Starting phenix.real_space_refine on Thu Nov 14 23:11:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/11_2024/8iw4_35762_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/11_2024/8iw4_35762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/11_2024/8iw4_35762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/11_2024/8iw4_35762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/11_2024/8iw4_35762_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw4_35762/11_2024/8iw4_35762_neut.cif" } resolution = 3.49 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5077 2.51 5 N 1338 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7900 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1408 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 177} Chain breaks: 6 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2230 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 239 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2226 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.56, per 1000 atoms: 0.58 Number of scatterers: 7900 At special positions: 0 Unit cell: (91.086, 113.411, 113.411, 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 49 16.00 O 1436 8.00 N 1338 7.00 C 5077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 32.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 removed outlier: 3.546A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 removed outlier: 4.309A pdb=" N GLY A 52 " --> pdb=" O ASP A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 269 through 278 Processing helix chain 'A' and resid 336 through 352 removed outlier: 3.826A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.681A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.966A 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 'R' and resid 35 through 57 removed outlier: 4.975A pdb=" N LEU R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 85 removed outlier: 4.114A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 96 Processing helix chain 'R' and resid 104 through 136 removed outlier: 3.657A pdb=" N THR R 109 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR R 113 " --> pdb=" O THR R 109 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER R 114 " --> pdb=" O CYS R 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE R 117 " --> pdb=" O THR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 removed outlier: 3.735A pdb=" N LYS R 143 " --> pdb=" O THR R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 169 removed outlier: 3.776A pdb=" N PHE R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 232 removed outlier: 4.340A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU R 201 " --> pdb=" O ASN R 197 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 3.991A pdb=" N VAL R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 283 removed outlier: 4.395A pdb=" N LYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR R 259 " --> pdb=" O LYS R 255 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU R 260 " --> pdb=" O ALA R 256 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA R 263 " --> pdb=" O THR R 259 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.772A pdb=" N ALA R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR R 283 " --> pdb=" O VAL R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 312 removed outlier: 3.610A pdb=" N TYR R 293 " --> pdb=" O PRO R 289 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 327 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.535A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.523A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.856A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.275A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.074A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.602A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.009A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP B 211 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.395A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.379A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.814A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.814A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.545A pdb=" N TYR S 190 " --> pdb=" O ASN S 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR S 175 " --> pdb=" O MET S 230 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 960 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: 2.27 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1372 1.33 - 1.45: 2261 1.45 - 1.57: 4380 1.57 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 8081 Sorted by residual: bond pdb=" CA ASN A 271 " pdb=" C ASN A 271 " ideal model delta sigma weight residual 1.522 1.445 0.077 1.36e-02 5.41e+03 3.24e+01 bond pdb=" C TYR A 360 " pdb=" O TYR A 360 " ideal model delta sigma weight residual 1.249 1.222 0.027 8.50e-03 1.38e+04 9.82e+00 bond pdb=" C VAL R 94 " pdb=" O VAL R 94 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.23e-02 6.61e+03 7.83e+00 bond pdb=" N GLN A 267 " pdb=" CA GLN A 267 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.28e-02 6.10e+03 4.92e+00 bond pdb=" CA VAL R 94 " pdb=" CB VAL R 94 " ideal model delta sigma weight residual 1.540 1.510 0.030 1.37e-02 5.33e+03 4.72e+00 ... (remaining 8076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 10762 2.56 - 5.12: 184 5.12 - 7.68: 29 7.68 - 10.25: 6 10.25 - 12.81: 2 Bond angle restraints: 10983 Sorted by residual: angle pdb=" N HIS A 357 " pdb=" CA HIS A 357 " pdb=" C HIS A 357 " ideal model delta sigma weight residual 111.14 123.05 -11.91 1.08e+00 8.57e-01 1.22e+02 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" C TYR A 358 " ideal model delta sigma weight residual 111.30 124.11 -12.81 1.36e+00 5.41e-01 8.87e+01 angle pdb=" N ASN R 303 " pdb=" CA ASN R 303 " pdb=" C ASN R 303 " ideal model delta sigma weight residual 112.38 103.43 8.95 1.22e+00 6.72e-01 5.38e+01 angle pdb=" N CYS A 359 " pdb=" CA CYS A 359 " pdb=" C CYS A 359 " ideal model delta sigma weight residual 110.24 119.64 -9.40 1.30e+00 5.92e-01 5.23e+01 angle pdb=" N ALA A 269 " pdb=" CA ALA A 269 " pdb=" C ALA A 269 " ideal model delta sigma weight residual 113.41 104.60 8.81 1.22e+00 6.72e-01 5.22e+01 ... (remaining 10978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 4141 17.16 - 34.31: 421 34.31 - 51.47: 101 51.47 - 68.62: 14 68.62 - 85.78: 6 Dihedral angle restraints: 4683 sinusoidal: 1663 harmonic: 3020 Sorted by residual: dihedral pdb=" C VAL R 279 " pdb=" N VAL R 279 " pdb=" CA VAL R 279 " pdb=" CB VAL R 279 " ideal model delta harmonic sigma weight residual -122.00 -137.52 15.52 0 2.50e+00 1.60e-01 3.85e+01 dihedral pdb=" N GLN A 267 " pdb=" C GLN A 267 " pdb=" CA GLN A 267 " pdb=" CB GLN A 267 " ideal model delta harmonic sigma weight residual 122.80 133.97 -11.17 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" C GLN A 267 " pdb=" N GLN A 267 " pdb=" CA GLN A 267 " pdb=" CB GLN A 267 " ideal model delta harmonic sigma weight residual -122.60 -133.05 10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1154 0.102 - 0.205: 75 0.205 - 0.307: 16 0.307 - 0.410: 6 0.410 - 0.512: 2 Chirality restraints: 1253 Sorted by residual: chirality pdb=" CA TYR A 358 " pdb=" N TYR A 358 " pdb=" C TYR A 358 " pdb=" CB TYR A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CA VAL R 279 " pdb=" N VAL R 279 " pdb=" C VAL R 279 " pdb=" CB VAL R 279 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA LYS A 216 " pdb=" N LYS A 216 " pdb=" C LYS A 216 " pdb=" CB LYS A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 1250 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 301 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C TYR R 301 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 301 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR R 302 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 351 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ALA A 351 " -0.036 2.00e-02 2.50e+03 pdb=" O ALA A 351 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 352 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 147 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C SER R 147 " -0.036 2.00e-02 2.50e+03 pdb=" O SER R 147 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 148 " 0.012 2.00e-02 2.50e+03 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 195 2.69 - 3.25: 7248 3.25 - 3.80: 11631 3.80 - 4.35: 15289 4.35 - 4.90: 26177 Nonbonded interactions: 60540 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.143 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP A 215 " pdb=" NH1 ARG A 373 " model vdw 2.224 3.120 nonbonded pdb=" ND2 ASN B 119 " pdb=" O GLY B 144 " model vdw 2.234 3.120 nonbonded pdb=" O SER S 105 " pdb=" NH2 ARG S 191 " model vdw 2.258 3.120 ... (remaining 60535 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.740 Find NCS groups from input model: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8081 Z= 0.223 Angle : 0.813 12.808 10983 Z= 0.544 Chirality : 0.063 0.512 1253 Planarity : 0.004 0.033 1381 Dihedral : 14.913 85.776 2728 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.39 % Allowed : 8.07 % Favored : 90.54 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 1013 helix: 0.78 (0.33), residues: 288 sheet: -0.04 (0.32), residues: 265 loop : -1.41 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 317 HIS 0.002 0.001 HIS S 232 PHE 0.012 0.001 PHE A 219 TYR 0.018 0.001 TYR S 235 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.072 Fit side-chains REVERT: R 94 VAL cc_start: 0.7301 (t) cc_final: 0.6964 (p) REVERT: R 98 TRP cc_start: 0.5655 (t-100) cc_final: 0.4917 (t-100) REVERT: R 128 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6256 (mt) REVERT: R 264 MET cc_start: 0.5059 (mmp) cc_final: 0.4741 (mmt) REVERT: S 6 GLU cc_start: 0.4100 (mm-30) cc_final: 0.3409 (mm-30) REVERT: S 160 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6732 (ttp80) outliers start: 11 outliers final: 4 residues processed: 124 average time/residue: 0.2328 time to fit residues: 37.8570 Evaluate side-chains 96 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.0030 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 218 ASN A 236 GLN B 119 ASN B 142 HIS B 225 HIS ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8081 Z= 0.198 Angle : 0.536 5.849 10983 Z= 0.283 Chirality : 0.043 0.148 1253 Planarity : 0.004 0.032 1381 Dihedral : 5.032 52.557 1136 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.14 % Allowed : 12.61 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 1013 helix: 1.10 (0.32), residues: 306 sheet: 0.08 (0.32), residues: 271 loop : -1.32 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 317 HIS 0.003 0.001 HIS A 362 PHE 0.014 0.001 PHE R 117 TYR 0.025 0.002 TYR S 235 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.846 Fit side-chains REVERT: B 312 ASP cc_start: 0.6474 (t70) cc_final: 0.6245 (t0) REVERT: R 52 LEU cc_start: 0.6772 (mt) cc_final: 0.6340 (mt) REVERT: R 264 MET cc_start: 0.5430 (mmp) cc_final: 0.5201 (mmt) REVERT: R 277 ASP cc_start: 0.6117 (t0) cc_final: 0.5774 (t0) REVERT: S 113 GLN cc_start: 0.6911 (mm110) cc_final: 0.6393 (pt0) outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 0.2150 time to fit residues: 33.4151 Evaluate side-chains 108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.0060 chunk 28 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 overall best weight: 2.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 230 ASN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8081 Z= 0.249 Angle : 0.561 5.956 10983 Z= 0.295 Chirality : 0.043 0.155 1253 Planarity : 0.004 0.050 1381 Dihedral : 5.138 58.160 1130 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.77 % Allowed : 15.26 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.27), residues: 1013 helix: 0.93 (0.32), residues: 311 sheet: 0.06 (0.32), residues: 266 loop : -1.41 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.017 0.002 PHE R 117 TYR 0.030 0.002 TYR S 235 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.904 Fit side-chains REVERT: B 66 ASP cc_start: 0.7203 (p0) cc_final: 0.6833 (p0) REVERT: R 179 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.6080 (pm20) REVERT: R 213 MET cc_start: 0.5869 (ttm) cc_final: 0.5610 (ttt) REVERT: S 113 GLN cc_start: 0.6966 (mm110) cc_final: 0.6164 (mm110) REVERT: S 230 MET cc_start: 0.7901 (tpt) cc_final: 0.7327 (tpt) outliers start: 22 outliers final: 18 residues processed: 112 average time/residue: 0.2118 time to fit residues: 32.1803 Evaluate side-chains 110 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 329 LYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8081 Z= 0.153 Angle : 0.490 5.539 10983 Z= 0.257 Chirality : 0.041 0.152 1253 Planarity : 0.003 0.042 1381 Dihedral : 4.854 55.440 1130 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.27 % Allowed : 18.41 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 1013 helix: 1.27 (0.32), residues: 308 sheet: -0.06 (0.31), residues: 284 loop : -1.36 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS C 44 PHE 0.010 0.001 PHE B 241 TYR 0.023 0.001 TYR S 235 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: B 66 ASP cc_start: 0.7162 (p0) cc_final: 0.6814 (p0) REVERT: R 179 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5959 (pm20) REVERT: R 213 MET cc_start: 0.5490 (ttm) cc_final: 0.5280 (ttt) REVERT: S 113 GLN cc_start: 0.6881 (mm110) cc_final: 0.6040 (mm110) REVERT: S 230 MET cc_start: 0.7844 (tpt) cc_final: 0.7233 (tpt) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 0.2063 time to fit residues: 33.4072 Evaluate side-chains 111 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 30.0000 chunk 88 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8081 Z= 0.234 Angle : 0.535 6.103 10983 Z= 0.282 Chirality : 0.043 0.158 1253 Planarity : 0.004 0.040 1381 Dihedral : 5.015 55.325 1130 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.40 % Allowed : 19.04 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.27), residues: 1013 helix: 1.15 (0.32), residues: 308 sheet: -0.15 (0.31), residues: 287 loop : -1.37 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 PHE 0.017 0.002 PHE B 241 TYR 0.028 0.001 TYR S 235 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7061 (ttmm) REVERT: B 66 ASP cc_start: 0.7157 (p0) cc_final: 0.6827 (p0) REVERT: R 179 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5570 (pm20) REVERT: R 213 MET cc_start: 0.5537 (ttm) cc_final: 0.5327 (ttt) REVERT: S 113 GLN cc_start: 0.6980 (mm110) cc_final: 0.6069 (mm110) REVERT: S 230 MET cc_start: 0.7899 (tpt) cc_final: 0.7406 (tpt) outliers start: 27 outliers final: 21 residues processed: 114 average time/residue: 0.2282 time to fit residues: 35.8995 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.0470 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8081 Z= 0.135 Angle : 0.468 5.561 10983 Z= 0.245 Chirality : 0.041 0.144 1253 Planarity : 0.003 0.034 1381 Dihedral : 4.718 52.814 1130 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.14 % Allowed : 21.06 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 1013 helix: 1.50 (0.32), residues: 307 sheet: 0.11 (0.32), residues: 268 loop : -1.44 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.010 0.001 PHE B 241 TYR 0.019 0.001 TYR S 235 ARG 0.001 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.986 Fit side-chains REVERT: B 66 ASP cc_start: 0.7062 (p0) cc_final: 0.6667 (p0) REVERT: B 234 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: S 113 GLN cc_start: 0.6957 (mm110) cc_final: 0.5833 (mm110) REVERT: S 230 MET cc_start: 0.7723 (tpt) cc_final: 0.7175 (tpt) outliers start: 17 outliers final: 10 residues processed: 112 average time/residue: 0.2044 time to fit residues: 31.4197 Evaluate side-chains 107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain S residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8081 Z= 0.166 Angle : 0.488 5.546 10983 Z= 0.255 Chirality : 0.041 0.145 1253 Planarity : 0.003 0.034 1381 Dihedral : 4.767 52.907 1130 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.90 % Allowed : 20.18 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 1013 helix: 1.50 (0.32), residues: 308 sheet: -0.00 (0.31), residues: 274 loop : -1.40 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.011 0.001 PHE B 241 TYR 0.021 0.001 TYR S 235 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.763 Fit side-chains REVERT: B 66 ASP cc_start: 0.7018 (p0) cc_final: 0.6640 (p0) REVERT: B 234 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: S 113 GLN cc_start: 0.6904 (mm110) cc_final: 0.5812 (mm110) REVERT: S 230 MET cc_start: 0.7772 (tpt) cc_final: 0.7270 (tpt) REVERT: S 234 GLU cc_start: 0.7067 (tt0) cc_final: 0.6788 (tt0) outliers start: 23 outliers final: 16 residues processed: 116 average time/residue: 0.2188 time to fit residues: 34.1610 Evaluate side-chains 114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 159 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8081 Z= 0.192 Angle : 0.503 5.550 10983 Z= 0.264 Chirality : 0.042 0.152 1253 Planarity : 0.003 0.034 1381 Dihedral : 4.899 54.460 1130 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.15 % Allowed : 19.80 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.27), residues: 1013 helix: 1.49 (0.32), residues: 308 sheet: -0.04 (0.32), residues: 275 loop : -1.38 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 PHE 0.013 0.001 PHE B 241 TYR 0.022 0.001 TYR S 235 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.858 Fit side-chains REVERT: B 234 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: S 113 GLN cc_start: 0.6901 (mm110) cc_final: 0.5755 (mm110) REVERT: S 230 MET cc_start: 0.7831 (tpt) cc_final: 0.7346 (tpt) REVERT: S 234 GLU cc_start: 0.6999 (tt0) cc_final: 0.6751 (tt0) outliers start: 25 outliers final: 21 residues processed: 121 average time/residue: 0.2174 time to fit residues: 35.4574 Evaluate side-chains 119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 159 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 HIS ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8081 Z= 0.135 Angle : 0.468 5.550 10983 Z= 0.244 Chirality : 0.041 0.141 1253 Planarity : 0.003 0.032 1381 Dihedral : 4.746 56.268 1130 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.65 % Allowed : 20.55 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 1013 helix: 1.68 (0.32), residues: 307 sheet: 0.15 (0.32), residues: 267 loop : -1.35 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.010 0.001 HIS C 44 PHE 0.011 0.001 PHE B 241 TYR 0.018 0.001 TYR S 235 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.875 Fit side-chains REVERT: B 66 ASP cc_start: 0.6899 (p0) cc_final: 0.6393 (p0) REVERT: B 234 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: S 113 GLN cc_start: 0.6841 (mm110) cc_final: 0.5667 (mm110) REVERT: S 230 MET cc_start: 0.7730 (tpt) cc_final: 0.7192 (tpt) REVERT: S 234 GLU cc_start: 0.6989 (tt0) cc_final: 0.6754 (tt0) outliers start: 21 outliers final: 17 residues processed: 113 average time/residue: 0.2272 time to fit residues: 34.8723 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 159 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8081 Z= 0.140 Angle : 0.467 5.546 10983 Z= 0.243 Chirality : 0.041 0.141 1253 Planarity : 0.003 0.032 1381 Dihedral : 4.712 58.750 1130 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.77 % Allowed : 20.68 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1013 helix: 1.79 (0.32), residues: 307 sheet: 0.19 (0.32), residues: 267 loop : -1.30 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 241 TYR 0.018 0.001 TYR S 235 ARG 0.003 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.821 Fit side-chains REVERT: B 234 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: R 286 PHE cc_start: 0.7339 (m-80) cc_final: 0.7058 (m-80) REVERT: S 113 GLN cc_start: 0.6773 (mm110) cc_final: 0.5639 (mm110) REVERT: S 230 MET cc_start: 0.7730 (tpt) cc_final: 0.7222 (tpt) REVERT: S 234 GLU cc_start: 0.6969 (tt0) cc_final: 0.6764 (tt0) outliers start: 22 outliers final: 18 residues processed: 112 average time/residue: 0.2202 time to fit residues: 32.9807 Evaluate side-chains 118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 191 GLN Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 159 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.0670 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.0770 chunk 54 optimal weight: 0.0570 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.163009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3527 r_free = 0.3527 target = 0.141487 restraints weight = 8683.787| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 0.93 r_work: 0.3405 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8081 Z= 0.115 Angle : 0.446 5.557 10983 Z= 0.232 Chirality : 0.040 0.133 1253 Planarity : 0.003 0.032 1381 Dihedral : 4.567 59.471 1130 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.40 % Allowed : 20.93 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.28), residues: 1013 helix: 2.04 (0.32), residues: 304 sheet: 0.32 (0.32), residues: 267 loop : -1.21 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.000 HIS B 142 PHE 0.010 0.001 PHE B 241 TYR 0.016 0.001 TYR S 235 ARG 0.003 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.98 seconds wall clock time: 35 minutes 15.18 seconds (2115.18 seconds total)