80) REVERT: B 157 ILE cc_start: 0.8829 (tt) cc_final: 0.8450 (tt) REVERT: B 211 TRP cc_start: 0.9063 (m100) cc_final: 0.8478 (m100) REVERT: B 234 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: B 258 ASP cc_start: 0.7886 (t0) cc_final: 0.7336 (t0) REVERT: C 13 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8281 (ptp-110) REVERT: C 25 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8654 (mp) REVERT: C 27 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7829 (mtt90) REVERT: D 6 ARG cc_start: 0.8581 (ttp-170) cc_final: 0.8293 (ptm160) REVERT: D 29 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7237 (tm-30) REVERT: E 47 ARG cc_start: 0.6694 (mtt-85) cc_final: 0.6451 (ttm110) REVERT: E 63 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7935 (mt-10) REVERT: R 50 PHE cc_start: 0.7979 (m-10) cc_final: 0.7541 (m-10) REVERT: R 55 TYR cc_start: 0.7845 (m-80) cc_final: 0.7528 (m-80) REVERT: R 126 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8161 (ttmm) REVERT: R 163 LYS cc_start: 0.8007 (mppt) cc_final: 0.7496 (mptt) REVERT: R 224 LEU cc_start: 0.8767 (tp) cc_final: 0.8388 (tp) REVERT: R 227 MET cc_start: 0.7865 (mtp) cc_final: 0.7601 (ttm) REVERT: R 228 LEU cc_start: 0.9070 (mm) cc_final: 0.8802 (mm) REVERT: R 287 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8024 (pp20) REVERT: R 306 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7746 (t70) REVERT: R 314 TYR cc_start: 0.8802 (m-80) cc_final: 0.8384 (m-80) REVERT: R 323 HIS cc_start: 0.8254 (m90) cc_final: 0.8043 (m-70) REVERT: R 327 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8101 (ptmt) REVERT: S 6 GLU cc_start: 0.7312 (pm20) cc_final: 0.6083 (pm20) REVERT: S 109 ASP cc_start: 0.8187 (p0) cc_final: 0.7981 (p0) REVERT: S 128 MET cc_start: 0.8677 (mmm) cc_final: 0.7869 (mmm) REVERT: S 130 GLN cc_start: 0.7577 (mt0) cc_final: 0.7240 (mt0) outliers start: 40 outliers final: 26 residues processed: 318 average time/residue: 0.2311 time to fit residues: 100.6659 Evaluate side-chains 306 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 277 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 40.0000 chunk 110 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN D 8 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10390 Z= 0.237 Angle : 0.625 8.970 14079 Z= 0.319 Chirality : 0.043 0.153 1621 Planarity : 0.004 0.069 1768 Dihedral : 5.233 37.982 1474 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.83 % Allowed : 20.51 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.60 (0.23), residues: 1284 helix: -0.75 (0.25), residues: 430 sheet: -2.24 (0.28), residues: 291 loop : -2.11 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 112 HIS 0.003 0.001 HIS A 213 PHE 0.020 0.001 PHE S 68 TYR 0.021 0.001 TYR A 302 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 289 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8936 (t70) cc_final: 0.8499 (t0) REVERT: A 29 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8752 (ttmm) REVERT: A 243 MET cc_start: 0.8763 (tpp) cc_final: 0.8283 (tpp) REVERT: A 305 CYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7861 (m) REVERT: A 341 ASP cc_start: 0.8598 (t0) cc_final: 0.8319 (t0) REVERT: A 349 LYS cc_start: 0.8934 (tttm) cc_final: 0.8718 (ttpp) REVERT: B 82 TRP cc_start: 0.8751 (m100) cc_final: 0.8437 (m100) REVERT: B 105 TYR cc_start: 0.9081 (t80) cc_final: 0.8797 (t80) REVERT: B 157 ILE cc_start: 0.8909 (tt) cc_final: 0.8546 (tt) REVERT: B 211 TRP cc_start: 0.9118 (m100) cc_final: 0.8485 (m100) REVERT: B 234 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: B 258 ASP cc_start: 0.7889 (t0) cc_final: 0.7374 (t0) REVERT: C 13 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8325 (ptp-110) REVERT: C 25 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8716 (mp) REVERT: C 27 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7950 (mpt-90) REVERT: C 32 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8742 (ttpp) REVERT: D 29 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7061 (tm-30) REVERT: E 47 ARG cc_start: 0.6831 (mtt-85) cc_final: 0.6549 (ttm110) REVERT: R 55 TYR cc_start: 0.8011 (m-80) cc_final: 0.7395 (m-80) REVERT: R 126 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8034 (ttpp) REVERT: R 224 LEU cc_start: 0.8793 (tp) cc_final: 0.8496 (tp) REVERT: R 227 MET cc_start: 0.7866 (mtp) cc_final: 0.7587 (ttm) REVERT: R 228 LEU cc_start: 0.9098 (mm) cc_final: 0.8819 (mm) REVERT: R 229 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: R 246 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8469 (ptmm) REVERT: R 287 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7820 (pp20) REVERT: R 306 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7728 (t70) REVERT: R 314 TYR cc_start: 0.8779 (m-80) cc_final: 0.8482 (m-80) REVERT: R 323 HIS cc_start: 0.8264 (m90) cc_final: 0.8041 (m-70) REVERT: S 6 GLU cc_start: 0.7388 (pm20) cc_final: 0.6175 (pm20) REVERT: S 128 MET cc_start: 0.8707 (mmm) cc_final: 0.8168 (mmm) REVERT: S 130 GLN cc_start: 0.7626 (mt0) cc_final: 0.7291 (mt0) outliers start: 53 outliers final: 36 residues processed: 315 average time/residue: 0.2395 time to fit residues: 102.5491 Evaluate side-chains 320 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 246 LYS Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN E 18 HIS R 66 ASN R 150 HIS R 247 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10390 Z= 0.176 Angle : 0.618 8.810 14079 Z= 0.311 Chirality : 0.042 0.147 1621 Planarity : 0.004 0.075 1768 Dihedral : 5.019 37.752 1474 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.10 % Allowed : 23.34 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.41 (0.23), residues: 1284 helix: -0.55 (0.25), residues: 434 sheet: -2.21 (0.28), residues: 287 loop : -2.00 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 112 HIS 0.003 0.000 HIS S 35 PHE 0.022 0.001 PHE S 200 TYR 0.019 0.001 TYR A 302 ARG 0.007 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 286 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7178 (mp0) cc_final: 0.6483 (mp0) REVERT: A 26 ASP cc_start: 0.8931 (t70) cc_final: 0.8495 (t0) REVERT: A 29 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8757 (ttmm) REVERT: A 243 MET cc_start: 0.8736 (tpp) cc_final: 0.8239 (tpp) REVERT: A 305 CYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8033 (m) REVERT: A 341 ASP cc_start: 0.8550 (t0) cc_final: 0.8290 (t0) REVERT: B 82 TRP cc_start: 0.8707 (m100) cc_final: 0.8035 (m100) REVERT: B 105 TYR cc_start: 0.9061 (t80) cc_final: 0.8798 (t80) REVERT: B 157 ILE cc_start: 0.8905 (tt) cc_final: 0.8476 (tt) REVERT: B 188 MET cc_start: 0.8286 (mmm) cc_final: 0.7526 (mpp) REVERT: B 211 TRP cc_start: 0.8984 (m100) cc_final: 0.8328 (m100) REVERT: B 226 GLU cc_start: 0.7488 (mp0) cc_final: 0.7167 (mp0) REVERT: B 234 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: B 258 ASP cc_start: 0.7885 (t0) cc_final: 0.7292 (t0) REVERT: C 13 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8343 (ptp-110) REVERT: C 25 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8540 (mp) REVERT: C 32 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8731 (ttpp) REVERT: D 6 ARG cc_start: 0.8652 (ttp-170) cc_final: 0.8352 (ptm160) REVERT: D 29 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6967 (tm-30) REVERT: E 47 ARG cc_start: 0.6691 (mtt-85) cc_final: 0.6467 (ttm110) REVERT: R 55 TYR cc_start: 0.8107 (m-80) cc_final: 0.7480 (m-80) REVERT: R 71 LEU cc_start: 0.8271 (tp) cc_final: 0.7867 (tt) REVERT: R 127 GLU cc_start: 0.8651 (tp30) cc_final: 0.8081 (tp30) REVERT: R 163 LYS cc_start: 0.8033 (mppt) cc_final: 0.7607 (mmtm) REVERT: R 212 ARG cc_start: 0.8708 (ttp-170) cc_final: 0.8394 (ttp-170) REVERT: R 224 LEU cc_start: 0.8722 (tp) cc_final: 0.8402 (tp) REVERT: R 227 MET cc_start: 0.7863 (mtp) cc_final: 0.7603 (ttm) REVERT: R 228 LEU cc_start: 0.9047 (mm) cc_final: 0.8797 (mm) REVERT: R 287 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7819 (pp20) REVERT: R 306 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7537 (t70) REVERT: R 323 HIS cc_start: 0.8289 (m90) cc_final: 0.8049 (m-70) REVERT: S 6 GLU cc_start: 0.7091 (pm20) cc_final: 0.6312 (pm20) REVERT: S 128 MET cc_start: 0.8696 (mmm) cc_final: 0.8129 (mmm) REVERT: S 130 GLN cc_start: 0.7621 (mt0) cc_final: 0.7289 (mt0) REVERT: S 210 GLU cc_start: 0.7800 (tp30) cc_final: 0.7497 (tp30) outliers start: 45 outliers final: 30 residues processed: 306 average time/residue: 0.2048 time to fit residues: 86.4453 Evaluate side-chains 300 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 266 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN D 8 GLN R 66 ASN R 150 HIS R 306 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10390 Z= 0.433 Angle : 0.720 8.610 14079 Z= 0.371 Chirality : 0.046 0.169 1621 Planarity : 0.005 0.074 1768 Dihedral : 5.538 38.516 1474 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.10 % Allowed : 22.97 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.44 (0.23), residues: 1284 helix: -0.46 (0.25), residues: 432 sheet: -2.09 (0.29), residues: 291 loop : -2.22 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 112 HIS 0.003 0.001 HIS D 33 PHE 0.022 0.002 PHE S 200 TYR 0.025 0.002 TYR A 302 ARG 0.007 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 268 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 26 ASP cc_start: 0.8951 (t70) cc_final: 0.8536 (t0) REVERT: A 29 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8789 (ttmm) REVERT: A 243 MET cc_start: 0.8842 (tpp) cc_final: 0.8380 (tpp) REVERT: A 341 ASP cc_start: 0.8692 (t0) cc_final: 0.8411 (t0) REVERT: B 82 TRP cc_start: 0.8785 (m100) cc_final: 0.8038 (m100) REVERT: B 105 TYR cc_start: 0.9071 (t80) cc_final: 0.8615 (t80) REVERT: B 111 TYR cc_start: 0.8886 (m-80) cc_final: 0.8620 (m-10) REVERT: B 157 ILE cc_start: 0.9153 (tt) cc_final: 0.8822 (tt) REVERT: B 188 MET cc_start: 0.8408 (mmm) cc_final: 0.8187 (mmm) REVERT: B 226 GLU cc_start: 0.7539 (mp0) cc_final: 0.7251 (mp0) REVERT: B 234 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: B 258 ASP cc_start: 0.8194 (t0) cc_final: 0.7673 (t0) REVERT: C 13 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8312 (ptp-110) REVERT: C 25 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8756 (mp) REVERT: C 32 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8761 (ttpp) REVERT: D 29 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7077 (tm-30) REVERT: D 45 ASP cc_start: 0.6774 (t0) cc_final: 0.6303 (t70) REVERT: E 47 ARG cc_start: 0.6872 (mtt-85) cc_final: 0.6553 (ttm110) REVERT: R 55 TYR cc_start: 0.8218 (m-80) cc_final: 0.7631 (m-80) REVERT: R 126 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8260 (ttpp) REVERT: R 127 GLU cc_start: 0.8621 (tp30) cc_final: 0.8022 (tp30) REVERT: R 184 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8184 (tpp80) REVERT: R 224 LEU cc_start: 0.8880 (tp) cc_final: 0.8613 (tp) REVERT: R 227 MET cc_start: 0.7936 (mtp) cc_final: 0.7644 (ttm) REVERT: R 228 LEU cc_start: 0.9191 (mm) cc_final: 0.8841 (mm) REVERT: R 229 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: R 306 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8027 (t-90) REVERT: S 6 GLU cc_start: 0.7913 (pm20) cc_final: 0.6956 (pm20) REVERT: S 13 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8048 (mm-40) REVERT: S 109 ASP cc_start: 0.8320 (p0) cc_final: 0.8090 (p0) REVERT: S 128 MET cc_start: 0.8849 (mmm) cc_final: 0.8002 (mmm) REVERT: S 130 GLN cc_start: 0.7732 (mt0) cc_final: 0.7434 (mt0) outliers start: 56 outliers final: 39 residues processed: 299 average time/residue: 0.2039 time to fit residues: 82.9840 Evaluate side-chains 303 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN R 66 ASN R 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10390 Z= 0.245 Angle : 0.670 9.318 14079 Z= 0.338 Chirality : 0.044 0.162 1621 Planarity : 0.004 0.073 1768 Dihedral : 5.296 38.356 1474 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.28 % Allowed : 23.79 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.27 (0.23), residues: 1284 helix: -0.24 (0.26), residues: 430 sheet: -1.99 (0.29), residues: 297 loop : -2.18 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 112 HIS 0.004 0.001 HIS R 306 PHE 0.021 0.001 PHE S 200 TYR 0.036 0.001 TYR A 302 ARG 0.008 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 275 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7641 (mp0) cc_final: 0.7057 (mp0) REVERT: A 26 ASP cc_start: 0.8950 (t70) cc_final: 0.8525 (t0) REVERT: A 29 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8801 (ttmm) REVERT: A 240 MET cc_start: 0.7329 (pmm) cc_final: 0.7062 (pmm) REVERT: A 243 MET cc_start: 0.8778 (tpp) cc_final: 0.8329 (tpp) REVERT: A 305 CYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 346 ASN cc_start: 0.8901 (m-40) cc_final: 0.8631 (m110) REVERT: B 82 TRP cc_start: 0.8746 (m100) cc_final: 0.8105 (m100) REVERT: B 105 TYR cc_start: 0.9065 (t80) cc_final: 0.8659 (t80) REVERT: B 111 TYR cc_start: 0.8839 (m-80) cc_final: 0.8569 (m-10) REVERT: B 147 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8902 (t) REVERT: B 157 ILE cc_start: 0.9060 (tt) cc_final: 0.8652 (tt) REVERT: B 172 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 188 MET cc_start: 0.8475 (mmm) cc_final: 0.8196 (mmm) REVERT: B 226 GLU cc_start: 0.7597 (mp0) cc_final: 0.7300 (mp0) REVERT: B 234 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: B 258 ASP cc_start: 0.8092 (t0) cc_final: 0.7466 (t0) REVERT: C 13 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8321 (ptp-110) REVERT: C 25 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8730 (mp) REVERT: C 32 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8718 (ttpp) REVERT: D 6 ARG cc_start: 0.8778 (ttp-170) cc_final: 0.8355 (ptm160) REVERT: D 29 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7049 (tm-30) REVERT: D 47 ARG cc_start: 0.7781 (ppt170) cc_final: 0.7517 (ppt170) REVERT: E 47 ARG cc_start: 0.6848 (mtt-85) cc_final: 0.6586 (ttm110) REVERT: R 55 TYR cc_start: 0.8268 (m-80) cc_final: 0.7570 (m-80) REVERT: R 71 LEU cc_start: 0.8272 (tp) cc_final: 0.7827 (tt) REVERT: R 126 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8167 (ttpp) REVERT: R 127 GLU cc_start: 0.8610 (tp30) cc_final: 0.8378 (mm-30) REVERT: R 163 LYS cc_start: 0.8121 (mppt) cc_final: 0.7602 (mptt) REVERT: R 184 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8003 (tpp80) REVERT: R 224 LEU cc_start: 0.8766 (tp) cc_final: 0.8478 (tp) REVERT: R 227 MET cc_start: 0.7891 (mtp) cc_final: 0.7557 (ttm) REVERT: R 228 LEU cc_start: 0.9129 (mm) cc_final: 0.8825 (mm) REVERT: R 229 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7181 (m-10) REVERT: R 277 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7772 (ttp) REVERT: R 287 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7850 (pp20) REVERT: R 306 HIS cc_start: 0.8100 (t70) cc_final: 0.7760 (t70) REVERT: R 323 HIS cc_start: 0.8268 (m90) cc_final: 0.7924 (m90) REVERT: S 6 GLU cc_start: 0.7998 (pm20) cc_final: 0.7452 (pm20) REVERT: S 109 ASP cc_start: 0.8253 (p0) cc_final: 0.8021 (p0) REVERT: S 128 MET cc_start: 0.8742 (mmm) cc_final: 0.7977 (mmm) REVERT: S 130 GLN cc_start: 0.7762 (mt0) cc_final: 0.7446 (mt0) outliers start: 47 outliers final: 33 residues processed: 303 average time/residue: 0.2341 time to fit residues: 96.9802 Evaluate side-chains 313 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 274 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN R 66 ASN R 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10390 Z= 0.209 Angle : 0.658 10.559 14079 Z= 0.329 Chirality : 0.043 0.151 1621 Planarity : 0.004 0.071 1768 Dihedral : 5.090 37.329 1474 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.92 % Allowed : 24.34 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.00 (0.23), residues: 1284 helix: -0.01 (0.26), residues: 431 sheet: -1.86 (0.31), residues: 279 loop : -2.02 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 112 HIS 0.005 0.001 HIS B 54 PHE 0.018 0.001 PHE S 200 TYR 0.024 0.001 TYR A 302 ARG 0.007 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 278 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: A 26 ASP cc_start: 0.8959 (t70) cc_final: 0.8530 (t0) REVERT: A 29 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8724 (ttmm) REVERT: A 243 MET cc_start: 0.8705 (tpp) cc_final: 0.8251 (tpp) REVERT: A 305 CYS cc_start: 0.8544 (t) cc_final: 0.8006 (m) REVERT: A 346 ASN cc_start: 0.8782 (m-40) cc_final: 0.8575 (m110) REVERT: B 82 TRP cc_start: 0.8740 (m100) cc_final: 0.8094 (m100) REVERT: B 105 TYR cc_start: 0.9078 (t80) cc_final: 0.8718 (t80) REVERT: B 147 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8875 (t) REVERT: B 157 ILE cc_start: 0.9050 (tt) cc_final: 0.8679 (tt) REVERT: B 172 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 188 MET cc_start: 0.8524 (mmm) cc_final: 0.8201 (mmm) REVERT: B 220 GLN cc_start: 0.8368 (mp-120) cc_final: 0.8130 (mp10) REVERT: B 226 GLU cc_start: 0.7613 (mp0) cc_final: 0.7296 (mp0) REVERT: B 234 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: B 258 ASP cc_start: 0.7872 (t0) cc_final: 0.7321 (t0) REVERT: C 13 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8294 (ptp-110) REVERT: C 25 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8613 (mp) REVERT: C 32 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8696 (ttpp) REVERT: D 6 ARG cc_start: 0.8644 (ttp-170) cc_final: 0.8285 (ptm160) REVERT: D 13 TYR cc_start: 0.7651 (t80) cc_final: 0.7164 (t80) REVERT: D 29 GLU cc_start: 0.7591 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 47 ARG cc_start: 0.7732 (ppt170) cc_final: 0.7528 (ppt170) REVERT: E 47 ARG cc_start: 0.6781 (mtt-85) cc_final: 0.6567 (ttm110) REVERT: R 55 TYR cc_start: 0.8255 (m-80) cc_final: 0.7591 (m-80) REVERT: R 126 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8134 (ttpp) REVERT: R 127 GLU cc_start: 0.8600 (tp30) cc_final: 0.8342 (tp30) REVERT: R 163 LYS cc_start: 0.8044 (mppt) cc_final: 0.7608 (mmtm) REVERT: R 184 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.7991 (tpp80) REVERT: R 212 ARG cc_start: 0.8721 (ttp-170) cc_final: 0.8191 (ttp-170) REVERT: R 224 LEU cc_start: 0.8734 (tp) cc_final: 0.8422 (tp) REVERT: R 227 MET cc_start: 0.7867 (mtp) cc_final: 0.7545 (ttm) REVERT: R 228 LEU cc_start: 0.9124 (mm) cc_final: 0.8858 (mm) REVERT: R 229 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7109 (m-10) REVERT: R 287 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7867 (pp20) REVERT: R 323 HIS cc_start: 0.8266 (m90) cc_final: 0.7934 (m90) REVERT: S 6 GLU cc_start: 0.7923 (pm20) cc_final: 0.7250 (pm20) REVERT: S 109 ASP cc_start: 0.8142 (p0) cc_final: 0.7928 (p0) REVERT: S 128 MET cc_start: 0.8716 (mmm) cc_final: 0.8158 (mmm) outliers start: 43 outliers final: 33 residues processed: 302 average time/residue: 0.2451 time to fit residues: 101.5086 Evaluate side-chains 305 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 267 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 150 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10390 Z= 0.198 Angle : 0.665 11.466 14079 Z= 0.332 Chirality : 0.043 0.149 1621 Planarity : 0.004 0.071 1768 Dihedral : 4.977 37.124 1474 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.83 % Allowed : 25.34 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.77 (0.23), residues: 1284 helix: 0.18 (0.26), residues: 429 sheet: -1.67 (0.31), residues: 280 loop : -1.91 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 112 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE S 200 TYR 0.030 0.001 TYR A 302 ARG 0.009 0.000 ARG C 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: A 26 ASP cc_start: 0.8962 (t70) cc_final: 0.8514 (t0) REVERT: A 240 MET cc_start: 0.7276 (pmm) cc_final: 0.7049 (pmm) REVERT: A 243 MET cc_start: 0.8701 (tpp) cc_final: 0.8253 (tpp) REVERT: A 305 CYS cc_start: 0.8565 (t) cc_final: 0.8073 (m) REVERT: B 19 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.7609 (mtm180) REVERT: B 82 TRP cc_start: 0.8728 (m100) cc_final: 0.8081 (m100) REVERT: B 105 TYR cc_start: 0.9055 (t80) cc_final: 0.8783 (t80) REVERT: B 147 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8872 (t) REVERT: B 157 ILE cc_start: 0.9054 (tt) cc_final: 0.8679 (tt) REVERT: B 172 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 188 MET cc_start: 0.8534 (mmm) cc_final: 0.8199 (mmm) REVERT: B 226 GLU cc_start: 0.7620 (mp0) cc_final: 0.7223 (mp0) REVERT: B 234 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: B 258 ASP cc_start: 0.7936 (t0) cc_final: 0.7382 (t0) REVERT: B 261 LEU cc_start: 0.9163 (mm) cc_final: 0.8933 (mm) REVERT: C 13 ARG cc_start: 0.8582 (ttm-80) cc_final: 0.8291 (ptp-110) REVERT: C 25 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8485 (mp) REVERT: C 27 ARG cc_start: 0.7942 (mpt180) cc_final: 0.7483 (mpt180) REVERT: C 32 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8691 (ttpp) REVERT: D 6 ARG cc_start: 0.8641 (ttp-170) cc_final: 0.8223 (ptm160) REVERT: D 13 TYR cc_start: 0.7629 (t80) cc_final: 0.7157 (t80) REVERT: R 55 TYR cc_start: 0.8257 (m-80) cc_final: 0.7575 (m-80) REVERT: R 126 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8123 (ttpp) REVERT: R 127 GLU cc_start: 0.8644 (tp30) cc_final: 0.8364 (tp30) REVERT: R 163 LYS cc_start: 0.8025 (mppt) cc_final: 0.7591 (mmtm) REVERT: R 184 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7994 (tpp80) REVERT: R 212 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8217 (ttp-170) REVERT: R 224 LEU cc_start: 0.8668 (tp) cc_final: 0.8314 (tp) REVERT: R 227 MET cc_start: 0.7870 (mtp) cc_final: 0.7540 (ttm) REVERT: R 228 LEU cc_start: 0.9113 (mm) cc_final: 0.8828 (mm) REVERT: R 229 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7121 (m-10) REVERT: R 287 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7788 (pp20) REVERT: R 323 HIS cc_start: 0.8225 (m90) cc_final: 0.7857 (m-70) REVERT: S 6 GLU cc_start: 0.8010 (pm20) cc_final: 0.7535 (pm20) REVERT: S 82 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7350 (tp-100) REVERT: S 128 MET cc_start: 0.8805 (mmm) cc_final: 0.7991 (mmm) outliers start: 42 outliers final: 31 residues processed: 300 average time/residue: 0.2406 time to fit residues: 97.9773 Evaluate side-chains 307 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 270 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 225 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN R 150 HIS S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.145163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.114581 restraints weight = 17021.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115818 restraints weight = 8227.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117955 restraints weight = 5556.989| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10390 Z= 0.219 Angle : 0.686 10.889 14079 Z= 0.342 Chirality : 0.044 0.160 1621 Planarity : 0.005 0.071 1768 Dihedral : 4.979 36.740 1474 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.74 % Allowed : 25.98 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.68 (0.24), residues: 1284 helix: 0.30 (0.26), residues: 427 sheet: -1.68 (0.31), residues: 280 loop : -1.87 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 112 HIS 0.009 0.001 HIS B 54 PHE 0.015 0.001 PHE S 200 TYR 0.028 0.001 TYR A 302 ARG 0.016 0.000 ARG E 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.03 seconds wall clock time: 56 minutes 28.12 seconds (3388.12 seconds total)