Starting phenix.real_space_refine on Fri Jan 19 23:31:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cag_30330/01_2024/7cag_30330_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cag_30330/01_2024/7cag_30330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cag_30330/01_2024/7cag_30330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cag_30330/01_2024/7cag_30330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cag_30330/01_2024/7cag_30330_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cag_30330/01_2024/7cag_30330_updated.pdb" } resolution = 3.78 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= 0.016 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 38 5.16 5 C 8302 2.51 5 N 2188 2.21 5 O 2459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 ASP 72": "OD1" <-> "OD2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ASP 138": "OD1" <-> "OD2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E ASP 297": "OD1" <-> "OD2" Residue "E ARG 343": "NH1" <-> "NH2" Residue "E ARG 371": "NH1" <-> "NH2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E GLU 449": "OE1" <-> "OE2" Residue "E ASP 459": "OD1" <-> "OD2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12995 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3298 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 31, 'TRANS': 403} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2155 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 270} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2051 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 256} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2704 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2700 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 40 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 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: 7.03, per 1000 atoms: 0.54 Number of scatterers: 12995 At special positions: 0 Unit cell: (81.18, 95.12, 168.1, 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 38 16.00 P 6 15.00 Mg 2 11.99 O 2459 8.00 N 2188 7.00 C 8302 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=2, symmetry=0 Links applied ALPHA1-1 " GLC H 1 " - " GLC H 2 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.5 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 9 sheets defined 35.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'E' and resid 42 through 52 Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 118 through 121 No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 166 through 178 removed outlier: 4.052A pdb=" N ASP E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 206 removed outlier: 4.274A pdb=" N THR E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU E 202 " --> pdb=" O TRP E 198 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 239 removed outlier: 4.347A pdb=" N ALA E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 removed outlier: 4.337A pdb=" N LEU E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 286 removed outlier: 5.165A pdb=" N VAL E 285 " --> pdb=" O LEU E 281 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 361 through 369 removed outlier: 4.035A pdb=" N ARG E 368 " --> pdb=" O PHE E 364 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 381 removed outlier: 4.388A pdb=" N SER E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 425 through 431 removed outlier: 4.042A pdb=" N THR E 429 " --> pdb=" O GLN E 425 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 430 " --> pdb=" O ALA E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 459 removed outlier: 4.214A pdb=" N ALA E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 37 removed outlier: 4.178A pdb=" N LEU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.678A pdb=" N SER A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 80 through 109 removed outlier: 3.804A pdb=" N THR A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.947A pdb=" N SER A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 181 removed outlier: 3.559A pdb=" N GLU A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 184 through 189 removed outlier: 4.263A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.933A pdb=" N ILE A 223 " --> pdb=" O LYS A 220 " (cutoff:3.500A) 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 260 Processing helix chain 'A' and resid 268 through 293 removed outlier: 4.216A pdb=" N ALA A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 15 removed outlier: 3.845A pdb=" N TRP B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TRP B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 4.159A pdb=" N LEU B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 67 through 74 removed outlier: 3.924A pdb=" N ASN B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 96 removed outlier: 4.560A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.697A pdb=" N LEU B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 removed outlier: 4.750A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 4.264A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 155 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.641A pdb=" N PHE B 183 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.634A pdb=" N ALA B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) Proline residue: B 193 - end of helix No H-bonds generated for 'chain 'B' and resid 189 through 194' Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'B' and resid 225 through 228 No H-bonds generated for 'chain 'B' and resid 225 through 228' Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 255 through 258 No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 260 through 263 No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 112 through 125 removed outlier: 4.140A pdb=" N ALA C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 removed outlier: 4.035A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 188 removed outlier: 3.692A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 235 through 238 No H-bonds generated for 'chain 'C' and resid 235 through 238' Processing helix chain 'C' and resid 267 through 276 removed outlier: 4.144A pdb=" N ASP C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 273 " --> pdb=" O MET C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 77 through 80 removed outlier: 3.696A pdb=" N ARG D 80 " --> pdb=" O PRO D 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 77 through 80' Processing helix chain 'D' and resid 97 through 106 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.725A pdb=" N ALA D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 removed outlier: 4.083A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 removed outlier: 3.588A pdb=" N ALA D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 No H-bonds generated for 'chain 'D' and resid 201 through 204' Processing helix chain 'D' and resid 225 through 228 No H-bonds generated for 'chain 'D' and resid 225 through 228' Processing helix chain 'D' and resid 267 through 273 removed outlier: 4.981A pdb=" N ASP D 271 " --> pdb=" O HIS D 268 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU D 272 " --> pdb=" O MET D 269 " (cutoff:3.500A) 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 297 No H-bonds generated for 'chain 'D' and resid 294 through 297' Processing sheet with id= A, first strand: chain 'E' and resid 90 through 94 removed outlier: 6.019A pdb=" N LEU E 351 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 269 through 272 removed outlier: 3.905A pdb=" N ASN E 272 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 151 " --> pdb=" O ASN E 272 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 331 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 4 through 7 Processing sheet with id= D, first strand: chain 'C' and resid 38 through 41 removed outlier: 3.602A pdb=" N MET C 212 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 219 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU C 213 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.061A pdb=" N VAL C 193 " --> pdb=" O MET C 162 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 314 through 316 removed outlier: 4.058A pdb=" N ILE C 314 " --> pdb=" O HIS C 325 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= H, first strand: chain 'D' and resid 193 through 195 removed outlier: 5.824A pdb=" N ILE D 37 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 219 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU D 213 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 321 through 324 301 hydrogen bonds defined for protein. 873 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: 3.07 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: 1.23 - 1.34: 4243 1.34 - 1.46: 2089 1.46 - 1.57: 6844 1.57 - 1.69: 10 1.69 - 1.81: 73 Bond restraints: 13259 Sorted by residual: bond pdb=" C1 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.410 1.499 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C ILE A 124 " pdb=" N PRO A 125 " ideal model delta sigma weight residual 1.334 1.367 -0.033 8.40e-03 1.42e+04 1.57e+01 bond pdb=" C5 GLC H 2 " pdb=" O5 GLC H 2 " ideal model delta sigma weight residual 1.410 1.487 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.410 1.479 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C3 GLC H 2 " pdb=" O3 GLC H 2 " ideal model delta sigma weight residual 1.410 1.478 -0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 13254 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.06: 343 105.06 - 112.30: 6628 112.30 - 119.55: 4465 119.55 - 126.80: 6472 126.80 - 134.04: 198 Bond angle restraints: 18106 Sorted by residual: angle pdb=" N GLN C 87 " pdb=" CA GLN C 87 " pdb=" C GLN C 87 " ideal model delta sigma weight residual 110.97 102.92 8.05 1.09e+00 8.42e-01 5.46e+01 angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 132.53 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 132.63 7.24 1.00e+00 1.00e+00 5.24e+01 angle pdb=" N GLN D 87 " pdb=" CA GLN D 87 " pdb=" C GLN D 87 " ideal model delta sigma weight residual 111.07 104.55 6.52 1.07e+00 8.73e-01 3.72e+01 angle pdb=" N THR D 190 " pdb=" CA THR D 190 " pdb=" C THR D 190 " ideal model delta sigma weight residual 108.52 115.20 -6.68 1.52e+00 4.33e-01 1.93e+01 ... (remaining 18101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7151 17.85 - 35.69: 653 35.69 - 53.54: 124 53.54 - 71.38: 19 71.38 - 89.23: 12 Dihedral angle restraints: 7959 sinusoidal: 3015 harmonic: 4944 Sorted by residual: dihedral pdb=" CA THR D 190 " pdb=" C THR D 190 " pdb=" N THR D 191 " pdb=" CA THR D 191 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY C 240 " pdb=" C GLY C 240 " pdb=" N SER C 241 " pdb=" CA SER C 241 " ideal model delta harmonic sigma weight residual 180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLN C 367 " pdb=" C GLN C 367 " pdb=" N ILE C 368 " pdb=" CA ILE C 368 " ideal model delta harmonic sigma weight residual 180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 7956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.939: 2145 0.939 - 1.878: 0 1.878 - 2.817: 0 2.817 - 3.756: 0 3.756 - 4.695: 1 Chirality restraints: 2146 Sorted by residual: chirality pdb=" C1 GLC H 2 " pdb=" C2 GLC H 2 " pdb=" O1 GLC H 2 " pdb=" O5 GLC H 2 " both_signs ideal model delta sigma weight residual False 2.33 -2.36 4.70 2.00e-01 2.50e+01 5.51e+02 chirality pdb=" CA GLN C 87 " pdb=" N GLN C 87 " pdb=" C GLN C 87 " pdb=" CB GLN C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLN D 87 " pdb=" N GLN D 87 " pdb=" C GLN D 87 " pdb=" CB GLN D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2143 not shown) Planarity restraints: 2322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 258 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO C 259 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 259 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 259 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 181 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO E 182 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 182 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 182 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 220 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 221 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.031 5.00e-02 4.00e+02 ... (remaining 2319 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 86 2.46 - 3.07: 9197 3.07 - 3.68: 19474 3.68 - 4.29: 27409 4.29 - 4.90: 44965 Nonbonded interactions: 101131 Sorted by model distance: nonbonded pdb="MG MG C 501 " pdb=" O3G ATP C 502 " model vdw 1.845 2.170 nonbonded pdb=" OE1 GLN D 87 " pdb="MG MG D 501 " model vdw 2.066 2.170 nonbonded pdb=" OG1 THR C 49 " pdb=" O1A ATP C 502 " model vdw 2.072 2.440 nonbonded pdb=" OG1 THR A 142 " pdb=" O THR A 145 " model vdw 2.158 2.440 nonbonded pdb=" OG SER C 48 " pdb="MG MG C 501 " model vdw 2.170 2.170 ... (remaining 101126 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 53 or (resid 54 through 55 and (name N or name C \ A or name C or name O or name CB )) or resid 56 through 63 or (resid 64 and (nam \ e N or name CA or name C or name O or name CB )) or resid 65 through 90 or (resi \ d 91 and (name N or name CA or name C or name O or name CB )) or resid 92 throug \ h 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or \ resid 110 through 130 or (resid 131 through 132 and (name N or name CA or name C \ or name O or name CB )) or resid 133 through 187 or (resid 188 and (name N or n \ ame CA or name C or name O or name CB )) or resid 189 or (resid 190 through 191 \ and (name N or name CA or name C or name O or name CB )) or resid 192 through 23 \ 2 or (resid 233 and (name N or name CA or name C or name O or name CB )) or resi \ d 234 through 259 or (resid 260 and (name N or name CA or name C or name O or na \ me CB )) or resid 261 through 303 or (resid 304 through 305 and (name N or name \ CA or name C or name O or name CB )) or resid 306 through 362 or (resid 363 and \ (name N or name CA or name C or name O or name CB )) or resid 364 through 387 or \ (resid 388 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 9 or (resid 390 and (name N or name CA or name C or name O or name CB )) or resi \ d 391 or resid 501 through 502)) selection = (chain 'D' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 44 or (resid 45 and (name N or na \ me CA or name C or name O or name CB )) or resid 46 through 52 or (resid 53 thro \ ugh 55 and (name N or name CA or name C or name O or name CB )) or resid 56 thro \ ugh 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or \ resid 67 through 69 or (resid 70 and (name N or name CA or name C or name O or n \ ame CB )) or resid 71 through 74 or (resid 75 through 76 and (name N or name CA \ or name C or name O or name CB )) or resid 77 through 114 or (resid 115 through \ 117 and (name N or name CA or name C or name O or name CB )) or resid 118 throug \ h 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or \ resid 167 through 288 or (resid 289 and (name N or name CA or name C or name O o \ r name CB )) or resid 290 through 297 or (resid 298 and (name N or name CA or na \ me C or name O or name CB )) or resid 299 through 309 or (resid 310 through 313 \ and (name N or name CA or name C or name O or name CB )) or resid 314 through 37 \ 5 or (resid 376 and (name N or name CA or name C or name O or name CB )) or resi \ d 377 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 12.630 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.800 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.004 0.089 13259 Z= 0.237 Angle : 0.758 9.830 18106 Z= 0.429 Chirality : 0.112 4.695 2146 Planarity : 0.005 0.085 2322 Dihedral : 14.531 89.228 4767 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 0.15 % Allowed : 6.73 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.72 (0.16), residues: 1699 helix: -3.20 (0.15), residues: 674 sheet: -4.33 (0.31), residues: 118 loop : -4.36 (0.16), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.003 0.001 HIS C 290 PHE 0.016 0.001 PHE C 326 TYR 0.016 0.001 TYR E 34 ARG 0.003 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 291 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLN cc_start: 0.7773 (pt0) cc_final: 0.7261 (tp40) REVERT: E 252 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8294 (tm-30) REVERT: E 297 ASP cc_start: 0.5801 (t0) cc_final: 0.5593 (t0) REVERT: E 405 TYR cc_start: 0.8508 (p90) cc_final: 0.8217 (p90) REVERT: A 52 GLN cc_start: 0.8316 (pp30) cc_final: 0.7008 (pp30) REVERT: A 55 ASN cc_start: 0.7877 (t0) cc_final: 0.7366 (t0) REVERT: A 58 GLU cc_start: 0.8394 (mp0) cc_final: 0.7835 (mp0) REVERT: A 267 ASN cc_start: 0.8204 (t0) cc_final: 0.7989 (m-40) REVERT: B 87 ILE cc_start: 0.9236 (pt) cc_final: 0.9010 (pt) REVERT: B 138 TRP cc_start: 0.8219 (m-10) cc_final: 0.7490 (m-90) REVERT: B 210 LEU cc_start: 0.8577 (pt) cc_final: 0.8261 (pt) REVERT: B 221 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7918 (ttm170) REVERT: C 158 LYS cc_start: 0.8537 (mttt) cc_final: 0.8050 (mtpt) REVERT: C 244 MET cc_start: 0.7423 (tmm) cc_final: 0.6947 (ttp) REVERT: C 379 ILE cc_start: 0.8246 (pt) cc_final: 0.7895 (tt) REVERT: C 390 ARG cc_start: 0.6879 (tpt90) cc_final: 0.5913 (tpt90) REVERT: D 158 LYS cc_start: 0.7919 (mttt) cc_final: 0.7449 (pttt) outliers start: 2 outliers final: 0 residues processed: 293 average time/residue: 0.2690 time to fit residues: 110.3480 Evaluate side-chains 213 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 0.0170 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 0.0020 chunk 154 optimal weight: 2.9990 overall best weight: 0.7828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN E 414 ASN E 455 GLN A 69 ASN B 56 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 138 GLN C 176 GLN C 350 ASN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN D 145 GLN D 164 GLN D 197 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13259 Z= 0.195 Angle : 0.698 9.971 18106 Z= 0.346 Chirality : 0.045 0.158 2146 Planarity : 0.005 0.075 2322 Dihedral : 7.380 63.548 1915 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 1.59 % Allowed : 15.81 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.18), residues: 1699 helix: -2.35 (0.18), residues: 682 sheet: -3.91 (0.37), residues: 109 loop : -3.87 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 138 HIS 0.002 0.001 HIS C 290 PHE 0.016 0.001 PHE B 126 TYR 0.016 0.001 TYR E 275 ARG 0.006 0.000 ARG E 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 252 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8235 (tm-30) REVERT: E 270 GLU cc_start: 0.8670 (pp20) cc_final: 0.7890 (pp20) REVERT: E 414 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7501 (p0) REVERT: A 26 TRP cc_start: 0.7809 (m100) cc_final: 0.7330 (m-90) REVERT: A 52 GLN cc_start: 0.8384 (pp30) cc_final: 0.7066 (pp30) REVERT: A 55 ASN cc_start: 0.7817 (t0) cc_final: 0.7577 (t0) REVERT: A 58 GLU cc_start: 0.8311 (mp0) cc_final: 0.7639 (mp0) REVERT: A 267 ASN cc_start: 0.8120 (t0) cc_final: 0.7868 (m-40) REVERT: B 87 ILE cc_start: 0.9363 (pt) cc_final: 0.9131 (pt) REVERT: B 97 ARG cc_start: 0.8574 (mmm160) cc_final: 0.8250 (mmm160) REVERT: B 138 TRP cc_start: 0.8555 (m-10) cc_final: 0.7713 (m-90) REVERT: B 197 THR cc_start: 0.8932 (t) cc_final: 0.8716 (t) REVERT: B 221 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7919 (ttm170) REVERT: B 264 GLN cc_start: 0.8648 (pp30) cc_final: 0.8347 (pp30) REVERT: C 168 ASN cc_start: 0.8380 (p0) cc_final: 0.8077 (p0) REVERT: C 244 MET cc_start: 0.7383 (tmm) cc_final: 0.6967 (ttp) REVERT: C 390 ARG cc_start: 0.6817 (tpt90) cc_final: 0.5904 (tpt90) REVERT: D 158 LYS cc_start: 0.7852 (mttt) cc_final: 0.7440 (pttt) REVERT: D 166 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8757 (pp) outliers start: 21 outliers final: 10 residues processed: 250 average time/residue: 0.2445 time to fit residues: 88.2947 Evaluate side-chains 217 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 205 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 166 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN E 414 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13259 Z= 0.263 Angle : 0.695 10.987 18106 Z= 0.346 Chirality : 0.047 0.234 2146 Planarity : 0.005 0.073 2322 Dihedral : 7.203 58.911 1915 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 2.50 % Allowed : 18.31 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.18), residues: 1699 helix: -2.02 (0.19), residues: 686 sheet: -3.45 (0.35), residues: 135 loop : -3.77 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 129 HIS 0.004 0.001 HIS C 290 PHE 0.015 0.001 PHE A 279 TYR 0.013 0.001 TYR E 275 ARG 0.004 0.000 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 166 TRP cc_start: 0.8071 (m100) cc_final: 0.7774 (m100) REVERT: E 252 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8226 (tm-30) REVERT: E 414 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7361 (p0) REVERT: A 52 GLN cc_start: 0.8448 (pp30) cc_final: 0.7086 (pp30) REVERT: A 55 ASN cc_start: 0.7906 (t0) cc_final: 0.7615 (t0) REVERT: A 58 GLU cc_start: 0.8370 (mp0) cc_final: 0.8005 (mp0) REVERT: A 267 ASN cc_start: 0.8105 (t0) cc_final: 0.7861 (m-40) REVERT: B 129 TRP cc_start: 0.8325 (m-90) cc_final: 0.8110 (m-90) REVERT: B 138 TRP cc_start: 0.8516 (m-10) cc_final: 0.7637 (m-90) REVERT: B 220 GLN cc_start: 0.8644 (mm110) cc_final: 0.8419 (mm-40) REVERT: B 221 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7937 (ttm170) REVERT: B 264 GLN cc_start: 0.8657 (pp30) cc_final: 0.8314 (pp30) REVERT: C 168 ASN cc_start: 0.8496 (p0) cc_final: 0.8250 (p0) REVERT: C 244 MET cc_start: 0.7588 (tmm) cc_final: 0.7065 (ttp) REVERT: C 390 ARG cc_start: 0.6835 (tpt90) cc_final: 0.5949 (tpt90) REVERT: D 166 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8799 (pp) outliers start: 33 outliers final: 21 residues processed: 240 average time/residue: 0.2371 time to fit residues: 83.7440 Evaluate side-chains 216 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 375 ASN Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.1980 chunk 116 optimal weight: 0.0370 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13259 Z= 0.193 Angle : 0.659 9.926 18106 Z= 0.328 Chirality : 0.045 0.204 2146 Planarity : 0.005 0.071 2322 Dihedral : 6.928 59.768 1915 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 3.40 % Allowed : 19.59 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.19), residues: 1699 helix: -1.72 (0.19), residues: 688 sheet: -3.26 (0.37), residues: 135 loop : -3.64 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 153 HIS 0.003 0.001 HIS C 290 PHE 0.012 0.001 PHE B 126 TYR 0.011 0.001 TYR A 45 ARG 0.006 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 252 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7771 (tm-30) REVERT: A 52 GLN cc_start: 0.8458 (pp30) cc_final: 0.7120 (pp30) REVERT: A 55 ASN cc_start: 0.7766 (t0) cc_final: 0.7505 (t0) REVERT: A 58 GLU cc_start: 0.8355 (mp0) cc_final: 0.7768 (mp0) REVERT: A 270 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8883 (tt) REVERT: B 130 ARG cc_start: 0.8255 (tpp-160) cc_final: 0.7927 (tpp80) REVERT: B 138 TRP cc_start: 0.8496 (m-10) cc_final: 0.7609 (m-90) REVERT: B 221 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7949 (ttm170) REVERT: B 250 MET cc_start: 0.8515 (mmm) cc_final: 0.7447 (mmm) REVERT: B 264 GLN cc_start: 0.8581 (pp30) cc_final: 0.8306 (pp30) REVERT: C 168 ASN cc_start: 0.8413 (p0) cc_final: 0.8205 (p0) REVERT: C 244 MET cc_start: 0.7432 (tmm) cc_final: 0.6968 (ttp) REVERT: C 390 ARG cc_start: 0.6785 (tpt90) cc_final: 0.5868 (tpt90) REVERT: D 29 MET cc_start: 0.7801 (ppp) cc_final: 0.7536 (ppp) REVERT: D 122 THR cc_start: 0.8920 (t) cc_final: 0.8635 (t) REVERT: D 166 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8779 (pp) outliers start: 45 outliers final: 26 residues processed: 247 average time/residue: 0.2235 time to fit residues: 83.2557 Evaluate side-chains 235 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.0870 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN A 201 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13259 Z= 0.199 Angle : 0.657 9.827 18106 Z= 0.326 Chirality : 0.045 0.209 2146 Planarity : 0.005 0.070 2322 Dihedral : 6.704 57.583 1915 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 3.86 % Allowed : 19.82 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.19), residues: 1699 helix: -1.53 (0.20), residues: 687 sheet: -3.05 (0.36), residues: 147 loop : -3.54 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 153 HIS 0.003 0.001 HIS C 290 PHE 0.021 0.001 PHE B 232 TYR 0.011 0.001 TYR E 378 ARG 0.006 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 217 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 93 LEU cc_start: 0.8609 (pp) cc_final: 0.8361 (pp) REVERT: E 252 GLN cc_start: 0.8501 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 52 GLN cc_start: 0.8466 (pp30) cc_final: 0.7112 (pp30) REVERT: A 55 ASN cc_start: 0.7744 (t0) cc_final: 0.7494 (t0) REVERT: A 58 GLU cc_start: 0.8357 (mp0) cc_final: 0.7761 (mp0) REVERT: A 139 TYR cc_start: 0.8351 (m-80) cc_final: 0.7561 (m-80) REVERT: A 270 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9008 (tt) REVERT: A 284 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8287 (tp) REVERT: B 43 LYS cc_start: 0.8676 (mmtp) cc_final: 0.7858 (mmtp) REVERT: B 130 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.8128 (tpp80) REVERT: B 138 TRP cc_start: 0.8523 (m-10) cc_final: 0.7565 (m-90) REVERT: B 264 GLN cc_start: 0.8529 (pp30) cc_final: 0.8262 (pp30) REVERT: C 168 ASN cc_start: 0.8406 (p0) cc_final: 0.8204 (p0) REVERT: C 232 ASN cc_start: 0.8161 (t0) cc_final: 0.7831 (t0) REVERT: C 244 MET cc_start: 0.7461 (tmm) cc_final: 0.6984 (ttp) REVERT: C 390 ARG cc_start: 0.6799 (tpt90) cc_final: 0.6054 (tpt90) REVERT: D 115 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8534 (mt) REVERT: D 122 THR cc_start: 0.8924 (t) cc_final: 0.8640 (t) REVERT: D 166 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8749 (pp) REVERT: D 351 GLN cc_start: 0.8164 (pm20) cc_final: 0.7949 (mp10) outliers start: 51 outliers final: 26 residues processed: 256 average time/residue: 0.2301 time to fit residues: 88.1906 Evaluate side-chains 235 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 96 optimal weight: 0.0770 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 0.3980 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13259 Z= 0.167 Angle : 0.656 12.036 18106 Z= 0.320 Chirality : 0.044 0.204 2146 Planarity : 0.005 0.067 2322 Dihedral : 6.460 59.266 1915 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 3.33 % Allowed : 21.03 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.19), residues: 1699 helix: -1.41 (0.20), residues: 698 sheet: -2.81 (0.36), residues: 141 loop : -3.47 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 166 HIS 0.003 0.001 HIS C 325 PHE 0.024 0.001 PHE B 232 TYR 0.013 0.001 TYR A 45 ARG 0.003 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: E 93 LEU cc_start: 0.8537 (pp) cc_final: 0.8263 (pp) REVERT: E 252 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 52 GLN cc_start: 0.8433 (pp30) cc_final: 0.7095 (pp30) REVERT: A 55 ASN cc_start: 0.7663 (t0) cc_final: 0.7409 (t0) REVERT: A 58 GLU cc_start: 0.8336 (mp0) cc_final: 0.7709 (mp0) REVERT: A 270 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8890 (tt) REVERT: A 284 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8303 (tp) REVERT: B 138 TRP cc_start: 0.8505 (m-10) cc_final: 0.7567 (m-90) REVERT: C 232 ASN cc_start: 0.8183 (t0) cc_final: 0.7891 (t0) REVERT: C 244 MET cc_start: 0.7467 (tmm) cc_final: 0.6959 (ttp) REVERT: C 390 ARG cc_start: 0.6843 (tpt90) cc_final: 0.5932 (tpt90) REVERT: D 29 MET cc_start: 0.7794 (ppp) cc_final: 0.7482 (ppp) REVERT: D 115 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8615 (mt) REVERT: D 122 THR cc_start: 0.8887 (t) cc_final: 0.8576 (t) REVERT: D 158 LYS cc_start: 0.7623 (mtpp) cc_final: 0.6925 (mmmt) REVERT: D 166 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8752 (pp) REVERT: D 351 GLN cc_start: 0.8214 (pm20) cc_final: 0.8007 (pm20) outliers start: 44 outliers final: 29 residues processed: 253 average time/residue: 0.2215 time to fit residues: 84.0119 Evaluate side-chains 237 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 0.0270 chunk 163 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 145 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13259 Z= 0.172 Angle : 0.651 9.681 18106 Z= 0.322 Chirality : 0.045 0.184 2146 Planarity : 0.005 0.067 2322 Dihedral : 6.299 59.755 1915 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 3.18 % Allowed : 21.86 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.19), residues: 1699 helix: -1.29 (0.20), residues: 697 sheet: -2.77 (0.39), residues: 134 loop : -3.34 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 166 HIS 0.002 0.001 HIS C 325 PHE 0.032 0.001 PHE B 183 TYR 0.027 0.001 TYR E 405 ARG 0.005 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 93 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8368 (pp) REVERT: E 252 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 52 GLN cc_start: 0.8426 (pp30) cc_final: 0.7058 (pp30) REVERT: A 55 ASN cc_start: 0.7619 (t0) cc_final: 0.7374 (t0) REVERT: A 58 GLU cc_start: 0.8315 (mp0) cc_final: 0.7697 (mp0) REVERT: A 270 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8880 (tt) REVERT: A 284 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8290 (tp) REVERT: B 138 TRP cc_start: 0.8500 (m-10) cc_final: 0.7586 (m-90) REVERT: C 168 ASN cc_start: 0.8094 (p0) cc_final: 0.7748 (p0) REVERT: C 232 ASN cc_start: 0.8170 (t0) cc_final: 0.7864 (t0) REVERT: C 244 MET cc_start: 0.7409 (tmm) cc_final: 0.7092 (ttp) REVERT: C 390 ARG cc_start: 0.6807 (tpt90) cc_final: 0.5846 (tpt90) REVERT: D 122 THR cc_start: 0.8861 (t) cc_final: 0.8647 (t) REVERT: D 158 LYS cc_start: 0.7571 (mtpp) cc_final: 0.6857 (mmmt) REVERT: D 166 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8759 (pp) REVERT: D 170 ASP cc_start: 0.7314 (p0) cc_final: 0.6708 (p0) REVERT: D 351 GLN cc_start: 0.8243 (pm20) cc_final: 0.7987 (pm20) outliers start: 42 outliers final: 30 residues processed: 246 average time/residue: 0.2206 time to fit residues: 82.7851 Evaluate side-chains 242 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 chunk 104 optimal weight: 0.0570 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 128 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.3250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 13259 Z= 0.165 Angle : 0.643 9.898 18106 Z= 0.317 Chirality : 0.044 0.189 2146 Planarity : 0.005 0.066 2322 Dihedral : 6.041 58.311 1915 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.87 % Allowed : 23.07 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.19), residues: 1699 helix: -1.13 (0.20), residues: 706 sheet: -2.66 (0.41), residues: 122 loop : -3.22 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS C 94 PHE 0.031 0.001 PHE A 279 TYR 0.015 0.001 TYR E 405 ARG 0.002 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 93 LEU cc_start: 0.8558 (pp) cc_final: 0.8264 (pp) REVERT: E 252 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7828 (tm-30) REVERT: E 297 ASP cc_start: 0.5844 (t0) cc_final: 0.5293 (t70) REVERT: A 26 TRP cc_start: 0.7682 (m100) cc_final: 0.7155 (m-90) REVERT: A 52 GLN cc_start: 0.8416 (pp30) cc_final: 0.7046 (pp30) REVERT: A 58 GLU cc_start: 0.8292 (mp0) cc_final: 0.7662 (mp0) REVERT: A 270 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8839 (tt) REVERT: A 284 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8283 (tp) REVERT: B 221 ARG cc_start: 0.8160 (ttm170) cc_final: 0.6892 (tpt170) REVERT: B 233 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7477 (p) REVERT: B 238 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.4981 (p90) REVERT: C 168 ASN cc_start: 0.8107 (p0) cc_final: 0.7796 (p0) REVERT: C 232 ASN cc_start: 0.8162 (t0) cc_final: 0.7888 (t0) REVERT: C 244 MET cc_start: 0.7385 (tmm) cc_final: 0.7060 (ttp) REVERT: C 390 ARG cc_start: 0.6777 (tpt90) cc_final: 0.5863 (tpt90) REVERT: D 29 MET cc_start: 0.7760 (ppp) cc_final: 0.7439 (ppp) REVERT: D 158 LYS cc_start: 0.7569 (mtpp) cc_final: 0.7246 (pttp) REVERT: D 170 ASP cc_start: 0.7128 (p0) cc_final: 0.6607 (p0) REVERT: D 222 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7434 (t) REVERT: D 351 GLN cc_start: 0.8257 (pm20) cc_final: 0.7945 (pm20) outliers start: 38 outliers final: 25 residues processed: 250 average time/residue: 0.2229 time to fit residues: 84.1381 Evaluate side-chains 235 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 368 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.0870 chunk 143 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 0.0270 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 0.0870 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13259 Z= 0.181 Angle : 0.660 14.892 18106 Z= 0.319 Chirality : 0.044 0.152 2146 Planarity : 0.005 0.067 2322 Dihedral : 5.961 57.277 1915 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.72 % Allowed : 24.28 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.19), residues: 1699 helix: -1.05 (0.20), residues: 704 sheet: -2.48 (0.38), residues: 141 loop : -3.19 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 166 HIS 0.002 0.001 HIS D 94 PHE 0.025 0.001 PHE A 279 TYR 0.011 0.001 TYR E 405 ARG 0.002 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 252 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 297 ASP cc_start: 0.5868 (t0) cc_final: 0.5297 (t70) REVERT: A 26 TRP cc_start: 0.7666 (m100) cc_final: 0.7135 (m-90) REVERT: A 45 TYR cc_start: 0.8493 (t80) cc_final: 0.8288 (t80) REVERT: A 52 GLN cc_start: 0.8492 (pp30) cc_final: 0.7163 (pp30) REVERT: A 270 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8837 (tt) REVERT: A 284 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8301 (tp) REVERT: B 221 ARG cc_start: 0.8152 (ttm170) cc_final: 0.6841 (tpt170) REVERT: B 233 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7411 (p) REVERT: B 238 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.4988 (p90) REVERT: C 168 ASN cc_start: 0.8160 (p0) cc_final: 0.7872 (p0) REVERT: C 232 ASN cc_start: 0.8217 (t0) cc_final: 0.7947 (t0) REVERT: C 244 MET cc_start: 0.7442 (tmm) cc_final: 0.7096 (ttp) REVERT: C 390 ARG cc_start: 0.6776 (tpt90) cc_final: 0.5859 (tpt90) REVERT: D 29 MET cc_start: 0.7765 (ppp) cc_final: 0.7445 (ppp) REVERT: D 158 LYS cc_start: 0.7645 (mtpp) cc_final: 0.7240 (pttt) REVERT: D 170 ASP cc_start: 0.7101 (p0) cc_final: 0.6582 (p0) REVERT: D 351 GLN cc_start: 0.8275 (pm20) cc_final: 0.7974 (pm20) outliers start: 36 outliers final: 27 residues processed: 235 average time/residue: 0.2190 time to fit residues: 77.9923 Evaluate side-chains 238 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 160 PHE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 169 optimal weight: 0.4980 chunk 155 optimal weight: 0.0770 chunk 134 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 GLN E 76 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13259 Z= 0.166 Angle : 0.651 13.753 18106 Z= 0.315 Chirality : 0.044 0.175 2146 Planarity : 0.004 0.064 2322 Dihedral : 5.828 56.142 1915 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 3.03 % Allowed : 24.05 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.20), residues: 1699 helix: -0.97 (0.20), residues: 701 sheet: -2.36 (0.41), residues: 127 loop : -3.08 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 166 HIS 0.003 0.001 HIS D 94 PHE 0.026 0.001 PHE A 279 TYR 0.010 0.001 TYR B 23 ARG 0.003 0.000 ARG A 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 252 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7874 (tm-30) REVERT: E 399 GLN cc_start: 0.7270 (pp30) cc_final: 0.7021 (pp30) REVERT: A 26 TRP cc_start: 0.7642 (m100) cc_final: 0.7135 (m-90) REVERT: A 52 GLN cc_start: 0.8506 (pp30) cc_final: 0.7200 (pp30) REVERT: A 218 MET cc_start: 0.8455 (mmm) cc_final: 0.8079 (mtt) REVERT: A 270 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8831 (tt) REVERT: A 284 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8296 (tp) REVERT: B 43 LYS cc_start: 0.8652 (mmtp) cc_final: 0.8353 (mmtp) REVERT: B 221 ARG cc_start: 0.8142 (ttm170) cc_final: 0.6867 (tpt170) REVERT: B 238 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.4959 (p90) REVERT: C 168 ASN cc_start: 0.8095 (p0) cc_final: 0.7877 (p0) REVERT: C 232 ASN cc_start: 0.8168 (t0) cc_final: 0.7918 (t0) REVERT: C 244 MET cc_start: 0.7385 (tmm) cc_final: 0.7048 (ttp) REVERT: C 390 ARG cc_start: 0.6741 (tpt90) cc_final: 0.5815 (tpt90) REVERT: D 29 MET cc_start: 0.7757 (ppp) cc_final: 0.7422 (ppp) REVERT: D 115 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8643 (mt) REVERT: D 158 LYS cc_start: 0.7560 (mtpp) cc_final: 0.7191 (pttp) REVERT: D 170 ASP cc_start: 0.7103 (p0) cc_final: 0.6571 (p0) REVERT: D 351 GLN cc_start: 0.8288 (pm20) cc_final: 0.7993 (pm20) outliers start: 40 outliers final: 28 residues processed: 243 average time/residue: 0.2179 time to fit residues: 79.9980 Evaluate side-chains 237 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 160 PHE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 0.0170 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 138 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.0070 chunk 118 optimal weight: 0.0070 chunk 7 optimal weight: 20.0000 overall best weight: 0.2232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120429 restraints weight = 25285.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123524 restraints weight = 13656.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.125598 restraints weight = 8828.130| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13259 Z= 0.164 Angle : 0.659 14.131 18106 Z= 0.319 Chirality : 0.044 0.154 2146 Planarity : 0.004 0.064 2322 Dihedral : 5.747 55.524 1915 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.50 % Allowed : 24.74 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.20), residues: 1699 helix: -0.81 (0.21), residues: 694 sheet: -2.28 (0.42), residues: 124 loop : -3.02 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 166 HIS 0.010 0.001 HIS A 109 PHE 0.025 0.001 PHE A 279 TYR 0.018 0.001 TYR A 45 ARG 0.003 0.000 ARG E 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2846.04 seconds wall clock time: 52 minutes 24.55 seconds (3144.55 seconds total)