Starting phenix.real_space_refine on Thu Feb 15 16:40:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpm_34933/02_2024/8hpm_34933_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpm_34933/02_2024/8hpm_34933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpm_34933/02_2024/8hpm_34933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpm_34933/02_2024/8hpm_34933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpm_34933/02_2024/8hpm_34933_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpm_34933/02_2024/8hpm_34933_updated.pdb" } resolution = 3.82 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= 0.011 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 29 5.16 5 C 8181 2.51 5 N 2157 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 390": "NH1" <-> "NH2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 175": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E ARG 343": "NH1" <-> "NH2" Residue "E ARG 368": "NH1" <-> "NH2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12803 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2115 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 267} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2007 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 254} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2657 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 176 Chain: "D" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2658 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 165 Chain: "E" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3281 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 31, 'TRANS': 405} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.00, per 1000 atoms: 0.55 Number of scatterers: 12803 At special positions: 0 Unit cell: (83.64, 93.48, 165.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 6 15.00 O 2430 8.00 N 2157 7.00 C 8181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-1 " GLC G 1 " - " GLC G 2 " Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 2.4 seconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 13 sheets defined 45.7% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 18 through 33 Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.620A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 77 through 110 removed outlier: 3.669A pdb=" N ALA A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.517A pdb=" N ARG A 119 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 122 " --> pdb=" O ARG A 119 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.784A pdb=" N TRP A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 162 through 189 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 216 through 235 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.460A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 292 removed outlier: 3.530A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 36 Proline residue: B 27 - end of helix removed outlier: 4.344A pdb=" N ILE B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 65 through 96 removed outlier: 4.294A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.523A pdb=" N ILE B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 removed outlier: 4.857A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 138 through 163 removed outlier: 4.923A pdb=" N ILE B 143 " --> pdb=" O GLY B 140 " (cutoff:3.500A) Proline residue: B 144 - end of helix removed outlier: 3.843A pdb=" N LEU B 150 " --> pdb=" O THR B 147 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.620A pdb=" N TYR B 155 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 157 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 179 through 207 removed outlier: 5.273A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Proline residue: B 189 - end of helix Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 242 through 262 Proline residue: B 255 - end of helix removed outlier: 3.789A pdb=" N ILE B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 97 through 107 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 112 through 125 removed outlier: 3.525A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.522A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 188 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 267 through 274 removed outlier: 5.312A pdb=" N LEU C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 97 through 107 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 112 through 125 Processing helix chain 'D' and resid 141 through 155 removed outlier: 5.124A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 188 removed outlier: 4.139A pdb=" N ARG D 178 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 267 through 275 removed outlier: 4.003A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'E' and resid 38 through 54 removed outlier: 5.742A pdb=" N ALA E 42 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 43 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 47 " --> pdb=" O PHE E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 82 removed outlier: 3.920A pdb=" N LEU E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 104 Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 128 through 134 removed outlier: 3.514A pdb=" N ALA E 134 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 193 through 206 removed outlier: 3.581A pdb=" N VAL E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 255 through 263 removed outlier: 3.705A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 285 Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 314 through 324 Processing helix chain 'E' and resid 361 through 370 Processing helix chain 'E' and resid 375 through 381 removed outlier: 3.790A pdb=" N THR E 379 " --> pdb=" O ASN E 375 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 405 through 413 removed outlier: 3.572A pdb=" N THR E 413 " --> pdb=" O ARG E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 435 Processing helix chain 'E' and resid 443 through 458 removed outlier: 3.509A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 29 through 31 Processing sheet with id= B, first strand: chain 'C' and resid 192 through 196 removed outlier: 6.525A pdb=" N ARG C 208 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL C 40 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL C 210 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 245 through 250 Processing sheet with id= D, first strand: chain 'C' and resid 308 through 312 removed outlier: 4.041A pdb=" N GLU C 366 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 321 through 327 Processing sheet with id= F, first strand: chain 'D' and resid 192 through 196 removed outlier: 6.811A pdb=" N ARG D 208 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL D 40 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 210 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU D 213 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 245 through 249 removed outlier: 3.785A pdb=" N SER D 378 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 256 through 258 Processing sheet with id= I, first strand: chain 'D' and resid 291 through 293 removed outlier: 4.062A pdb=" N GLU D 366 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 322 through 327 Processing sheet with id= K, first strand: chain 'E' and resid 31 through 37 removed outlier: 6.877A pdb=" N GLN E 60 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR E 34 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA E 62 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR E 36 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG E 64 " --> pdb=" O THR E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 90 through 94 removed outlier: 3.515A pdb=" N THR E 146 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU E 351 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 152 through 155 529 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2432 1.32 - 1.45: 2961 1.45 - 1.57: 7600 1.57 - 1.70: 10 1.70 - 1.82: 54 Bond restraints: 13057 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 GLC G 1 " pdb=" O5 GLC G 1 " ideal model delta sigma weight residual 1.415 1.549 -0.134 2.00e-02 2.50e+03 4.50e+01 ... (remaining 13052 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.76: 434 105.76 - 113.35: 6635 113.35 - 120.93: 6654 120.93 - 128.52: 4097 128.52 - 136.10: 66 Bond angle restraints: 17886 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.30 19.57 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.33 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.39 16.44 1.00e+00 1.00e+00 2.70e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.68e+01 ... (remaining 17881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7249 17.61 - 35.23: 458 35.23 - 52.84: 90 52.84 - 70.46: 23 70.46 - 88.07: 4 Dihedral angle restraints: 7824 sinusoidal: 2776 harmonic: 5048 Sorted by residual: dihedral pdb=" CA ASP C 321 " pdb=" C ASP C 321 " pdb=" N LYS C 322 " pdb=" CA LYS C 322 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LEU A 151 " pdb=" C LEU A 151 " pdb=" N LEU A 152 " pdb=" CA LEU A 152 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER D 156 " pdb=" C SER D 156 " pdb=" N PRO D 157 " pdb=" CA PRO D 157 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 7821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1836 0.130 - 0.260: 310 0.260 - 0.390: 20 0.390 - 0.520: 4 0.520 - 0.650: 1 Chirality restraints: 2171 Sorted by residual: chirality pdb=" C1 GLC G 1 " pdb=" C2 GLC G 1 " pdb=" O5 GLC G 1 " pdb=" O1 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 3.03e+01 chirality pdb=" C5 GLC G 2 " pdb=" C4 GLC G 2 " pdb=" C6 GLC G 2 " pdb=" O5 GLC G 2 " both_signs ideal model delta sigma weight residual False -2.50 -1.85 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA LYS C 109 " pdb=" N LYS C 109 " pdb=" C LYS C 109 " pdb=" CB LYS C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 2168 not shown) Planarity restraints: 2300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 106 " -0.118 2.00e-02 2.50e+03 6.65e-02 1.11e+02 pdb=" CG TRP E 106 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP E 106 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP E 106 " 0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP E 106 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP E 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 106 " 0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 106 " -0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 106 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP E 106 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 333 " -0.120 2.00e-02 2.50e+03 6.73e-02 9.06e+01 pdb=" CG TYR E 333 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 333 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR E 333 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR E 333 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR E 333 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR E 333 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 333 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 80 " 0.100 2.00e-02 2.50e+03 5.74e-02 8.24e+01 pdb=" CG TRP A 80 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 80 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 80 " -0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP A 80 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP A 80 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A 80 " -0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 80 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 80 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 80 " 0.074 2.00e-02 2.50e+03 ... (remaining 2297 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 784 2.76 - 3.29: 14598 3.29 - 3.83: 20156 3.83 - 4.36: 25345 4.36 - 4.90: 40667 Nonbonded interactions: 101550 Sorted by model distance: nonbonded pdb=" O ALA D 23 " pdb=" C VAL D 24 " model vdw 2.225 3.270 nonbonded pdb=" O ALA C 90 " pdb=" NH1 ARG C 151 " model vdw 2.249 2.520 nonbonded pdb=" O ALA D 23 " pdb=" O VAL D 24 " model vdw 2.261 3.040 nonbonded pdb=" CG PRO E 37 " pdb=" NE2 GLN E 73 " model vdw 2.282 3.520 nonbonded pdb=" N LYS D 11 " pdb=" O VAL D 24 " model vdw 2.302 2.520 ... (remaining 101545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 or (resid 75 through 76 and (n \ ame N or name CA or name C or name O or name CB )) or resid 77 through 79 or (re \ sid 80 through 81 and (name N or name CA or name C or name O or name CB )) or re \ sid 82 through 95 or (resid 96 and (name N or name CA or name C or name O or nam \ e CB )) or resid 97 through 126 or (resid 127 and (name N or name CA or name C o \ r name O or name CB )) or resid 128 through 143 or (resid 144 and (name N or nam \ e CA or name C or name O or name CB )) or resid 145 through 165 or (resid 166 an \ d (name N or name CA or name C or name O or name CB )) or resid 167 through 168 \ or (resid 169 through 172 and (name N or name CA or name C or name O or name CB \ )) or resid 173 through 176 or (resid 177 through 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 204 or (resid 205 and (name \ N or name CA or name C or name O or name CB )) or resid 206 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or (resid 232 through 233 and (name N or name CA or name C or name O or \ name CB )) or resid 234 through 244 or (resid 245 and (name N or name CA or name \ C or name O or name CB )) or resid 246 through 286 or (resid 287 and (name N or \ name CA or name C or name O or name CB )) or resid 288 through 316 or (resid 31 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) or re \ sid 341 through 367 or (resid 368 through 369 and (name N or name CA or name C o \ r name O or name CB )) or resid 370 through 391 or resid 501)) selection = (chain 'D' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 14 or (resid 21 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 131 or (res \ id 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thr \ ough 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) \ or resid 173 through 177 or (resid 178 through 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 180 through 190 or (resid 191 through 192 a \ nd (name N or name CA or name C or name O or name CB )) or resid 193 or (resid 1 \ 94 through 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 226 or (resid 227 and (name N or name CA or name C or name O or nam \ e CB )) or resid 228 or (resid 229 and (name N or name CA or name C or name O or \ name CB )) or resid 230 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 289 or (resid 290 and (name N o \ r name CA or name C or name O or name CB )) or resid 291 through 292 or (resid 2 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 294 through \ 325 or (resid 326 and (name N or name CA or name C or name O or name CB )) or r \ esid 327 through 365 or (resid 366 and (name N or name CA or name C or name O or \ name CB )) or resid 367 through 391 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.850 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: 12.300 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 35.620 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 0.134 13057 Z= 0.816 Angle : 1.823 19.566 17886 Z= 1.236 Chirality : 0.095 0.650 2171 Planarity : 0.012 0.120 2300 Dihedral : 12.983 88.073 4564 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 0.65 % Allowed : 4.95 % Favored : 94.40 % Cbeta Deviations : 0.31 % 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: -2.52 (0.18), residues: 1744 helix: -1.59 (0.15), residues: 810 sheet: -1.15 (0.43), residues: 143 loop : -1.74 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.023 TRP E 106 HIS 0.013 0.003 HIS C 94 PHE 0.062 0.012 PHE D 238 TYR 0.120 0.015 TYR E 333 ARG 0.011 0.001 ARG E 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 361 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7553 (ttt180) cc_final: 0.7203 (tmm160) REVERT: A 186 LEU cc_start: 0.9459 (tp) cc_final: 0.9247 (tt) REVERT: A 203 ASP cc_start: 0.8131 (m-30) cc_final: 0.7925 (t0) REVERT: A 279 PHE cc_start: 0.8653 (t80) cc_final: 0.8356 (t80) REVERT: B 13 TRP cc_start: 0.8172 (m100) cc_final: 0.7916 (m100) REVERT: B 68 SER cc_start: 0.8177 (t) cc_final: 0.7429 (t) REVERT: C 91 LEU cc_start: 0.8082 (mt) cc_final: 0.7825 (mp) REVERT: C 149 MET cc_start: 0.8851 (mtp) cc_final: 0.8483 (mtp) REVERT: C 316 GLU cc_start: 0.8770 (pt0) cc_final: 0.8388 (tt0) REVERT: C 380 PHE cc_start: 0.7776 (m-80) cc_final: 0.7025 (m-80) REVERT: D 99 GLN cc_start: 0.8718 (mt0) cc_final: 0.8267 (mt0) REVERT: D 100 ASN cc_start: 0.8012 (m-40) cc_final: 0.7762 (m110) REVERT: D 101 ILE cc_start: 0.8197 (mt) cc_final: 0.7906 (mm) REVERT: D 269 MET cc_start: 0.4923 (mmp) cc_final: 0.4378 (mtt) REVERT: D 386 LEU cc_start: 0.8926 (mt) cc_final: 0.8705 (mm) REVERT: E 76 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7257 (mm-40) REVERT: E 281 LEU cc_start: 0.9194 (mt) cc_final: 0.8807 (mm) outliers start: 8 outliers final: 1 residues processed: 368 average time/residue: 0.2691 time to fit residues: 138.4893 Evaluate side-chains 223 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 275 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 136 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 127 ASN B 231 ASN C 87 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13057 Z= 0.221 Angle : 0.745 8.643 17886 Z= 0.386 Chirality : 0.048 0.222 2171 Planarity : 0.005 0.085 2300 Dihedral : 8.334 88.708 1965 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 3.17 % Allowed : 13.07 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1744 helix: -0.44 (0.17), residues: 835 sheet: -1.44 (0.35), residues: 185 loop : -1.42 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 12 HIS 0.010 0.002 HIS C 325 PHE 0.035 0.002 PHE A 83 TYR 0.022 0.002 TYR D 194 ARG 0.008 0.001 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 260 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7244 (tmm160) REVERT: A 270 LEU cc_start: 0.8809 (mt) cc_final: 0.8598 (pp) REVERT: B 68 SER cc_start: 0.8206 (t) cc_final: 0.6866 (t) REVERT: B 127 ASN cc_start: 0.8779 (t0) cc_final: 0.8365 (t0) REVERT: B 128 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.6023 (ttm) REVERT: C 66 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7248 (mmm160) REVERT: C 86 PHE cc_start: 0.7161 (m-80) cc_final: 0.6323 (m-80) REVERT: C 149 MET cc_start: 0.8640 (mtp) cc_final: 0.8417 (mtp) REVERT: C 380 PHE cc_start: 0.7636 (m-80) cc_final: 0.6907 (m-80) REVERT: D 269 MET cc_start: 0.5267 (mmp) cc_final: 0.4764 (mtt) REVERT: D 390 ARG cc_start: 0.7858 (tpt170) cc_final: 0.7646 (mmt-90) REVERT: E 281 LEU cc_start: 0.9103 (mt) cc_final: 0.8865 (mm) outliers start: 39 outliers final: 15 residues processed: 282 average time/residue: 0.2495 time to fit residues: 101.9752 Evaluate side-chains 235 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 218 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 50.0000 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN E 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13057 Z= 0.295 Angle : 0.701 8.224 17886 Z= 0.362 Chirality : 0.046 0.239 2171 Planarity : 0.005 0.047 2300 Dihedral : 7.726 83.285 1963 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.06 % Allowed : 17.21 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1744 helix: -0.15 (0.17), residues: 824 sheet: -1.42 (0.36), residues: 191 loop : -1.53 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 207 HIS 0.008 0.002 HIS C 325 PHE 0.022 0.002 PHE E 328 TYR 0.014 0.002 TYR D 89 ARG 0.007 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 227 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7891 (ttt180) cc_final: 0.7193 (tmm160) REVERT: B 68 SER cc_start: 0.8241 (t) cc_final: 0.7734 (t) REVERT: B 170 LYS cc_start: 0.9355 (ttmt) cc_final: 0.8865 (mptt) REVERT: B 256 ILE cc_start: 0.8806 (pt) cc_final: 0.8421 (mt) REVERT: C 66 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7273 (mmm160) REVERT: C 149 MET cc_start: 0.8734 (mtp) cc_final: 0.8514 (mtp) REVERT: C 164 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 316 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: C 380 PHE cc_start: 0.7663 (m-80) cc_final: 0.6896 (m-80) REVERT: D 100 ASN cc_start: 0.8338 (m-40) cc_final: 0.7726 (t0) REVERT: D 265 LEU cc_start: 0.5835 (mt) cc_final: 0.5573 (mt) REVERT: D 269 MET cc_start: 0.5355 (mmp) cc_final: 0.4607 (mtt) REVERT: D 367 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8863 (mm-40) REVERT: D 390 ARG cc_start: 0.7863 (tpt170) cc_final: 0.7026 (tpp-160) outliers start: 50 outliers final: 27 residues processed: 262 average time/residue: 0.2453 time to fit residues: 92.6083 Evaluate side-chains 231 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0470 chunk 119 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13057 Z= 0.328 Angle : 0.703 9.961 17886 Z= 0.359 Chirality : 0.046 0.197 2171 Planarity : 0.005 0.040 2300 Dihedral : 7.364 80.910 1963 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.36 % Allowed : 18.83 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1744 helix: -0.03 (0.18), residues: 820 sheet: -1.37 (0.36), residues: 191 loop : -1.60 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 207 HIS 0.006 0.001 HIS C 325 PHE 0.026 0.002 PHE A 83 TYR 0.022 0.002 TYR B 145 ARG 0.010 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 204 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7946 (ttt180) cc_final: 0.7280 (tmm160) REVERT: A 45 TYR cc_start: 0.8731 (t80) cc_final: 0.8506 (t80) REVERT: A 173 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: A 279 PHE cc_start: 0.8745 (t80) cc_final: 0.8319 (t80) REVERT: B 64 ASP cc_start: 0.6371 (OUTLIER) cc_final: 0.6079 (t70) REVERT: B 66 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7335 (t80) REVERT: B 68 SER cc_start: 0.8395 (t) cc_final: 0.8095 (t) REVERT: B 170 LYS cc_start: 0.9353 (ttmt) cc_final: 0.8829 (mptt) REVERT: B 256 ILE cc_start: 0.8858 (pt) cc_final: 0.8527 (mt) REVERT: C 66 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7276 (mmm160) REVERT: C 149 MET cc_start: 0.8725 (mtp) cc_final: 0.8514 (mtp) REVERT: C 164 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 316 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: C 380 PHE cc_start: 0.7718 (m-80) cc_final: 0.6941 (m-80) REVERT: D 99 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8452 (mm-40) REVERT: D 100 ASN cc_start: 0.8453 (m-40) cc_final: 0.7909 (t0) REVERT: D 265 LEU cc_start: 0.5900 (mt) cc_final: 0.5626 (mt) REVERT: D 269 MET cc_start: 0.5225 (mmp) cc_final: 0.4857 (mtt) REVERT: D 380 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8736 (m-80) REVERT: E 266 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8068 (mttp) outliers start: 66 outliers final: 44 residues processed: 250 average time/residue: 0.2418 time to fit residues: 88.2601 Evaluate side-chains 247 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 196 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13057 Z= 0.184 Angle : 0.635 8.753 17886 Z= 0.320 Chirality : 0.044 0.201 2171 Planarity : 0.004 0.041 2300 Dihedral : 6.888 79.186 1963 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.73 % Allowed : 21.43 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1744 helix: 0.31 (0.18), residues: 823 sheet: -1.23 (0.36), residues: 190 loop : -1.59 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 207 HIS 0.004 0.001 HIS C 325 PHE 0.023 0.002 PHE C 234 TYR 0.014 0.002 TYR E 34 ARG 0.008 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7228 (tmm160) REVERT: B 64 ASP cc_start: 0.6333 (OUTLIER) cc_final: 0.6074 (t70) REVERT: B 66 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7201 (t80) REVERT: B 68 SER cc_start: 0.8309 (t) cc_final: 0.7512 (t) REVERT: B 170 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8767 (mptt) REVERT: B 173 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8009 (mmtm) REVERT: C 66 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7179 (mmm160) REVERT: C 103 PHE cc_start: 0.9171 (t80) cc_final: 0.8943 (t80) REVERT: C 149 MET cc_start: 0.8725 (mtp) cc_final: 0.8523 (mtp) REVERT: C 164 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 316 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: C 380 PHE cc_start: 0.7718 (m-80) cc_final: 0.6893 (m-80) REVERT: D 100 ASN cc_start: 0.8416 (m-40) cc_final: 0.7995 (t0) outliers start: 46 outliers final: 27 residues processed: 253 average time/residue: 0.2367 time to fit residues: 86.5966 Evaluate side-chains 235 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.0980 chunk 33 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13057 Z= 0.178 Angle : 0.631 8.856 17886 Z= 0.315 Chirality : 0.043 0.200 2171 Planarity : 0.004 0.043 2300 Dihedral : 6.584 78.385 1963 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.73 % Allowed : 22.48 % Favored : 73.78 % 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: -0.87 (0.20), residues: 1744 helix: 0.43 (0.18), residues: 825 sheet: -1.08 (0.38), residues: 176 loop : -1.57 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 207 HIS 0.003 0.001 HIS C 94 PHE 0.022 0.001 PHE A 83 TYR 0.023 0.001 TYR D 194 ARG 0.003 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7876 (ttt180) cc_final: 0.7186 (tmm160) REVERT: B 66 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 68 SER cc_start: 0.8126 (t) cc_final: 0.7850 (t) REVERT: B 127 ASN cc_start: 0.9010 (t0) cc_final: 0.8436 (t0) REVERT: B 170 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8744 (mptt) REVERT: C 95 MET cc_start: 0.8291 (ppp) cc_final: 0.7038 (tmm) REVERT: C 164 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 212 MET cc_start: 0.7664 (mmp) cc_final: 0.7222 (mmp) REVERT: C 316 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: D 86 PHE cc_start: 0.8241 (m-80) cc_final: 0.7923 (m-80) REVERT: D 100 ASN cc_start: 0.8437 (m-40) cc_final: 0.8054 (t0) REVERT: D 367 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8751 (tp40) REVERT: E 266 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7794 (tptp) REVERT: E 310 PHE cc_start: 0.8806 (t80) cc_final: 0.8587 (t80) outliers start: 46 outliers final: 28 residues processed: 245 average time/residue: 0.2838 time to fit residues: 104.7082 Evaluate side-chains 238 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 141 optimal weight: 0.0570 chunk 94 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 overall best weight: 0.8304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13057 Z= 0.182 Angle : 0.646 10.250 17886 Z= 0.324 Chirality : 0.044 0.191 2171 Planarity : 0.004 0.043 2300 Dihedral : 6.361 78.025 1963 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.14 % Allowed : 21.59 % Favored : 74.27 % 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: -0.88 (0.20), residues: 1744 helix: 0.40 (0.18), residues: 827 sheet: -1.09 (0.37), residues: 176 loop : -1.55 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 141 HIS 0.005 0.001 HIS C 94 PHE 0.030 0.001 PHE C 103 TYR 0.016 0.001 TYR D 92 ARG 0.005 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8300 (pp) REVERT: B 68 SER cc_start: 0.8281 (t) cc_final: 0.7994 (t) REVERT: B 127 ASN cc_start: 0.8991 (t0) cc_final: 0.8406 (t0) REVERT: B 170 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8746 (mptt) REVERT: B 173 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7634 (mmtm) REVERT: C 66 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7249 (mmm160) REVERT: C 164 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 212 MET cc_start: 0.7636 (mmp) cc_final: 0.7295 (mmp) REVERT: C 273 LEU cc_start: 0.8470 (tt) cc_final: 0.8153 (pp) REVERT: C 380 PHE cc_start: 0.8162 (m-80) cc_final: 0.7388 (m-80) REVERT: D 99 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8643 (tm-30) REVERT: D 100 ASN cc_start: 0.8503 (m-40) cc_final: 0.8126 (t0) REVERT: D 367 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8746 (tp40) REVERT: E 310 PHE cc_start: 0.8827 (t80) cc_final: 0.8598 (t80) outliers start: 51 outliers final: 35 residues processed: 254 average time/residue: 0.2499 time to fit residues: 92.3884 Evaluate side-chains 240 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 0.0040 chunk 160 optimal weight: 4.9990 chunk 146 optimal weight: 0.0570 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13057 Z= 0.163 Angle : 0.646 9.459 17886 Z= 0.319 Chirality : 0.043 0.200 2171 Planarity : 0.004 0.047 2300 Dihedral : 6.119 77.905 1963 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.68 % Allowed : 23.70 % Favored : 73.62 % 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: -0.79 (0.20), residues: 1744 helix: 0.48 (0.19), residues: 825 sheet: -1.06 (0.38), residues: 176 loop : -1.50 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 141 HIS 0.004 0.001 HIS D 94 PHE 0.037 0.001 PHE A 83 TYR 0.023 0.002 TYR D 194 ARG 0.006 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 SER cc_start: 0.8303 (t) cc_final: 0.7687 (t) REVERT: B 127 ASN cc_start: 0.8923 (t0) cc_final: 0.8342 (t0) REVERT: B 170 LYS cc_start: 0.9234 (ttmt) cc_final: 0.8731 (mptt) REVERT: B 173 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7565 (mmtm) REVERT: C 164 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 212 MET cc_start: 0.7600 (mmp) cc_final: 0.7094 (mmp) REVERT: C 269 MET cc_start: 0.8869 (tpt) cc_final: 0.7998 (mtt) REVERT: C 380 PHE cc_start: 0.8184 (m-80) cc_final: 0.7476 (m-80) REVERT: D 99 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8754 (tm-30) REVERT: D 100 ASN cc_start: 0.8589 (m-40) cc_final: 0.8378 (t0) REVERT: D 367 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8740 (tp40) REVERT: E 266 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8176 (pttm) REVERT: E 310 PHE cc_start: 0.8801 (t80) cc_final: 0.8542 (t80) REVERT: E 438 ILE cc_start: 0.9117 (tp) cc_final: 0.8899 (tp) outliers start: 33 outliers final: 22 residues processed: 257 average time/residue: 0.2389 time to fit residues: 90.4495 Evaluate side-chains 230 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 102 optimal weight: 0.0040 chunk 165 optimal weight: 5.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13057 Z= 0.196 Angle : 0.666 14.890 17886 Z= 0.330 Chirality : 0.044 0.195 2171 Planarity : 0.004 0.047 2300 Dihedral : 6.099 78.126 1963 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.76 % Allowed : 24.68 % Favored : 72.56 % 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: -0.78 (0.20), residues: 1744 helix: 0.49 (0.18), residues: 833 sheet: -1.03 (0.38), residues: 176 loop : -1.52 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 141 HIS 0.005 0.001 HIS D 94 PHE 0.027 0.001 PHE C 234 TYR 0.015 0.001 TYR D 92 ARG 0.004 0.000 ARG C 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8486 (t80) cc_final: 0.8097 (t80) REVERT: B 68 SER cc_start: 0.8200 (t) cc_final: 0.7884 (t) REVERT: B 127 ASN cc_start: 0.8999 (t0) cc_final: 0.8417 (t0) REVERT: B 170 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8742 (mptt) REVERT: B 173 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7591 (mmtm) REVERT: C 164 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 380 PHE cc_start: 0.8192 (m-80) cc_final: 0.7407 (m-80) outliers start: 34 outliers final: 29 residues processed: 227 average time/residue: 0.2386 time to fit residues: 79.5575 Evaluate side-chains 227 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 0.0000 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 0.0370 chunk 147 optimal weight: 1.9990 overall best weight: 0.5262 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13057 Z= 0.179 Angle : 0.675 11.746 17886 Z= 0.331 Chirality : 0.044 0.193 2171 Planarity : 0.004 0.048 2300 Dihedral : 6.013 78.105 1963 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.19 % Allowed : 25.08 % Favored : 72.73 % 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: -0.73 (0.20), residues: 1744 helix: 0.52 (0.19), residues: 813 sheet: -0.94 (0.38), residues: 176 loop : -1.46 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 141 HIS 0.002 0.001 HIS C 94 PHE 0.025 0.001 PHE C 234 TYR 0.021 0.001 TYR D 194 ARG 0.007 0.000 ARG E 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASN cc_start: 0.8962 (t0) cc_final: 0.8358 (t0) REVERT: B 170 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8713 (mptt) REVERT: B 173 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7617 (mmtm) REVERT: C 164 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8233 (tm-30) REVERT: C 212 MET cc_start: 0.7204 (tpp) cc_final: 0.6835 (tpp) REVERT: C 216 GLU cc_start: 0.7667 (pt0) cc_final: 0.6399 (mm-30) REVERT: C 269 MET cc_start: 0.8739 (tpt) cc_final: 0.8095 (mmt) REVERT: C 380 PHE cc_start: 0.8211 (m-80) cc_final: 0.7585 (m-80) REVERT: D 367 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8589 (tp-100) outliers start: 27 outliers final: 24 residues processed: 229 average time/residue: 0.2333 time to fit residues: 78.4296 Evaluate side-chains 227 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 141 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.139181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102955 restraints weight = 33690.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.105072 restraints weight = 17315.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107197 restraints weight = 10876.148| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13057 Z= 0.181 Angle : 0.658 11.181 17886 Z= 0.324 Chirality : 0.043 0.210 2171 Planarity : 0.004 0.049 2300 Dihedral : 5.924 78.015 1963 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.35 % Allowed : 25.81 % Favored : 71.83 % 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: -0.71 (0.20), residues: 1744 helix: 0.51 (0.19), residues: 817 sheet: -1.08 (0.37), residues: 182 loop : -1.38 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 141 HIS 0.003 0.001 HIS C 94 PHE 0.025 0.001 PHE C 234 TYR 0.016 0.001 TYR D 92 ARG 0.003 0.000 ARG E 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2914.44 seconds wall clock time: 53 minutes 22.39 seconds (3202.39 seconds total)