Starting phenix.real_space_refine on Thu Feb 15 15:27:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/02_2024/8hpr_34941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/02_2024/8hpr_34941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/02_2024/8hpr_34941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/02_2024/8hpr_34941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/02_2024/8hpr_34941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpr_34941/02_2024/8hpr_34941_updated.pdb" } resolution = 3.75 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 8071 2.51 5 N 2147 2.21 5 O 2386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 146": "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 187": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 361": "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 GLU 100": "OE1" <-> "OE2" 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 PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E ARG 343": "NH1" <-> "NH2" Residue "E ARG 368": "NH1" <-> "NH2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E ARG 377": "NH1" <-> "NH2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 445": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12645 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2013 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 14, 'TRANS': 262} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1848 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 16, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2695 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 345} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2719 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 3283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3283 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 405} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "H" 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.63, per 1000 atoms: 0.60 Number of scatterers: 12645 At special positions: 0 Unit cell: (82.82, 84.46, 169.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 6 15.00 Mg 2 11.99 O 2386 8.00 N 2147 7.00 C 8071 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 H 1 " - " GLC H 2 " Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 2.2 seconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3154 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 17 sheets defined 48.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 29 through 51 removed outlier: 4.478A pdb=" N LEU A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 77 through 109 removed outlier: 3.770A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.183A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 127 No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 130 through 141 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 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 190 Proline residue: A 179 - end of helix removed outlier: 3.648A pdb=" N LEU A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 215 through 236 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: 3.603A pdb=" N TYR A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 4.384A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 36 removed outlier: 4.263A pdb=" N TRP B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.859A pdb=" N GLY B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 removed outlier: 3.977A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 118 through 132 Proline residue: B 124 - end of helix removed outlier: 3.570A pdb=" N ASN B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 removed outlier: 4.707A pdb=" N ILE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 155 through 163 removed outlier: 5.016A pdb=" N GLU B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 179 through 186 removed outlier: 4.010A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 206 Proline residue: B 193 - end of helix removed outlier: 5.104A pdb=" N THR B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.759A pdb=" N ILE B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 97 through 107 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.675A pdb=" N ARG C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 153 " --> pdb=" O MET C 149 " (cutoff:3.500A) removed outlier: 3.865A 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 205 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 273 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 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 299 through 304 removed outlier: 4.713A pdb=" N ARG C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 77 through 80 No H-bonds generated for 'chain 'D' and resid 77 through 80' Processing helix chain 'D' and resid 97 through 100 No H-bonds generated for 'chain 'D' and resid 97 through 100' Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 112 through 125 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 144 through 153 removed outlier: 3.566A pdb=" N ARG D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 188 removed outlier: 3.863A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.554A pdb=" N THR D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 288 through 290 No H-bonds generated for 'chain 'D' and resid 288 through 290' Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 299 through 304 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 55 removed outlier: 5.498A pdb=" N ALA E 42 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR E 43 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS E 45 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 47 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 55 " --> pdb=" O ASN E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 Processing helix chain 'E' and resid 95 through 103 removed outlier: 4.176A pdb=" N THR E 98 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA E 99 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 102 " --> pdb=" O ALA E 99 " (cutoff:3.500A) 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 118 through 123 Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.762A pdb=" N PHE E 199 " --> pdb=" O MET E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 277 through 285 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 325 Processing helix chain 'E' and resid 360 through 370 Processing helix chain 'E' and resid 373 through 383 Processing helix chain 'E' and resid 391 through 394 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 403 through 414 removed outlier: 4.368A pdb=" N GLU E 406 " --> pdb=" O PRO E 403 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN E 410 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 435 removed outlier: 4.637A pdb=" N GLN E 425 " --> pdb=" O PRO E 422 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 430 " --> pdb=" O VAL E 427 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET E 431 " --> pdb=" O SER E 428 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E 432 " --> pdb=" O THR E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 443 through 459 removed outlier: 3.659A pdb=" N GLN E 455 " --> pdb=" O THR E 451 " (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 216 through 221 removed outlier: 6.827A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 220 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 209 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR C 192 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU C 39 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C 194 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N GLY C 41 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 245 through 249 Processing sheet with id= D, first strand: chain 'C' and resid 250 through 252 Processing sheet with id= E, first strand: chain 'C' and resid 305 through 311 removed outlier: 3.996A pdb=" N LEU C 306 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 372 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 314 through 317 removed outlier: 3.967A pdb=" N ILE C 314 " --> pdb=" O HIS C 325 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.870A pdb=" N TYR C 13 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA C 22 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 29 through 31 Processing sheet with id= I, first strand: chain 'D' and resid 36 through 38 removed outlier: 6.771A pdb=" N THR D 192 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 245 through 249 removed outlier: 3.910A pdb=" N ILE D 282 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 250 through 252 Processing sheet with id= L, first strand: chain 'D' and resid 306 through 312 removed outlier: 4.285A pdb=" N LEU D 306 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE D 372 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU D 366 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.998A pdb=" N ILE D 314 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.449A pdb=" N TYR D 13 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA D 22 " --> pdb=" O TYR D 13 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 209 through 213 removed outlier: 3.685A pdb=" N GLN D 219 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU D 213 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 60 through 66 removed outlier: 7.291A pdb=" N TYR E 35 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET E 91 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N LEU E 93 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU E 351 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 328 through 331 removed outlier: 7.488A pdb=" N ALA E 268 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TRP E 184 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU E 270 " --> pdb=" O TRP E 184 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 186 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN E 272 " --> pdb=" O ALA E 186 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1524 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: 3.89 Time building geometry restraints manager: 5.73 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: 2377 1.32 - 1.45: 2987 1.45 - 1.57: 7465 1.57 - 1.69: 10 1.69 - 1.82: 62 Bond restraints: 12901 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.73e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.41e+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 5.37e+01 bond pdb=" C5 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.415 1.549 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 12896 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.54: 390 105.54 - 113.19: 6432 113.19 - 120.83: 6675 120.83 - 128.47: 4076 128.47 - 136.11: 65 Bond angle restraints: 17638 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 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.56 16.27 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.72 16.11 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.67 8.13 1.00e+00 1.00e+00 6.61e+01 ... (remaining 17633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 7440 24.83 - 49.66: 280 49.66 - 74.49: 23 74.49 - 99.32: 12 99.32 - 124.15: 2 Dihedral angle restraints: 7757 sinusoidal: 2875 harmonic: 4882 Sorted by residual: dihedral pdb=" CA GLU A 58 " pdb=" C GLU A 58 " pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLU D 130 " pdb=" C GLU D 130 " pdb=" N LEU D 131 " pdb=" CA LEU D 131 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LYS D 322 " pdb=" C LYS D 322 " pdb=" N TYR D 323 " pdb=" CA TYR D 323 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 7754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1148 0.070 - 0.140: 670 0.140 - 0.210: 218 0.210 - 0.280: 50 0.280 - 0.350: 15 Chirality restraints: 2101 Sorted by residual: chirality pdb=" C1 GLC H 1 " pdb=" C2 GLC H 1 " pdb=" O5 GLC H 1 " pdb=" O1 GLC H 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.81e+01 chirality pdb=" CA TYR D 89 " pdb=" N TYR D 89 " pdb=" C TYR D 89 " pdb=" CB TYR D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PHE B 161 " pdb=" N PHE B 161 " pdb=" C PHE B 161 " pdb=" CB PHE B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2098 not shown) Planarity restraints: 2269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 97 " 0.161 2.00e-02 2.50e+03 9.03e-02 2.04e+02 pdb=" CG TRP E 97 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP E 97 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP E 97 " -0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP E 97 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP E 97 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP E 97 " -0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 97 " 0.103 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 97 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP E 97 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " 0.121 2.00e-02 2.50e+03 6.04e-02 9.12e+01 pdb=" CG TRP E 153 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " -0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " -0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " 0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " -0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 35 " 0.103 2.00e-02 2.50e+03 5.99e-02 7.18e+01 pdb=" CG TYR E 35 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 35 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR E 35 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR E 35 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR E 35 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR E 35 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR E 35 " 0.103 2.00e-02 2.50e+03 ... (remaining 2266 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 509 2.74 - 3.28: 13910 3.28 - 3.82: 19995 3.82 - 4.36: 25739 4.36 - 4.90: 41108 Nonbonded interactions: 101261 Sorted by model distance: nonbonded pdb=" O GLY D 46 " pdb=" SD MET D 212 " model vdw 2.201 3.400 nonbonded pdb=" OE1 GLN C 87 " pdb="MG MG C 502 " model vdw 2.222 2.170 nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 502 " model vdw 2.230 2.170 nonbonded pdb=" OG SER D 48 " pdb="MG MG D 502 " model vdw 2.241 2.170 nonbonded pdb=" NE2 GLN C 87 " pdb="MG MG C 502 " model vdw 2.256 2.250 ... (remaining 101256 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 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB )) or resid 85 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 273 or (resid 274 thro \ ugh 278 and (name N or name CA or name C or name O or name CB )) or resid 279 th \ rough 327 or resid 352 through 388 or (resid 389 and (name N or name CA or name \ C or name O or name CB )) or resid 390 through 391 or resid 501 through 502)) selection = (chain 'D' and (resid 2 through 20 or (resid 21 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 81 or (resid 82 through \ 84 and (name N or name CA or name C or name O or name CB )) or resid 85 through \ 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or re \ sid 110 through 118 or (resid 119 through 120 and (name N or name CA or name C o \ r name O or name CB )) or resid 121 through 123 or (resid 124 through 125 and (n \ ame N or name CA or name C or name O or name CB )) or resid 126 through 130 or ( \ resid 131 through 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 through 143 or (resid 144 and (name N or name CA or name C or name O \ or name CB )) or resid 145 through 179 or (resid 180 and (name N or name CA or \ name C or name O or name CB )) or resid 181 through 232 or (resid 233 and (name \ N or name CA or name C or name O or name CB )) or resid 234 through 356 or (resi \ d 357 through 358 and (name N or name CA or name C or name O or name CB )) or re \ sid 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) o \ r resid 361 through 377 or (resid 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 through 386 or (resid 387 and (name N or name CA or \ name C or name O or name CB )) or resid 388 through 391 or resid 501 through 502 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.020 Extract box with map and model: 12.510 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.400 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 12901 Z= 0.818 Angle : 1.778 19.356 17638 Z= 1.213 Chirality : 0.096 0.350 2101 Planarity : 0.013 0.113 2269 Dihedral : 13.559 124.146 4603 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 0.64 % Allowed : 6.65 % Favored : 92.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.19 % 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: -2.19 (0.18), residues: 1676 helix: -1.74 (0.15), residues: 813 sheet: -0.56 (0.43), residues: 133 loop : -1.06 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.161 0.022 TRP E 97 HIS 0.013 0.003 HIS D 290 PHE 0.080 0.012 PHE D 234 TYR 0.106 0.018 TYR B 23 ARG 0.016 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 395 time to evaluate : 1.493 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: A 45 TYR cc_start: 0.8793 (t80) cc_final: 0.8157 (t80) REVERT: A 137 TRP cc_start: 0.8796 (m100) cc_final: 0.8560 (m100) REVERT: A 147 TYR cc_start: 0.8611 (p90) cc_final: 0.8345 (p90) REVERT: A 180 PHE cc_start: 0.8658 (t80) cc_final: 0.8358 (t80) REVERT: A 195 ASP cc_start: 0.8221 (m-30) cc_final: 0.7993 (m-30) REVERT: A 219 ILE cc_start: 0.8959 (mt) cc_final: 0.8693 (pt) REVERT: A 233 ASP cc_start: 0.8351 (t70) cc_final: 0.8126 (t0) REVERT: A 255 SER cc_start: 0.9476 (m) cc_final: 0.9043 (t) REVERT: A 291 LYS cc_start: 0.8660 (tppp) cc_final: 0.8295 (tttt) REVERT: B 25 LEU cc_start: 0.7742 (mt) cc_final: 0.7502 (mm) REVERT: B 175 ASP cc_start: 0.7731 (m-30) cc_final: 0.7390 (m-30) REVERT: B 260 VAL cc_start: 0.8362 (t) cc_final: 0.8144 (p) REVERT: C 13 TYR cc_start: 0.8247 (m-80) cc_final: 0.7786 (m-10) REVERT: C 51 LEU cc_start: 0.9141 (tp) cc_final: 0.8493 (tp) REVERT: C 87 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: C 149 MET cc_start: 0.8817 (ttt) cc_final: 0.8590 (ttp) REVERT: C 172 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8762 (ttmm) REVERT: C 244 MET cc_start: 0.6770 (ttm) cc_final: 0.6569 (tpt) REVERT: D 92 TYR cc_start: 0.8017 (m-80) cc_final: 0.7766 (m-10) REVERT: D 197 HIS cc_start: 0.8575 (m170) cc_final: 0.8235 (m-70) REVERT: D 198 ASP cc_start: 0.8036 (t0) cc_final: 0.7686 (t0) REVERT: D 244 MET cc_start: 0.5617 (ttm) cc_final: 0.5377 (tpp) REVERT: D 281 ASN cc_start: 0.7478 (m-40) cc_final: 0.7113 (m110) REVERT: E 315 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9215 (pp20) REVERT: E 322 ASP cc_start: 0.8902 (m-30) cc_final: 0.8684 (p0) outliers start: 8 outliers final: 3 residues processed: 400 average time/residue: 0.2919 time to fit residues: 161.1265 Evaluate side-chains 262 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 258 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain E residue 148 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN B 17 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS C 219 GLN C 290 HIS D 99 GLN D 199 GLN E 49 ASN E 283 ASN E 359 HIS E 375 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12901 Z= 0.230 Angle : 0.738 8.548 17638 Z= 0.382 Chirality : 0.047 0.192 2101 Planarity : 0.005 0.040 2269 Dihedral : 8.570 56.984 1927 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.28 % Allowed : 14.41 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.65 (0.20), residues: 1676 helix: -0.08 (0.18), residues: 812 sheet: -0.58 (0.37), residues: 174 loop : -0.63 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 12 HIS 0.006 0.001 HIS D 290 PHE 0.023 0.002 PHE B 161 TYR 0.024 0.002 TYR C 194 ARG 0.006 0.001 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 285 time to evaluate : 1.707 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 45 TYR cc_start: 0.8621 (t80) cc_final: 0.8256 (t80) REVERT: A 134 SER cc_start: 0.8699 (t) cc_final: 0.8268 (p) REVERT: A 137 TRP cc_start: 0.8753 (m100) cc_final: 0.8548 (m100) REVERT: A 147 TYR cc_start: 0.8742 (p90) cc_final: 0.8530 (p90) REVERT: A 219 ILE cc_start: 0.8874 (mt) cc_final: 0.8530 (pt) REVERT: A 233 ASP cc_start: 0.8339 (t70) cc_final: 0.8099 (t0) REVERT: B 36 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8808 (mm) REVERT: C 81 ASP cc_start: 0.6100 (t0) cc_final: 0.5729 (m-30) REVERT: C 184 LEU cc_start: 0.9183 (tp) cc_final: 0.8778 (tp) REVERT: C 224 ASP cc_start: 0.8203 (m-30) cc_final: 0.7969 (p0) REVERT: D 198 ASP cc_start: 0.8100 (t0) cc_final: 0.7823 (t0) REVERT: E 315 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9196 (pp20) outliers start: 41 outliers final: 22 residues processed: 305 average time/residue: 0.2630 time to fit residues: 114.7029 Evaluate side-chains 254 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 231 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 164 optimal weight: 0.1980 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN D 199 GLN D 290 HIS E 148 ASN E 283 ASN E 411 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12901 Z= 0.197 Angle : 0.656 9.728 17638 Z= 0.333 Chirality : 0.045 0.184 2101 Planarity : 0.005 0.047 2269 Dihedral : 8.585 70.017 1921 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.60 % Allowed : 16.01 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: -0.34 (0.20), residues: 1676 helix: 0.29 (0.18), residues: 805 sheet: -0.26 (0.37), residues: 179 loop : -0.70 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 129 HIS 0.008 0.001 HIS C 325 PHE 0.025 0.002 PHE B 161 TYR 0.026 0.002 TYR E 393 ARG 0.005 0.001 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 252 time to evaluate : 1.341 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 45 TYR cc_start: 0.8635 (t80) cc_final: 0.8165 (t80) REVERT: A 58 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7660 (mt-10) REVERT: A 134 SER cc_start: 0.8679 (t) cc_final: 0.8241 (p) REVERT: A 219 ILE cc_start: 0.8876 (mt) cc_final: 0.8515 (pt) REVERT: A 233 ASP cc_start: 0.8374 (t70) cc_final: 0.8085 (t0) REVERT: A 262 LEU cc_start: 0.9315 (tp) cc_final: 0.8979 (tt) REVERT: B 174 MET cc_start: 0.7288 (tpt) cc_final: 0.6540 (tpp) REVERT: C 186 ASP cc_start: 0.7953 (p0) cc_final: 0.7639 (m-30) REVERT: C 361 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7282 (mmm160) REVERT: D 198 ASP cc_start: 0.8125 (t0) cc_final: 0.7900 (t0) REVERT: D 361 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6923 (mmm160) REVERT: E 315 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9197 (pp20) outliers start: 45 outliers final: 24 residues processed: 279 average time/residue: 0.2522 time to fit residues: 101.4610 Evaluate side-chains 249 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12901 Z= 0.191 Angle : 0.622 8.457 17638 Z= 0.315 Chirality : 0.045 0.195 2101 Planarity : 0.005 0.047 2269 Dihedral : 8.001 71.106 1918 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.44 % Allowed : 16.81 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1676 helix: 0.47 (0.19), residues: 799 sheet: 0.04 (0.38), residues: 179 loop : -0.57 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 30 HIS 0.004 0.001 HIS D 290 PHE 0.025 0.002 PHE B 161 TYR 0.021 0.002 TYR C 194 ARG 0.010 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 242 time to evaluate : 1.581 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 34 LEU cc_start: 0.9239 (tp) cc_final: 0.9032 (tt) REVERT: A 45 TYR cc_start: 0.8618 (t80) cc_final: 0.8261 (t80) REVERT: A 58 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 134 SER cc_start: 0.8669 (t) cc_final: 0.8257 (p) REVERT: A 229 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7391 (t80) REVERT: A 233 ASP cc_start: 0.8437 (t70) cc_final: 0.8134 (t0) REVERT: A 262 LEU cc_start: 0.9339 (tp) cc_final: 0.8994 (tt) REVERT: B 128 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8131 (ttm) REVERT: B 239 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7404 (mm-30) REVERT: C 13 TYR cc_start: 0.8055 (m-80) cc_final: 0.7387 (m-10) REVERT: C 53 MET cc_start: 0.8633 (mtm) cc_final: 0.8358 (mtm) REVERT: C 184 LEU cc_start: 0.8985 (tp) cc_final: 0.8691 (mt) REVERT: C 244 MET cc_start: 0.6506 (ttm) cc_final: 0.6253 (mmm) REVERT: C 380 PHE cc_start: 0.8243 (m-80) cc_final: 0.7892 (m-80) REVERT: D 198 ASP cc_start: 0.8197 (t0) cc_final: 0.7986 (t0) REVERT: D 361 ARG cc_start: 0.7376 (mmm160) cc_final: 0.7065 (mmm160) REVERT: E 315 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9201 (pp20) outliers start: 43 outliers final: 30 residues processed: 264 average time/residue: 0.2407 time to fit residues: 92.2521 Evaluate side-chains 255 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 0.0010 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 overall best weight: 1.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12901 Z= 0.243 Angle : 0.636 7.887 17638 Z= 0.319 Chirality : 0.044 0.191 2101 Planarity : 0.005 0.050 2269 Dihedral : 7.704 74.004 1918 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.24 % Allowed : 17.37 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1676 helix: 0.59 (0.19), residues: 802 sheet: 0.06 (0.39), residues: 179 loop : -0.59 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 30 HIS 0.003 0.001 HIS C 94 PHE 0.025 0.002 PHE B 161 TYR 0.025 0.002 TYR C 194 ARG 0.009 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 231 time to evaluate : 1.482 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: A 45 TYR cc_start: 0.8696 (t80) cc_final: 0.8300 (t80) REVERT: A 134 SER cc_start: 0.8725 (t) cc_final: 0.8282 (p) REVERT: A 229 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7664 (t80) REVERT: A 233 ASP cc_start: 0.8517 (t70) cc_final: 0.8189 (t0) REVERT: A 262 LEU cc_start: 0.9361 (tp) cc_final: 0.9041 (tt) REVERT: B 128 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8041 (mtp) REVERT: B 239 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7516 (mm-30) REVERT: C 13 TYR cc_start: 0.8044 (m-80) cc_final: 0.7489 (m-10) REVERT: C 244 MET cc_start: 0.6525 (ttm) cc_final: 0.6255 (mmm) REVERT: C 282 ILE cc_start: 0.9219 (mp) cc_final: 0.8852 (mp) REVERT: C 361 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7298 (mmm160) REVERT: C 379 ILE cc_start: 0.9244 (pp) cc_final: 0.8962 (tp) REVERT: D 198 ASP cc_start: 0.8109 (t0) cc_final: 0.7906 (t0) REVERT: D 361 ARG cc_start: 0.7516 (mmm160) cc_final: 0.7195 (mmm160) REVERT: E 315 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9211 (pp20) outliers start: 53 outliers final: 38 residues processed: 257 average time/residue: 0.2486 time to fit residues: 91.4410 Evaluate side-chains 260 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 0.0030 chunk 84 optimal weight: 9.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12901 Z= 0.172 Angle : 0.612 10.637 17638 Z= 0.304 Chirality : 0.044 0.240 2101 Planarity : 0.005 0.048 2269 Dihedral : 7.039 73.938 1918 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.60 % Allowed : 18.73 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.08 (0.21), residues: 1676 helix: 0.66 (0.19), residues: 804 sheet: 0.31 (0.39), residues: 173 loop : -0.64 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 30 HIS 0.002 0.001 HIS C 325 PHE 0.021 0.001 PHE B 161 TYR 0.017 0.002 TYR E 192 ARG 0.008 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 235 time to evaluate : 1.386 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 45 TYR cc_start: 0.8609 (t80) cc_final: 0.8187 (t80) REVERT: A 134 SER cc_start: 0.8676 (t) cc_final: 0.8261 (p) REVERT: A 229 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7581 (t80) REVERT: A 233 ASP cc_start: 0.8483 (t70) cc_final: 0.8090 (t0) REVERT: A 262 LEU cc_start: 0.9338 (tp) cc_final: 0.9017 (tt) REVERT: B 128 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8011 (mtp) REVERT: B 174 MET cc_start: 0.7357 (tpt) cc_final: 0.6626 (tpt) REVERT: B 239 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7654 (mm-30) REVERT: C 13 TYR cc_start: 0.8003 (m-80) cc_final: 0.7512 (m-10) REVERT: C 244 MET cc_start: 0.6588 (ttm) cc_final: 0.6292 (mmm) REVERT: C 282 ILE cc_start: 0.9179 (mp) cc_final: 0.8778 (mp) REVERT: C 361 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7345 (mmm160) REVERT: C 379 ILE cc_start: 0.9332 (pp) cc_final: 0.9081 (tp) REVERT: D 361 ARG cc_start: 0.7521 (mmm160) cc_final: 0.7205 (mmm160) REVERT: E 315 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9207 (pp20) outliers start: 45 outliers final: 31 residues processed: 260 average time/residue: 0.2369 time to fit residues: 89.4600 Evaluate side-chains 254 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 100 optimal weight: 0.0060 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12901 Z= 0.199 Angle : 0.616 9.617 17638 Z= 0.307 Chirality : 0.044 0.219 2101 Planarity : 0.005 0.047 2269 Dihedral : 6.672 73.715 1918 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.84 % Allowed : 19.22 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.16 (0.21), residues: 1676 helix: 0.78 (0.19), residues: 791 sheet: 0.45 (0.39), residues: 177 loop : -0.67 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 30 HIS 0.002 0.001 HIS C 325 PHE 0.036 0.002 PHE A 83 TYR 0.020 0.002 TYR C 194 ARG 0.008 0.001 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 1.474 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 45 TYR cc_start: 0.8612 (t80) cc_final: 0.8200 (t80) REVERT: A 60 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8183 (p90) REVERT: A 134 SER cc_start: 0.8694 (t) cc_final: 0.8277 (p) REVERT: A 229 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7665 (t80) REVERT: A 233 ASP cc_start: 0.8525 (t70) cc_final: 0.8129 (t0) REVERT: A 262 LEU cc_start: 0.9361 (tp) cc_final: 0.9048 (tt) REVERT: B 128 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: B 239 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7671 (mm-30) REVERT: C 13 TYR cc_start: 0.8008 (m-80) cc_final: 0.7476 (m-10) REVERT: C 244 MET cc_start: 0.6586 (ttm) cc_final: 0.6276 (mmm) REVERT: C 282 ILE cc_start: 0.9147 (mp) cc_final: 0.8703 (mp) REVERT: C 379 ILE cc_start: 0.9514 (pp) cc_final: 0.9254 (tp) REVERT: D 361 ARG cc_start: 0.7530 (mmm160) cc_final: 0.7191 (mmm160) REVERT: E 235 ARG cc_start: 0.9146 (ttm110) cc_final: 0.8919 (mtp85) REVERT: E 315 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9214 (pp20) outliers start: 48 outliers final: 36 residues processed: 260 average time/residue: 0.2451 time to fit residues: 92.5563 Evaluate side-chains 267 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 247 PHE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12901 Z= 0.176 Angle : 0.622 9.929 17638 Z= 0.308 Chirality : 0.044 0.330 2101 Planarity : 0.004 0.048 2269 Dihedral : 6.356 73.221 1918 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.76 % Allowed : 19.78 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.11 (0.21), residues: 1676 helix: 0.71 (0.19), residues: 812 sheet: 0.57 (0.40), residues: 174 loop : -0.74 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 30 HIS 0.009 0.001 HIS D 94 PHE 0.022 0.001 PHE D 380 TYR 0.015 0.002 TYR C 194 ARG 0.007 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 235 time to evaluate : 1.457 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: A 45 TYR cc_start: 0.8594 (t80) cc_final: 0.8142 (t80) REVERT: A 60 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8184 (p90) REVERT: A 134 SER cc_start: 0.8674 (t) cc_final: 0.8254 (p) REVERT: A 195 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7927 (t0) REVERT: A 229 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7647 (t80) REVERT: A 233 ASP cc_start: 0.8511 (t70) cc_final: 0.8078 (t0) REVERT: A 262 LEU cc_start: 0.9344 (tp) cc_final: 0.9027 (tt) REVERT: A 292 ILE cc_start: 0.8489 (mm) cc_final: 0.8260 (tt) REVERT: B 51 GLU cc_start: 0.8275 (mp0) cc_final: 0.8013 (mp0) REVERT: B 128 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: B 239 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 13 TYR cc_start: 0.8006 (m-80) cc_final: 0.7431 (m-10) REVERT: C 244 MET cc_start: 0.6574 (ttm) cc_final: 0.6306 (mmm) REVERT: D 361 ARG cc_start: 0.7482 (mmm160) cc_final: 0.7165 (mmm160) REVERT: E 315 GLU cc_start: 0.9499 (mt-10) cc_final: 0.9211 (pp20) outliers start: 47 outliers final: 38 residues processed: 260 average time/residue: 0.2408 time to fit residues: 90.8210 Evaluate side-chains 263 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 176 GLN Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 0.0570 chunk 140 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 46 optimal weight: 0.0010 chunk 135 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.7306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12901 Z= 0.170 Angle : 0.640 11.481 17638 Z= 0.312 Chirality : 0.044 0.384 2101 Planarity : 0.004 0.048 2269 Dihedral : 6.112 72.680 1918 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.52 % Allowed : 20.66 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1676 helix: 0.70 (0.19), residues: 822 sheet: 0.61 (0.38), residues: 178 loop : -0.80 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 30 HIS 0.003 0.001 HIS D 94 PHE 0.034 0.001 PHE A 83 TYR 0.015 0.001 TYR C 194 ARG 0.007 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 1.471 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: A 45 TYR cc_start: 0.8566 (t80) cc_final: 0.8135 (t80) REVERT: A 60 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8180 (p90) REVERT: A 134 SER cc_start: 0.8645 (t) cc_final: 0.8234 (p) REVERT: A 229 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7647 (t80) REVERT: A 233 ASP cc_start: 0.8498 (t70) cc_final: 0.8030 (t0) REVERT: A 262 LEU cc_start: 0.9325 (tp) cc_final: 0.8997 (tt) REVERT: A 292 ILE cc_start: 0.8475 (mm) cc_final: 0.8264 (tt) REVERT: B 51 GLU cc_start: 0.8255 (mp0) cc_final: 0.8001 (mp0) REVERT: B 128 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8047 (mtp) REVERT: B 239 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7700 (mm-30) REVERT: C 13 TYR cc_start: 0.8013 (m-80) cc_final: 0.7509 (m-10) REVERT: C 98 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8503 (ttm-80) REVERT: C 244 MET cc_start: 0.6566 (ttm) cc_final: 0.6293 (mmm) REVERT: C 269 MET cc_start: 0.8698 (mtp) cc_final: 0.8479 (ptp) REVERT: D 361 ARG cc_start: 0.7567 (mmm160) cc_final: 0.7214 (mmm160) REVERT: E 315 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9219 (pp20) outliers start: 44 outliers final: 36 residues processed: 255 average time/residue: 0.2422 time to fit residues: 89.4290 Evaluate side-chains 260 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 221 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 176 GLN Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12901 Z= 0.196 Angle : 0.648 12.134 17638 Z= 0.316 Chirality : 0.045 0.428 2101 Planarity : 0.004 0.047 2269 Dihedral : 6.026 72.947 1918 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.44 % Allowed : 21.06 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.12 (0.21), residues: 1676 helix: 0.73 (0.19), residues: 820 sheet: 0.59 (0.39), residues: 178 loop : -0.80 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 30 HIS 0.002 0.001 HIS D 94 PHE 0.021 0.001 PHE D 380 TYR 0.026 0.002 TYR E 192 ARG 0.007 0.000 ARG D 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 225 time to evaluate : 1.382 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: A 45 TYR cc_start: 0.8620 (t80) cc_final: 0.8171 (t80) REVERT: A 60 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.8167 (p90) REVERT: A 134 SER cc_start: 0.8662 (t) cc_final: 0.8244 (p) REVERT: A 195 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7919 (t0) REVERT: A 233 ASP cc_start: 0.8517 (t70) cc_final: 0.8057 (t0) REVERT: A 262 LEU cc_start: 0.9347 (tp) cc_final: 0.9027 (tt) REVERT: A 292 ILE cc_start: 0.8472 (mm) cc_final: 0.8266 (tt) REVERT: B 51 GLU cc_start: 0.8296 (mp0) cc_final: 0.7991 (mp0) REVERT: B 128 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8030 (mtp) REVERT: B 239 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7691 (mm-30) REVERT: C 13 TYR cc_start: 0.8006 (m-80) cc_final: 0.7515 (m-10) REVERT: C 98 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8480 (ttm-80) REVERT: C 177 MET cc_start: 0.8852 (mmm) cc_final: 0.8643 (mmt) REVERT: C 203 MET cc_start: 0.9020 (tpp) cc_final: 0.8786 (tpt) REVERT: C 244 MET cc_start: 0.6498 (ttm) cc_final: 0.6233 (mmm) REVERT: C 269 MET cc_start: 0.8725 (mtp) cc_final: 0.8506 (ptp) REVERT: D 361 ARG cc_start: 0.7504 (mmm160) cc_final: 0.7194 (mmm160) REVERT: E 315 GLU cc_start: 0.9497 (mt-10) cc_final: 0.9188 (pp20) outliers start: 43 outliers final: 37 residues processed: 249 average time/residue: 0.2412 time to fit residues: 87.0968 Evaluate side-chains 256 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 71 PHE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.0070 chunk 132 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.130475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.097920 restraints weight = 31674.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101240 restraints weight = 17693.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.103443 restraints weight = 12311.252| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12901 Z= 0.163 Angle : 0.643 10.916 17638 Z= 0.312 Chirality : 0.044 0.387 2101 Planarity : 0.004 0.048 2269 Dihedral : 5.842 71.609 1918 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.96 % Allowed : 22.34 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1676 helix: 0.73 (0.19), residues: 823 sheet: 0.65 (0.38), residues: 178 loop : -0.81 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 30 HIS 0.001 0.000 HIS C 325 PHE 0.021 0.001 PHE D 380 TYR 0.022 0.001 TYR E 192 ARG 0.007 0.000 ARG D 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.82 seconds wall clock time: 55 minutes 32.70 seconds (3332.70 seconds total)