Starting phenix.real_space_refine on Tue Feb 13 19:37:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1t_32949/02_2024/7x1t_32949_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1t_32949/02_2024/7x1t_32949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1t_32949/02_2024/7x1t_32949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1t_32949/02_2024/7x1t_32949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1t_32949/02_2024/7x1t_32949_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1t_32949/02_2024/7x1t_32949_updated.pdb" } resolution = 3.26 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= 0.003 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4790 2.51 5 N 1282 2.21 5 O 1373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2": not complete - not flipped Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7488 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 299 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1958 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1578 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 148 Chain: "C" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2288 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 324} Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 13, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 178 Chain: "D" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1336 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 4 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 188 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {'NH2': 1, 'RGI': 1} Classifications: {'peptide': 3, 'undetermined': 2} Link IDs: {'NH2_CTERM': 1, 'PCIS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="RGI E 1 " pdbres="ASP E 2 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'RGI:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 4.70, per 1000 atoms: 0.63 Number of scatterers: 7488 At special positions: 0 Unit cell: (86.67, 114.49, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1373 8.00 N 1282 7.00 C 4790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB HIS E 3 " pdb=" CB PRO E 4 " Number of C-beta restraints generated: 2024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 20.0% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'F' and resid 30 through 43 removed outlier: 3.687A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 35 removed outlier: 3.558A pdb=" N THR A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.650A pdb=" N VAL A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 62 No H-bonds generated for 'chain 'A' and resid 59 through 62' Processing helix chain 'A' and resid 65 through 68 No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 70 through 73 No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.876A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 139 through 163 removed outlier: 3.737A pdb=" N LYS A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 161 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 190 through 193 No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 196 through 199 No H-bonds generated for 'chain 'A' and resid 196 through 199' Processing helix chain 'A' and resid 202 through 205 No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 209 through 218 removed outlier: 4.397A pdb=" N ILE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.572A pdb=" N VAL A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 4.367A pdb=" N VAL A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.580A pdb=" N PHE A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 316 through 319 No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.753A pdb=" N ASN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 119 through 123' Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 184 through 201 removed outlier: 3.949A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.527A pdb=" N LYS B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.572A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 15 through 19' Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing sheet with id= A, first strand: chain 'B' and resid 36 through 39 removed outlier: 7.347A pdb=" N ALA B 105 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU B 39 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE B 107 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER B 138 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE B 108 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE B 140 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL B 110 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B 142 " --> pdb=" O VAL B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 69 through 75 Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.574A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 121 through 125 removed outlier: 3.508A pdb=" N ALA C 113 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 178 through 180 removed outlier: 3.735A pdb=" N THR C 159 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 220 through 223 removed outlier: 3.885A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.626A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 275 through 277 removed outlier: 3.606A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 337 through 339 Processing sheet with id= J, first strand: chain 'D' and resid 194 through 196 removed outlier: 3.562A pdb=" N SER D 196 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1215 1.29 - 1.43: 1986 1.43 - 1.56: 4364 1.56 - 1.69: 5 1.69 - 1.83: 57 Bond restraints: 7627 Sorted by residual: bond pdb=" C HIS E 3 " pdb=" N PRO E 4 " ideal model delta sigma weight residual 1.341 1.492 -0.151 1.60e-02 3.91e+03 8.94e+01 bond pdb=" N PRO E 4 " pdb=" CD PRO E 4 " ideal model delta sigma weight residual 1.473 1.352 0.121 1.40e-02 5.10e+03 7.52e+01 bond pdb=" C ASP E 2 " pdb=" N HIS E 3 " ideal model delta sigma weight residual 1.331 1.485 -0.154 2.07e-02 2.33e+03 5.55e+01 bond pdb=" C PRO E 4 " pdb=" N NH2 E 5 " ideal model delta sigma weight residual 1.329 1.431 -0.102 1.40e-02 5.10e+03 5.32e+01 bond pdb=" CA HIS E 3 " pdb=" C HIS E 3 " ideal model delta sigma weight residual 1.524 1.607 -0.083 1.26e-02 6.30e+03 4.38e+01 ... (remaining 7622 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.36: 174 106.36 - 113.26: 4158 113.26 - 120.17: 2707 120.17 - 127.08: 3333 127.08 - 133.98: 75 Bond angle restraints: 10447 Sorted by residual: angle pdb=" CA ASP E 2 " pdb=" CB ASP E 2 " pdb=" CG ASP E 2 " ideal model delta sigma weight residual 112.60 119.53 -6.93 1.00e+00 1.00e+00 4.81e+01 angle pdb=" N ASP E 2 " pdb=" CA ASP E 2 " pdb=" CB ASP E 2 " ideal model delta sigma weight residual 110.50 120.02 -9.52 1.70e+00 3.46e-01 3.14e+01 angle pdb=" C VAL D 64 " pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C TRP A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta sigma weight residual 120.38 126.62 -6.24 1.37e+00 5.33e-01 2.08e+01 angle pdb=" N ASP A 173 " pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 114.62 109.66 4.96 1.14e+00 7.69e-01 1.89e+01 ... (remaining 10442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 4166 21.88 - 43.76: 235 43.76 - 65.64: 18 65.64 - 87.53: 2 87.53 - 109.41: 2 Dihedral angle restraints: 4423 sinusoidal: 1294 harmonic: 3129 Sorted by residual: dihedral pdb=" CA LEU A 80 " pdb=" C LEU A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual 180.00 134.70 45.30 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA TRP D 47 " pdb=" C TRP D 47 " pdb=" N VAL D 48 " pdb=" CA VAL D 48 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP E 2 " pdb=" CB ASP E 2 " pdb=" CG ASP E 2 " pdb=" OD1 ASP E 2 " ideal model delta sinusoidal sigma weight residual 70.00 179.41 -109.41 1 2.00e+01 2.50e-03 3.20e+01 ... (remaining 4420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.196: 1285 1.196 - 2.392: 0 2.392 - 3.589: 0 3.589 - 4.785: 1 4.785 - 5.981: 1 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CA PRO E 4 " pdb=" N PRO E 4 " pdb=" C PRO E 4 " pdb=" CB PRO E 4 " both_signs ideal model delta sigma weight residual False 2.72 -3.26 5.98 2.00e-01 2.50e+01 8.94e+02 chirality pdb=" CA HIS E 3 " pdb=" N HIS E 3 " pdb=" C HIS E 3 " pdb=" CB HIS E 3 " both_signs ideal model delta sigma weight residual False 2.51 -2.16 4.67 2.00e-01 2.50e+01 5.45e+02 chirality pdb=" CB ILE D 204 " pdb=" CA ILE D 204 " pdb=" CG1 ILE D 204 " pdb=" CG2 ILE D 204 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 1284 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 80 " 0.076 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 81 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 316 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO A 317 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 50 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C TYR D 50 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR D 50 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE D 51 " 0.017 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 1549 2.77 - 3.48: 9690 3.48 - 4.19: 17123 4.19 - 4.90: 29911 Nonbonded interactions: 58275 Sorted by model distance: nonbonded pdb=" NH1 ARG A 306 " pdb=" N HIS E 3 " model vdw 1.351 3.200 nonbonded pdb=" C RGI E 1 " pdb=" N ASP E 2 " model vdw 1.509 3.350 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.251 2.440 nonbonded pdb=" NH1 ARG A 123 " pdb=" OH TYR A 211 " model vdw 2.314 2.520 nonbonded pdb=" OG1 THR C 321 " pdb=" OD1 ASP C 323 " model vdw 2.316 2.440 ... (remaining 58270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.170 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.900 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 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 : 0.007 0.186 7627 Z= 0.486 Angle : 0.977 11.451 10447 Z= 0.544 Chirality : 0.219 5.981 1287 Planarity : 0.007 0.116 1330 Dihedral : 13.895 109.407 2393 Min Nonbonded Distance : 1.351 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.93 % Favored : 90.98 % Rotamer: Outliers : 0.92 % Allowed : 10.08 % Favored : 89.01 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -5.73 (0.19), residues: 1053 helix: -5.02 (0.09), residues: 314 sheet: -3.30 (0.32), residues: 170 loop : -3.25 (0.22), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 96 HIS 0.014 0.002 HIS C 225 PHE 0.020 0.002 PHE C 234 TYR 0.027 0.002 TYR D 178 ARG 0.007 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6974 (mmt180) REVERT: A 93 TYR cc_start: 0.7569 (m-80) cc_final: 0.7260 (m-80) REVERT: A 143 LYS cc_start: 0.8097 (mttt) cc_final: 0.7485 (mmtt) REVERT: A 162 PHE cc_start: 0.7406 (m-80) cc_final: 0.7139 (m-10) REVERT: A 221 ASN cc_start: 0.7158 (p0) cc_final: 0.6941 (p0) REVERT: A 322 LEU cc_start: 0.8062 (tp) cc_final: 0.7738 (tp) REVERT: C 45 MET cc_start: 0.8382 (mpp) cc_final: 0.8154 (mmt) REVERT: C 61 MET cc_start: 0.7847 (ppp) cc_final: 0.7612 (ppp) REVERT: C 127 LYS cc_start: 0.8332 (mttm) cc_final: 0.7850 (mmtt) REVERT: D 216 TYR cc_start: 0.4209 (m-80) cc_final: 0.3931 (m-80) REVERT: E 3 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.6880 (m90) outliers start: 6 outliers final: 2 residues processed: 182 average time/residue: 0.1751 time to fit residues: 43.5285 Evaluate side-chains 144 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 312 ASN A 321 ASN B 22 ASN C 32 GLN C 62 HIS C 295 ASN D 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7627 Z= 0.315 Angle : 0.738 15.648 10447 Z= 0.380 Chirality : 0.053 0.878 1287 Planarity : 0.006 0.099 1330 Dihedral : 6.691 46.742 1142 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.80 % Allowed : 16.64 % Favored : 77.56 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -5.11 (0.21), residues: 1053 helix: -4.31 (0.16), residues: 314 sheet: -3.00 (0.34), residues: 181 loop : -2.95 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.020 0.002 PHE A 331 TYR 0.022 0.002 TYR D 178 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7586 (m-80) cc_final: 0.7259 (m-80) REVERT: A 143 LYS cc_start: 0.8105 (mttt) cc_final: 0.7545 (mmtt) REVERT: B 29 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7629 (mtmm) REVERT: C 45 MET cc_start: 0.8492 (mpp) cc_final: 0.8228 (mmp) REVERT: C 61 MET cc_start: 0.8056 (ppp) cc_final: 0.7563 (ppp) REVERT: C 220 GLN cc_start: 0.8751 (mt0) cc_final: 0.8409 (mt0) REVERT: C 290 ASP cc_start: 0.6079 (m-30) cc_final: 0.5358 (m-30) outliers start: 38 outliers final: 24 residues processed: 165 average time/residue: 0.1660 time to fit residues: 38.2788 Evaluate side-chains 159 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 3 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 103 optimal weight: 0.0010 chunk 85 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN D 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7627 Z= 0.164 Angle : 0.637 18.017 10447 Z= 0.318 Chirality : 0.045 0.265 1287 Planarity : 0.005 0.093 1330 Dihedral : 5.881 41.797 1140 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.19 % Allowed : 20.00 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -4.58 (0.22), residues: 1053 helix: -3.77 (0.20), residues: 318 sheet: -2.71 (0.36), residues: 180 loop : -2.67 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS D 220 PHE 0.010 0.001 PHE B 192 TYR 0.019 0.001 TYR D 103 ARG 0.003 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7413 (m-80) cc_final: 0.7106 (m-80) REVERT: A 143 LYS cc_start: 0.8086 (mttt) cc_final: 0.7536 (mmtt) REVERT: B 29 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7565 (mtmm) REVERT: C 45 MET cc_start: 0.8416 (mpp) cc_final: 0.8174 (mmp) REVERT: C 127 LYS cc_start: 0.8273 (mttm) cc_final: 0.7918 (mmtt) REVERT: C 220 GLN cc_start: 0.8728 (mt0) cc_final: 0.8233 (tt0) REVERT: C 225 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.5751 (m170) REVERT: C 273 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7868 (mp) REVERT: C 290 ASP cc_start: 0.5727 (m-30) cc_final: 0.5236 (m-30) outliers start: 34 outliers final: 26 residues processed: 166 average time/residue: 0.1722 time to fit residues: 39.4369 Evaluate side-chains 162 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 3 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 0.0020 chunk 64 optimal weight: 0.0170 chunk 95 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 overall best weight: 0.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7627 Z= 0.139 Angle : 0.592 16.900 10447 Z= 0.295 Chirality : 0.043 0.200 1287 Planarity : 0.005 0.088 1330 Dihedral : 5.371 38.235 1140 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.34 % Allowed : 21.68 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -4.22 (0.23), residues: 1053 helix: -3.40 (0.22), residues: 321 sheet: -2.36 (0.36), residues: 188 loop : -2.54 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 225 PHE 0.018 0.001 PHE A 139 TYR 0.015 0.001 TYR D 103 ARG 0.004 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7331 (m-80) cc_final: 0.7076 (m-80) REVERT: A 143 LYS cc_start: 0.8099 (mttt) cc_final: 0.7580 (mmtt) REVERT: A 162 PHE cc_start: 0.7373 (m-80) cc_final: 0.7137 (m-10) REVERT: C 45 MET cc_start: 0.8401 (mpp) cc_final: 0.8164 (mmp) REVERT: C 61 MET cc_start: 0.7791 (ppp) cc_final: 0.7419 (ppp) REVERT: C 87 THR cc_start: 0.7626 (m) cc_final: 0.7424 (p) REVERT: C 127 LYS cc_start: 0.8248 (mttm) cc_final: 0.7900 (mmtt) REVERT: C 220 GLN cc_start: 0.8652 (mt0) cc_final: 0.8197 (tt0) REVERT: C 228 ASP cc_start: 0.7950 (p0) cc_final: 0.7280 (p0) REVERT: C 273 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7850 (mp) REVERT: C 290 ASP cc_start: 0.5438 (m-30) cc_final: 0.4994 (m-30) outliers start: 35 outliers final: 26 residues processed: 166 average time/residue: 0.1721 time to fit residues: 39.4591 Evaluate side-chains 156 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 3 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.0470 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7627 Z= 0.344 Angle : 0.700 15.885 10447 Z= 0.354 Chirality : 0.048 0.315 1287 Planarity : 0.006 0.093 1330 Dihedral : 5.907 40.148 1140 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 7.79 % Allowed : 21.68 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -4.17 (0.24), residues: 1053 helix: -3.28 (0.23), residues: 314 sheet: -2.52 (0.35), residues: 192 loop : -2.50 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 82 HIS 0.005 0.002 HIS B 209 PHE 0.019 0.002 PHE B 108 TYR 0.028 0.002 TYR D 50 ARG 0.006 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 141 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7652 (m-80) cc_final: 0.7322 (m-80) REVERT: A 143 LYS cc_start: 0.8117 (mttt) cc_final: 0.7541 (mmtt) REVERT: A 162 PHE cc_start: 0.7499 (m-80) cc_final: 0.7157 (m-10) REVERT: B 29 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7470 (mtmm) REVERT: B 230 ASP cc_start: 0.8389 (t0) cc_final: 0.8097 (t0) REVERT: C 45 MET cc_start: 0.8539 (mpp) cc_final: 0.8276 (mmp) REVERT: C 61 MET cc_start: 0.8112 (ppp) cc_final: 0.7782 (ppp) REVERT: C 220 GLN cc_start: 0.8740 (mt0) cc_final: 0.8248 (tt0) REVERT: C 234 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: C 273 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7895 (mp) outliers start: 51 outliers final: 40 residues processed: 167 average time/residue: 0.1771 time to fit residues: 40.8327 Evaluate side-chains 179 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 3 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 ASN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7627 Z= 0.233 Angle : 0.635 14.941 10447 Z= 0.322 Chirality : 0.046 0.275 1287 Planarity : 0.005 0.093 1330 Dihedral : 5.640 39.892 1140 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 6.56 % Allowed : 23.82 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -4.05 (0.24), residues: 1053 helix: -3.08 (0.24), residues: 315 sheet: -2.56 (0.35), residues: 196 loop : -2.44 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 225 PHE 0.019 0.001 PHE A 139 TYR 0.024 0.002 TYR D 50 ARG 0.003 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7592 (m-80) cc_final: 0.7276 (m-80) REVERT: A 143 LYS cc_start: 0.8083 (mttt) cc_final: 0.7529 (mmtt) REVERT: A 162 PHE cc_start: 0.7503 (m-80) cc_final: 0.7127 (m-10) REVERT: B 29 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7472 (mtmm) REVERT: B 154 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5353 (pp) REVERT: C 45 MET cc_start: 0.8458 (mpp) cc_final: 0.8220 (mmp) REVERT: C 61 MET cc_start: 0.8071 (ppp) cc_final: 0.7792 (ppp) REVERT: C 220 GLN cc_start: 0.8691 (mt0) cc_final: 0.8242 (tt0) REVERT: C 234 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.6228 (m-80) REVERT: C 273 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7895 (mp) REVERT: D 4 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7351 (tt) outliers start: 43 outliers final: 33 residues processed: 170 average time/residue: 0.1676 time to fit residues: 39.5606 Evaluate side-chains 167 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7627 Z= 0.179 Angle : 0.594 13.969 10447 Z= 0.302 Chirality : 0.044 0.236 1287 Planarity : 0.005 0.089 1330 Dihedral : 5.245 37.733 1138 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 6.26 % Allowed : 23.51 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -3.84 (0.24), residues: 1053 helix: -2.83 (0.25), residues: 318 sheet: -2.26 (0.35), residues: 197 loop : -2.44 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS C 225 PHE 0.014 0.001 PHE A 327 TYR 0.028 0.001 TYR D 50 ARG 0.002 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7451 (m-80) cc_final: 0.7153 (m-80) REVERT: A 143 LYS cc_start: 0.8023 (mttt) cc_final: 0.7489 (mmtt) REVERT: A 162 PHE cc_start: 0.7517 (m-80) cc_final: 0.7160 (m-10) REVERT: B 29 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7390 (mtmm) REVERT: C 45 MET cc_start: 0.8434 (mpp) cc_final: 0.8207 (mmp) REVERT: C 61 MET cc_start: 0.7969 (ppp) cc_final: 0.7754 (ppp) REVERT: C 127 LYS cc_start: 0.8179 (mttm) cc_final: 0.7865 (mmtt) REVERT: C 220 GLN cc_start: 0.8653 (mt0) cc_final: 0.8234 (tt0) REVERT: C 234 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.6122 (m-80) REVERT: C 273 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7903 (mp) REVERT: D 4 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7204 (tt) outliers start: 41 outliers final: 31 residues processed: 171 average time/residue: 0.1605 time to fit residues: 38.8098 Evaluate side-chains 169 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.0770 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 50 optimal weight: 0.0370 chunk 9 optimal weight: 0.0470 chunk 79 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7627 Z= 0.210 Angle : 0.612 13.938 10447 Z= 0.310 Chirality : 0.045 0.245 1287 Planarity : 0.005 0.089 1330 Dihedral : 5.255 37.394 1138 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 6.72 % Allowed : 23.97 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -3.71 (0.24), residues: 1053 helix: -2.69 (0.25), residues: 317 sheet: -2.20 (0.35), residues: 199 loop : -2.37 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.005 0.001 HIS C 225 PHE 0.023 0.001 PHE A 139 TYR 0.030 0.002 TYR D 50 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7513 (m-80) cc_final: 0.7226 (m-80) REVERT: A 143 LYS cc_start: 0.8020 (mttt) cc_final: 0.7486 (mmtt) REVERT: A 162 PHE cc_start: 0.7541 (m-80) cc_final: 0.7146 (m-10) REVERT: C 45 MET cc_start: 0.8534 (mpp) cc_final: 0.8331 (mmp) REVERT: C 127 LYS cc_start: 0.8170 (mttm) cc_final: 0.7900 (mmtt) REVERT: C 220 GLN cc_start: 0.8656 (mt0) cc_final: 0.8243 (tt0) REVERT: C 234 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: C 273 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7926 (mp) REVERT: D 4 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7277 (tt) outliers start: 44 outliers final: 39 residues processed: 169 average time/residue: 0.1664 time to fit residues: 39.1362 Evaluate side-chains 179 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0370 chunk 94 optimal weight: 0.8980 chunk 96 optimal weight: 0.0010 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN B 209 HIS C 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7627 Z= 0.157 Angle : 0.585 13.278 10447 Z= 0.293 Chirality : 0.044 0.244 1287 Planarity : 0.004 0.086 1330 Dihedral : 4.884 34.922 1138 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.89 % Allowed : 26.11 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -3.48 (0.25), residues: 1053 helix: -2.48 (0.26), residues: 317 sheet: -2.05 (0.35), residues: 204 loop : -2.26 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS C 225 PHE 0.016 0.001 PHE A 327 TYR 0.025 0.001 TYR D 50 ARG 0.003 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 37 LEU cc_start: 0.7885 (mm) cc_final: 0.7176 (mp) REVERT: A 93 TYR cc_start: 0.7319 (m-80) cc_final: 0.7084 (m-80) REVERT: A 143 LYS cc_start: 0.7989 (mttt) cc_final: 0.7465 (mmtt) REVERT: A 162 PHE cc_start: 0.7451 (m-80) cc_final: 0.7062 (m-10) REVERT: B 29 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7416 (mtmm) REVERT: B 75 GLN cc_start: 0.7545 (tm130) cc_final: 0.7001 (tm-30) REVERT: C 45 MET cc_start: 0.8445 (mpp) cc_final: 0.8204 (mmp) REVERT: C 48 ARG cc_start: 0.7268 (mmt180) cc_final: 0.7062 (mmt90) REVERT: C 61 MET cc_start: 0.7532 (ppp) cc_final: 0.6528 (ppp) REVERT: C 127 LYS cc_start: 0.8139 (mttm) cc_final: 0.7899 (mmtt) REVERT: C 220 GLN cc_start: 0.8553 (mt0) cc_final: 0.8271 (tt0) REVERT: C 228 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7240 (p0) REVERT: C 273 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7862 (mp) outliers start: 32 outliers final: 29 residues processed: 164 average time/residue: 0.1598 time to fit residues: 36.9600 Evaluate side-chains 174 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7627 Z= 0.167 Angle : 0.585 13.363 10447 Z= 0.291 Chirality : 0.044 0.239 1287 Planarity : 0.005 0.084 1330 Dihedral : 4.777 33.729 1138 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.50 % Allowed : 25.34 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -3.31 (0.25), residues: 1053 helix: -2.32 (0.27), residues: 312 sheet: -1.89 (0.36), residues: 203 loop : -2.20 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.004 0.001 HIS C 225 PHE 0.026 0.001 PHE A 139 TYR 0.023 0.001 TYR D 50 ARG 0.003 0.000 ARG C 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7365 (m-80) cc_final: 0.7107 (m-80) REVERT: A 143 LYS cc_start: 0.7988 (mttt) cc_final: 0.7475 (mmtt) REVERT: A 162 PHE cc_start: 0.7447 (m-80) cc_final: 0.7058 (m-10) REVERT: A 322 LEU cc_start: 0.8140 (mm) cc_final: 0.7555 (mm) REVERT: B 29 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7369 (mtmm) REVERT: B 75 GLN cc_start: 0.7524 (tm130) cc_final: 0.7026 (tm-30) REVERT: C 48 ARG cc_start: 0.7238 (mmt180) cc_final: 0.7030 (mmt90) REVERT: C 127 LYS cc_start: 0.8130 (mttm) cc_final: 0.7856 (mmtt) REVERT: C 220 GLN cc_start: 0.8540 (mt0) cc_final: 0.8272 (tt0) REVERT: C 234 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: C 273 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7890 (mp) outliers start: 36 outliers final: 30 residues processed: 173 average time/residue: 0.1693 time to fit residues: 40.7937 Evaluate side-chains 178 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN C 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.188556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158358 restraints weight = 10752.925| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.53 r_work: 0.3866 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7627 Z= 0.194 Angle : 0.599 13.580 10447 Z= 0.300 Chirality : 0.046 0.334 1287 Planarity : 0.005 0.083 1330 Dihedral : 4.814 34.304 1138 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.65 % Allowed : 25.65 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -3.24 (0.25), residues: 1053 helix: -2.23 (0.27), residues: 308 sheet: -1.87 (0.36), residues: 203 loop : -2.17 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.005 0.001 HIS C 225 PHE 0.013 0.001 PHE A 327 TYR 0.023 0.001 TYR D 50 ARG 0.002 0.000 ARG C 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1956.75 seconds wall clock time: 36 minutes 3.12 seconds (2163.12 seconds total)