Starting phenix.real_space_refine on Fri Feb 16 02:44:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxe_15009/02_2024/7zxe_15009.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxe_15009/02_2024/7zxe_15009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxe_15009/02_2024/7zxe_15009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxe_15009/02_2024/7zxe_15009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxe_15009/02_2024/7zxe_15009.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxe_15009/02_2024/7zxe_15009.pdb" } resolution = 3.5 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= 0.002 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 Zn 2 6.06 5 P 93 5.49 5 S 68 5.16 5 C 8676 2.51 5 N 2504 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 120": "OE1" <-> "OE2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M ASP 157": "OD1" <-> "OD2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 171": "OE1" <-> "OE2" Residue "M PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 243": "OD1" <-> "OD2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 276": "OD1" <-> "OD2" Residue "M TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 307": "OD1" <-> "OD2" Residue "O ASP 179": "OD1" <-> "OD2" Residue "O GLU 191": "OE1" <-> "OE2" Residue "O TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 196": "NH1" <-> "NH2" Residue "O ARG 203": "NH1" <-> "NH2" Residue "O GLU 206": "OE1" <-> "OE2" Residue "O ARG 208": "NH1" <-> "NH2" Residue "O ARG 235": "NH1" <-> "NH2" Residue "O TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 263": "OD1" <-> "OD2" Residue "O ARG 269": "NH1" <-> "NH2" Residue "O PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 284": "OE1" <-> "OE2" Residue "O TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 294": "NH1" <-> "NH2" Residue "O ARG 299": "NH1" <-> "NH2" Residue "O ARG 318": "NH1" <-> "NH2" Residue "O ARG 336": "NH1" <-> "NH2" Residue "U TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 340": "OD1" <-> "OD2" Residue "U ARG 363": "NH1" <-> "NH2" Residue "U TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 20": "OD1" <-> "OD2" Residue "V GLU 21": "OE1" <-> "OE2" Residue "V ASP 69": "OD1" <-> "OD2" Residue "a GLU 12": "OE1" <-> "OE2" Residue "a ASP 22": "OD1" <-> "OD2" Residue "a ASP 28": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 121": "OD1" <-> "OD2" Residue "a TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 60": "OD1" <-> "OD2" Residue "b GLU 65": "OE1" <-> "OE2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b GLU 82": "OE1" <-> "OE2" Residue "b ASP 89": "OD1" <-> "OD2" Residue "b GLU 138": "OE1" <-> "OE2" Residue "b ARG 140": "NH1" <-> "NH2" Residue "b GLU 141": "OE1" <-> "OE2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 217": "OD1" <-> "OD2" Residue "b PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 276": "OE1" <-> "OE2" Residue "b PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 318": "OE1" <-> "OE2" Residue "b ASP 325": "OD1" <-> "OD2" Residue "b TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 369": "OD1" <-> "OD2" Residue "b GLU 374": "OE1" <-> "OE2" Residue "b GLU 398": "OE1" <-> "OE2" Residue "b TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 84": "OE1" <-> "OE2" Residue "c GLU 95": "OE1" <-> "OE2" Residue "c GLU 116": "OE1" <-> "OE2" Residue "c ASP 121": "OD1" <-> "OD2" Residue "c TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 152": "OD1" <-> "OD2" Residue "c GLU 178": "OE1" <-> "OE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c GLU 225": "OE1" <-> "OE2" Residue "c GLU 239": "OE1" <-> "OE2" Residue "c GLU 251": "OE1" <-> "OE2" Residue "c ARG 257": "NH1" <-> "NH2" Residue "c ASP 262": "OD1" <-> "OD2" Residue "c GLU 279": "OE1" <-> "OE2" Residue "c GLU 301": "OE1" <-> "OE2" Residue "c GLU 323": "OE1" <-> "OE2" Residue "c TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 7": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 32": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14150 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1567 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 10, 'TRANS': 190} Chain: "N" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 987 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "T" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 921 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1807 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "b" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2977 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2516 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 1 Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 424 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9621 SG CYS b 221 76.488 68.528 26.048 1.00139.75 S ATOM 10418 SG CYS b 317 72.705 68.101 26.856 1.00147.72 S ATOM 10740 SG CYS b 354 88.563 47.824 28.607 1.00133.30 S ATOM 10764 SG CYS b 357 92.447 47.927 28.524 1.00131.82 S ATOM 10955 SG CYS b 380 90.426 48.557 25.390 1.00131.89 S ATOM 10976 SG CYS b 383 90.645 45.098 26.867 1.00134.69 S Time building chain proxies: 7.61, per 1000 atoms: 0.54 Number of scatterers: 14150 At special positions: 0 Unit cell: (135.45, 164.85, 110.25, 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) Zn 2 29.99 S 68 16.00 P 93 15.00 O 2807 8.00 N 2504 7.00 C 8676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 313 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 319 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 317 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 221 " pdb=" ZN b 502 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 380 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 383 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 357 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 354 " Number of angles added : 8 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2874 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 53.3% alpha, 11.4% beta 38 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'M' and resid 117 through 129 removed outlier: 3.866A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.800A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 211 through 222 removed outlier: 4.067A pdb=" N MET M 215 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER M 220 " --> pdb=" O SER M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 265 Processing helix chain 'M' and resid 270 through 279 removed outlier: 3.828A pdb=" N ILE M 274 " --> pdb=" O THR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 292 removed outlier: 3.640A pdb=" N ILE M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.773A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 244 Processing helix chain 'O' and resid 269 through 277 Processing helix chain 'O' and resid 317 through 335 removed outlier: 3.506A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) Proline residue: O 330 - end of helix Processing helix chain 'U' and resid 10 through 33 removed outlier: 4.422A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 51 removed outlier: 3.654A pdb=" N LEU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 49 Processing helix chain 'a' and resid 6 through 20 removed outlier: 4.582A pdb=" N ASP a 10 " --> pdb=" O GLY a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 37 removed outlier: 3.903A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 42 removed outlier: 3.993A pdb=" N PHE a 42 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 67 Processing helix chain 'a' and resid 71 through 88 Processing helix chain 'a' and resid 100 through 117 removed outlier: 4.186A pdb=" N ASP a 105 " --> pdb=" O LEU a 101 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 132 Processing helix chain 'a' and resid 166 through 172 removed outlier: 4.218A pdb=" N LYS a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 195 removed outlier: 3.686A pdb=" N SER a 195 " --> pdb=" O LYS a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 232 removed outlier: 4.384A pdb=" N ASP a 214 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 55 Processing helix chain 'b' and resid 77 through 91 removed outlier: 3.634A pdb=" N ARG b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 104 Processing helix chain 'b' and resid 127 through 144 Processing helix chain 'b' and resid 150 through 161 Processing helix chain 'b' and resid 192 through 196 removed outlier: 3.698A pdb=" N LYS b 196 " --> pdb=" O HIS b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 226 removed outlier: 3.717A pdb=" N GLN b 226 " --> pdb=" O SER b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 242 through 247 Processing helix chain 'b' and resid 270 through 280 removed outlier: 4.448A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.650A pdb=" N TYR b 389 " --> pdb=" O ARG b 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 123 removed outlier: 4.229A pdb=" N CYS c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 171 Processing helix chain 'c' and resid 185 through 221 Proline residue: c 207 - end of helix Processing helix chain 'c' and resid 225 through 247 Processing helix chain 'c' and resid 249 through 255 removed outlier: 4.287A pdb=" N GLY c 255 " --> pdb=" O GLU c 251 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 267 removed outlier: 3.808A pdb=" N ILE c 266 " --> pdb=" O ASP c 262 " (cutoff:3.500A) Processing helix chain 'c' and resid 276 through 287 Processing helix chain 'c' and resid 298 through 313 Processing helix chain 'c' and resid 316 through 324 Processing helix chain 'c' and resid 329 through 340 Processing helix chain 'c' and resid 350 through 365 Processing helix chain 'c' and resid 371 through 376 Processing helix chain 'c' and resid 383 through 394 Processing helix chain 'd' and resid 2 through 45 Processing sheet with id=AA1, first strand: chain 'O' and resid 190 through 191 removed outlier: 4.052A pdb=" N LYS O 218 " --> pdb=" O PHE O 214 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU O 165 " --> pdb=" O GLY O 260 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY O 260 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN O 167 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET O 258 " --> pdb=" O ASN O 167 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL O 169 " --> pdb=" O GLN O 256 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN O 173 " --> pdb=" O ASP O 252 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP O 252 " --> pdb=" O ASN O 173 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 363 through 367 removed outlier: 4.280A pdb=" N PHE V 58 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE V 58 " --> pdb=" O PHE V 81 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE V 81 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY V 60 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL V 79 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN V 77 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL U 335 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS V 98 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS U 337 " --> pdb=" O CYS V 98 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL U 335 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET U 358 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS U 337 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY U 356 " --> pdb=" O CYS U 337 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR U 339 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS U 354 " --> pdb=" O TYR U 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'b' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 'b' and resid 290 through 291 removed outlier: 6.846A pdb=" N PHE b 258 " --> pdb=" O ALA b 291 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL b 320 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR b 324 " --> pdb=" O SER b 183 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER b 183 " --> pdb=" O THR b 324 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE b 326 " --> pdb=" O ILE b 181 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE b 181 " --> pdb=" O ILE b 326 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR b 203 " --> pdb=" O ILE b 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 377 through 379 652 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3567 1.33 - 1.45: 3101 1.45 - 1.57: 7662 1.57 - 1.69: 184 1.69 - 1.81: 105 Bond restraints: 14619 Sorted by residual: bond pdb=" N MET d 1 " pdb=" CA MET d 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" CG PRO b 308 " pdb=" CD PRO b 308 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.69e+00 bond pdb=" C3' DC T -6 " pdb=" O3' DC T -6 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" C1' DC T 24 " pdb=" N1 DC T 24 " ideal model delta sigma weight residual 1.490 1.521 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" C4' DC T -6 " pdb=" C3' DC T -6 " ideal model delta sigma weight residual 1.523 1.543 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 14614 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.77: 668 105.77 - 112.83: 7773 112.83 - 119.88: 4937 119.88 - 126.93: 6364 126.93 - 133.98: 370 Bond angle restraints: 20112 Sorted by residual: angle pdb=" N ILE M 180 " pdb=" CA ILE M 180 " pdb=" C ILE M 180 " ideal model delta sigma weight residual 111.58 107.59 3.99 1.06e+00 8.90e-01 1.42e+01 angle pdb=" CA PRO b 308 " pdb=" N PRO b 308 " pdb=" CD PRO b 308 " ideal model delta sigma weight residual 112.00 107.85 4.15 1.40e+00 5.10e-01 8.80e+00 angle pdb=" N GLU a 31 " pdb=" CA GLU a 31 " pdb=" CB GLU a 31 " ideal model delta sigma weight residual 110.12 114.27 -4.15 1.47e+00 4.63e-01 7.98e+00 angle pdb=" C ARG V 82 " pdb=" N GLU V 83 " pdb=" CA GLU V 83 " ideal model delta sigma weight residual 122.03 116.91 5.12 2.01e+00 2.48e-01 6.49e+00 angle pdb=" C TYR c 141 " pdb=" N MET c 142 " pdb=" CA MET c 142 " ideal model delta sigma weight residual 120.29 123.88 -3.59 1.42e+00 4.96e-01 6.40e+00 ... (remaining 20107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 8000 31.18 - 62.36: 596 62.36 - 93.54: 35 93.54 - 124.72: 1 124.72 - 155.90: 2 Dihedral angle restraints: 8634 sinusoidal: 4224 harmonic: 4410 Sorted by residual: dihedral pdb=" CA VAL V 52 " pdb=" C VAL V 52 " pdb=" N ARG V 53 " pdb=" CA ARG V 53 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR b 32 " pdb=" C TYR b 32 " pdb=" N GLU b 33 " pdb=" CA GLU b 33 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 8631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1739 0.041 - 0.081: 353 0.081 - 0.122: 99 0.122 - 0.162: 14 0.162 - 0.203: 1 Chirality restraints: 2206 Sorted by residual: chirality pdb=" CG LEU d 22 " pdb=" CB LEU d 22 " pdb=" CD1 LEU d 22 " pdb=" CD2 LEU d 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE b 321 " pdb=" N ILE b 321 " pdb=" C ILE b 321 " pdb=" CB ILE b 321 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE b 186 " pdb=" N ILE b 186 " pdb=" C ILE b 186 " pdb=" CB ILE b 186 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2203 not shown) Planarity restraints: 2263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE b 307 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO b 308 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO b 308 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO b 308 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 130 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO M 131 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO M 131 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO M 131 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 226 " 0.010 2.00e-02 2.50e+03 1.01e-02 2.55e+00 pdb=" CG TRP a 226 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP a 226 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP a 226 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 226 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 226 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP a 226 " -0.002 2.00e-02 2.50e+03 ... (remaining 2260 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 142 2.56 - 3.15: 11688 3.15 - 3.73: 23746 3.73 - 4.32: 32168 4.32 - 4.90: 51251 Nonbonded interactions: 118995 Sorted by model distance: nonbonded pdb=" O LEU a 207 " pdb=" NH2 ARG d 28 " model vdw 1.978 2.520 nonbonded pdb=" OP1 DG N 8 " pdb=" OG SER O 216 " model vdw 2.016 2.440 nonbonded pdb=" OH TYR V 3 " pdb=" O CYS V 98 " model vdw 2.044 2.440 nonbonded pdb=" O SER M 216 " pdb=" OG SER M 220 " model vdw 2.095 2.440 nonbonded pdb=" OG SER b 209 " pdb=" OD1 ASN b 299 " model vdw 2.104 2.440 ... (remaining 118990 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=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: 2.730 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: 13.180 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.480 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14619 Z= 0.164 Angle : 0.548 6.319 20112 Z= 0.323 Chirality : 0.037 0.203 2206 Planarity : 0.004 0.103 2263 Dihedral : 19.337 155.905 5760 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1474 helix: 1.79 (0.20), residues: 747 sheet: -0.34 (0.42), residues: 136 loop : -1.07 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP a 226 HIS 0.006 0.001 HIS c 369 PHE 0.025 0.001 PHE V 81 TYR 0.018 0.001 TYR c 141 ARG 0.006 0.000 ARG V 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 129 ASN cc_start: 0.8640 (m110) cc_final: 0.7964 (t0) REVERT: M 227 GLN cc_start: 0.9361 (mp10) cc_final: 0.9150 (mp10) REVERT: M 259 TYR cc_start: 0.9308 (t80) cc_final: 0.8919 (t80) REVERT: O 229 GLN cc_start: 0.8435 (mp10) cc_final: 0.8199 (mp10) REVERT: U 24 ASP cc_start: 0.8080 (p0) cc_final: 0.7791 (p0) REVERT: U 35 ASP cc_start: 0.7804 (p0) cc_final: 0.7463 (p0) REVERT: U 37 GLN cc_start: 0.9118 (mp-120) cc_final: 0.8340 (mp10) REVERT: U 43 LYS cc_start: 0.9262 (ttpp) cc_final: 0.9013 (ttpt) REVERT: U 47 GLU cc_start: 0.8976 (mp0) cc_final: 0.8634 (mp0) REVERT: V 21 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8670 (mm-30) REVERT: V 83 GLU cc_start: 0.7587 (pp20) cc_final: 0.7384 (pp20) REVERT: a 53 MET cc_start: 0.8920 (tmm) cc_final: 0.8687 (tmm) REVERT: a 57 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8201 (tt0) REVERT: a 83 TYR cc_start: 0.8783 (t80) cc_final: 0.8368 (t80) REVERT: a 119 HIS cc_start: 0.8874 (m-70) cc_final: 0.8161 (m90) REVERT: a 226 TRP cc_start: 0.8955 (t60) cc_final: 0.8739 (t60) REVERT: c 248 LEU cc_start: 0.9070 (tp) cc_final: 0.8769 (tp) REVERT: c 259 ASP cc_start: 0.7831 (p0) cc_final: 0.7522 (p0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2450 time to fit residues: 75.9160 Evaluate side-chains 140 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 GLN b 139 HIS ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14619 Z= 0.275 Angle : 0.634 10.236 20112 Z= 0.342 Chirality : 0.042 0.178 2206 Planarity : 0.005 0.069 2263 Dihedral : 21.912 149.514 2641 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.05 % Allowed : 8.39 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1474 helix: 1.55 (0.19), residues: 763 sheet: -0.31 (0.46), residues: 118 loop : -1.03 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 277 HIS 0.011 0.001 HIS a 223 PHE 0.023 0.002 PHE U 351 TYR 0.033 0.002 TYR O 237 ARG 0.010 0.001 ARG d 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8516 (mmt) cc_final: 0.8294 (mmt) REVERT: M 259 TYR cc_start: 0.9425 (t80) cc_final: 0.8968 (t80) REVERT: M 290 ARG cc_start: 0.8604 (mpt90) cc_final: 0.8310 (mmt180) REVERT: O 228 GLU cc_start: 0.8737 (mp0) cc_final: 0.8488 (mp0) REVERT: O 229 GLN cc_start: 0.8419 (mp10) cc_final: 0.8122 (mp10) REVERT: O 237 TYR cc_start: 0.7781 (m-80) cc_final: 0.7575 (m-80) REVERT: O 286 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7840 (tm-30) REVERT: U 24 ASP cc_start: 0.8010 (p0) cc_final: 0.7800 (p0) REVERT: U 37 GLN cc_start: 0.9165 (mp-120) cc_final: 0.8553 (mp10) REVERT: U 40 MET cc_start: 0.8794 (ptt) cc_final: 0.8349 (ptt) REVERT: U 348 LYS cc_start: 0.8938 (mppt) cc_final: 0.8570 (mppt) REVERT: V 83 GLU cc_start: 0.7827 (pp20) cc_final: 0.7444 (pp20) REVERT: V 84 VAL cc_start: 0.8736 (t) cc_final: 0.7885 (p) REVERT: a 31 GLU cc_start: 0.9209 (mp0) cc_final: 0.8960 (mp0) REVERT: a 35 ASN cc_start: 0.9381 (m110) cc_final: 0.9106 (m110) REVERT: a 57 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8304 (tt0) REVERT: a 83 TYR cc_start: 0.8791 (t80) cc_final: 0.8463 (t80) REVERT: a 119 HIS cc_start: 0.8979 (m-70) cc_final: 0.8091 (m90) REVERT: a 226 TRP cc_start: 0.8958 (t60) cc_final: 0.8665 (t60) REVERT: b 143 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8289 (p) REVERT: c 148 PRO cc_start: 0.6663 (Cg_endo) cc_final: 0.6295 (Cg_exo) REVERT: c 149 TYR cc_start: 0.7744 (t80) cc_final: 0.7438 (t80) REVERT: c 248 LEU cc_start: 0.9119 (tp) cc_final: 0.8810 (tp) REVERT: c 356 MET cc_start: 0.9075 (ttt) cc_final: 0.8642 (tpp) REVERT: d 17 ARG cc_start: 0.8672 (mtm180) cc_final: 0.8407 (ptt180) outliers start: 14 outliers final: 9 residues processed: 172 average time/residue: 0.2536 time to fit residues: 65.4216 Evaluate side-chains 150 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain c residue 164 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 112 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 116 ASN M 221 ASN O 166 GLN a 52 ASN a 73 GLN a 95 GLN a 116 ASN a 232 ASN ** b 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14619 Z= 0.193 Angle : 0.579 8.394 20112 Z= 0.311 Chirality : 0.039 0.178 2206 Planarity : 0.004 0.060 2263 Dihedral : 21.803 146.983 2641 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.42 % Allowed : 10.04 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1474 helix: 1.64 (0.19), residues: 768 sheet: 0.01 (0.48), residues: 111 loop : -0.99 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 226 HIS 0.006 0.001 HIS c 261 PHE 0.014 0.001 PHE U 351 TYR 0.015 0.001 TYR O 237 ARG 0.004 0.000 ARG V 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 244 LEU cc_start: 0.9218 (mt) cc_final: 0.8833 (tp) REVERT: M 259 TYR cc_start: 0.9422 (t80) cc_final: 0.9001 (t80) REVERT: M 290 ARG cc_start: 0.8599 (mpt90) cc_final: 0.8324 (mmt180) REVERT: O 229 GLN cc_start: 0.8475 (mp10) cc_final: 0.8254 (mp10) REVERT: O 286 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7717 (tm-30) REVERT: U 35 ASP cc_start: 0.7778 (p0) cc_final: 0.7499 (p0) REVERT: U 37 GLN cc_start: 0.9130 (mp-120) cc_final: 0.8627 (mp10) REVERT: U 40 MET cc_start: 0.8728 (ptt) cc_final: 0.8479 (ptt) REVERT: U 346 LYS cc_start: 0.8040 (tptt) cc_final: 0.7821 (tptt) REVERT: U 348 LYS cc_start: 0.8931 (mppt) cc_final: 0.8516 (mppt) REVERT: a 35 ASN cc_start: 0.9360 (m110) cc_final: 0.9080 (m110) REVERT: a 57 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8265 (tt0) REVERT: a 119 HIS cc_start: 0.8922 (m-70) cc_final: 0.8026 (m90) REVERT: a 140 MET cc_start: 0.8796 (mmt) cc_final: 0.7547 (mmt) REVERT: b 340 TYR cc_start: 0.7078 (t80) cc_final: 0.6618 (t80) REVERT: c 142 MET cc_start: 0.8182 (tpp) cc_final: 0.7354 (mpp) REVERT: c 149 TYR cc_start: 0.8107 (t80) cc_final: 0.7755 (t80) REVERT: c 248 LEU cc_start: 0.9123 (tp) cc_final: 0.8808 (tp) REVERT: c 356 MET cc_start: 0.9104 (ttt) cc_final: 0.8857 (tpp) outliers start: 19 outliers final: 10 residues processed: 169 average time/residue: 0.2623 time to fit residues: 65.9035 Evaluate side-chains 153 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 369 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14619 Z= 0.217 Angle : 0.596 11.114 20112 Z= 0.319 Chirality : 0.040 0.178 2206 Planarity : 0.004 0.058 2263 Dihedral : 21.880 149.252 2641 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.95 % Allowed : 12.43 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1474 helix: 1.60 (0.19), residues: 764 sheet: 0.32 (0.48), residues: 107 loop : -0.98 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 317 HIS 0.007 0.001 HIS U 343 PHE 0.016 0.001 PHE U 351 TYR 0.034 0.001 TYR a 83 ARG 0.006 0.000 ARG V 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8736 (mmt) cc_final: 0.8412 (mmt) REVERT: M 179 GLU cc_start: 0.8825 (tt0) cc_final: 0.8156 (tt0) REVERT: M 244 LEU cc_start: 0.9259 (mt) cc_final: 0.8810 (tp) REVERT: M 259 TYR cc_start: 0.9428 (t80) cc_final: 0.9061 (t80) REVERT: O 229 GLN cc_start: 0.8614 (mp10) cc_final: 0.8408 (mp10) REVERT: O 286 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7623 (tm-30) REVERT: U 36 GLU cc_start: 0.8595 (tp30) cc_final: 0.6999 (tp30) REVERT: U 37 GLN cc_start: 0.9232 (mp-120) cc_final: 0.8716 (mm-40) REVERT: U 348 LYS cc_start: 0.9017 (mppt) cc_final: 0.8754 (mmtm) REVERT: V 86 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8205 (tm-30) REVERT: a 35 ASN cc_start: 0.9379 (m110) cc_final: 0.9081 (m-40) REVERT: a 57 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8331 (tt0) REVERT: a 119 HIS cc_start: 0.8947 (m-70) cc_final: 0.8547 (m90) REVERT: a 140 MET cc_start: 0.8802 (mmt) cc_final: 0.7535 (mmt) REVERT: b 340 TYR cc_start: 0.7371 (t80) cc_final: 0.7008 (t80) REVERT: c 149 TYR cc_start: 0.8450 (t80) cc_final: 0.8135 (t80) REVERT: c 248 LEU cc_start: 0.9125 (tp) cc_final: 0.8814 (tp) outliers start: 26 outliers final: 15 residues processed: 162 average time/residue: 0.2317 time to fit residues: 57.4746 Evaluate side-chains 151 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 0.0020 chunk 102 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14619 Z= 0.164 Angle : 0.587 12.225 20112 Z= 0.312 Chirality : 0.039 0.195 2206 Planarity : 0.004 0.058 2263 Dihedral : 21.779 147.569 2641 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.65 % Allowed : 13.56 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1474 helix: 1.69 (0.19), residues: 769 sheet: 0.52 (0.49), residues: 107 loop : -0.92 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 72 HIS 0.005 0.001 HIS c 261 PHE 0.013 0.001 PHE U 351 TYR 0.040 0.001 TYR O 237 ARG 0.007 0.000 ARG d 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8617 (mmt) cc_final: 0.8374 (mmt) REVERT: M 244 LEU cc_start: 0.9226 (mt) cc_final: 0.8820 (tp) REVERT: M 259 TYR cc_start: 0.9435 (t80) cc_final: 0.9054 (t80) REVERT: O 229 GLN cc_start: 0.8609 (mp10) cc_final: 0.8382 (mp10) REVERT: O 237 TYR cc_start: 0.7844 (m-80) cc_final: 0.7622 (m-80) REVERT: O 286 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7568 (tm-30) REVERT: U 35 ASP cc_start: 0.8067 (p0) cc_final: 0.6610 (p0) REVERT: U 37 GLN cc_start: 0.9102 (mp-120) cc_final: 0.8483 (mp10) REVERT: U 348 LYS cc_start: 0.9010 (mppt) cc_final: 0.8766 (mmtm) REVERT: V 48 LEU cc_start: 0.9125 (tt) cc_final: 0.8917 (tt) REVERT: V 86 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8079 (tm-30) REVERT: a 7 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8494 (tt) REVERT: a 11 CYS cc_start: 0.9196 (m) cc_final: 0.8723 (m) REVERT: a 35 ASN cc_start: 0.9360 (m110) cc_final: 0.9065 (m110) REVERT: a 57 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8301 (tt0) REVERT: a 119 HIS cc_start: 0.8934 (m-70) cc_final: 0.8541 (m90) REVERT: a 140 MET cc_start: 0.8751 (mmt) cc_final: 0.7398 (mmt) REVERT: b 204 MET cc_start: 0.8570 (mtp) cc_final: 0.8210 (mmm) REVERT: b 340 TYR cc_start: 0.7266 (t80) cc_final: 0.7014 (t80) REVERT: c 142 MET cc_start: 0.8307 (tpp) cc_final: 0.7779 (mpp) REVERT: c 149 TYR cc_start: 0.8325 (t80) cc_final: 0.8049 (t80) REVERT: c 248 LEU cc_start: 0.9099 (tp) cc_final: 0.8781 (tp) outliers start: 22 outliers final: 15 residues processed: 171 average time/residue: 0.2352 time to fit residues: 61.6231 Evaluate side-chains 159 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 354 CYS Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain d residue 48 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 256 GLN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 219 GLN c 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 14619 Z= 0.397 Angle : 0.703 11.002 20112 Z= 0.375 Chirality : 0.043 0.188 2206 Planarity : 0.005 0.058 2263 Dihedral : 22.183 155.075 2641 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.55 % Allowed : 14.23 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1474 helix: 1.51 (0.19), residues: 770 sheet: 0.19 (0.49), residues: 111 loop : -1.10 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 348 HIS 0.007 0.001 HIS b 313 PHE 0.027 0.002 PHE U 351 TYR 0.025 0.002 TYR O 237 ARG 0.012 0.001 ARG V 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 227 GLN cc_start: 0.9130 (mp10) cc_final: 0.8774 (pm20) REVERT: M 259 TYR cc_start: 0.9467 (t80) cc_final: 0.9058 (t80) REVERT: O 229 GLN cc_start: 0.8670 (mp10) cc_final: 0.8314 (mp10) REVERT: O 237 TYR cc_start: 0.8013 (m-80) cc_final: 0.7723 (m-80) REVERT: U 35 ASP cc_start: 0.8085 (p0) cc_final: 0.6751 (p0) REVERT: U 37 GLN cc_start: 0.9058 (mp-120) cc_final: 0.8428 (mp10) REVERT: V 86 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8375 (tm-30) REVERT: V 89 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8922 (tptt) REVERT: a 35 ASN cc_start: 0.9376 (m110) cc_final: 0.9104 (m110) REVERT: a 57 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8450 (tt0) REVERT: b 340 TYR cc_start: 0.7686 (t80) cc_final: 0.7177 (t80) REVERT: c 142 MET cc_start: 0.8524 (tpp) cc_final: 0.7889 (tpp) REVERT: c 248 LEU cc_start: 0.9099 (tp) cc_final: 0.8817 (tp) REVERT: c 315 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6135 (tp) REVERT: d 9 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8185 (tmm160) outliers start: 34 outliers final: 17 residues processed: 166 average time/residue: 0.2318 time to fit residues: 59.4639 Evaluate side-chains 151 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 354 CYS Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 216 HIS Chi-restraints excluded: chain c residue 315 LEU Chi-restraints excluded: chain d residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 63 ASN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14619 Z= 0.262 Angle : 0.653 12.315 20112 Z= 0.345 Chirality : 0.041 0.228 2206 Planarity : 0.004 0.061 2263 Dihedral : 22.128 154.053 2641 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.87 % Allowed : 15.96 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1474 helix: 1.57 (0.19), residues: 772 sheet: 0.23 (0.49), residues: 113 loop : -1.10 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 72 HIS 0.012 0.001 HIS d 23 PHE 0.019 0.001 PHE U 351 TYR 0.019 0.001 TYR O 237 ARG 0.008 0.000 ARG V 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8864 (mmt) cc_final: 0.8312 (mmt) REVERT: M 227 GLN cc_start: 0.9070 (mp10) cc_final: 0.8783 (pm20) REVERT: M 229 GLN cc_start: 0.9356 (tp40) cc_final: 0.9111 (tp40) REVERT: M 259 TYR cc_start: 0.9473 (t80) cc_final: 0.9148 (t80) REVERT: O 229 GLN cc_start: 0.8669 (mp10) cc_final: 0.8333 (mp10) REVERT: U 35 ASP cc_start: 0.7997 (p0) cc_final: 0.6702 (p0) REVERT: U 37 GLN cc_start: 0.9087 (mp-120) cc_final: 0.8525 (mp10) REVERT: V 86 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8586 (tm-30) REVERT: V 89 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8885 (tptt) REVERT: a 11 CYS cc_start: 0.9406 (m) cc_final: 0.8911 (m) REVERT: a 35 ASN cc_start: 0.9382 (m110) cc_final: 0.9108 (m110) REVERT: a 57 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8438 (tt0) REVERT: b 204 MET cc_start: 0.8784 (mmm) cc_final: 0.8130 (mmm) REVERT: b 340 TYR cc_start: 0.7594 (t80) cc_final: 0.7098 (t80) REVERT: b 386 MET cc_start: 0.9097 (mmm) cc_final: 0.8759 (mmm) REVERT: c 142 MET cc_start: 0.8500 (tpp) cc_final: 0.7991 (tpp) REVERT: c 248 LEU cc_start: 0.9147 (tp) cc_final: 0.8858 (tp) outliers start: 25 outliers final: 19 residues processed: 162 average time/residue: 0.2483 time to fit residues: 61.1525 Evaluate side-chains 160 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 354 CYS Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 216 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14619 Z= 0.214 Angle : 0.640 12.645 20112 Z= 0.338 Chirality : 0.040 0.173 2206 Planarity : 0.004 0.063 2263 Dihedral : 22.046 153.574 2641 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.87 % Allowed : 16.10 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1474 helix: 1.61 (0.19), residues: 773 sheet: 0.80 (0.51), residues: 102 loop : -0.99 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 72 HIS 0.014 0.001 HIS d 23 PHE 0.016 0.001 PHE U 351 TYR 0.022 0.001 TYR a 83 ARG 0.006 0.000 ARG d 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8827 (mmt) cc_final: 0.8293 (mmt) REVERT: M 179 GLU cc_start: 0.8740 (tt0) cc_final: 0.8431 (mm-30) REVERT: M 227 GLN cc_start: 0.9062 (mp10) cc_final: 0.8830 (pm20) REVERT: M 229 GLN cc_start: 0.9346 (tp40) cc_final: 0.9134 (tp40) REVERT: M 259 TYR cc_start: 0.9478 (t80) cc_final: 0.9147 (t80) REVERT: O 229 GLN cc_start: 0.8644 (mp10) cc_final: 0.8326 (mp10) REVERT: O 237 TYR cc_start: 0.7966 (m-80) cc_final: 0.7577 (m-80) REVERT: U 35 ASP cc_start: 0.7893 (p0) cc_final: 0.6503 (p0) REVERT: U 37 GLN cc_start: 0.9132 (mp-120) cc_final: 0.8539 (mp10) REVERT: V 86 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8513 (tm-30) REVERT: V 89 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8858 (tptt) REVERT: a 7 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8452 (tt) REVERT: a 11 CYS cc_start: 0.9399 (m) cc_final: 0.8895 (m) REVERT: a 35 ASN cc_start: 0.9383 (m110) cc_final: 0.9087 (m110) REVERT: a 57 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8384 (tt0) REVERT: b 204 MET cc_start: 0.8674 (mmm) cc_final: 0.7994 (mmm) REVERT: b 340 TYR cc_start: 0.7597 (t80) cc_final: 0.7241 (t80) REVERT: b 386 MET cc_start: 0.9105 (mmm) cc_final: 0.8778 (mmm) REVERT: c 315 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6077 (tp) outliers start: 25 outliers final: 21 residues processed: 161 average time/residue: 0.2478 time to fit residues: 60.6121 Evaluate side-chains 162 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 354 CYS Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 119 HIS ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14619 Z= 0.210 Angle : 0.641 12.366 20112 Z= 0.337 Chirality : 0.040 0.181 2206 Planarity : 0.004 0.060 2263 Dihedral : 22.003 152.864 2641 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.95 % Allowed : 16.40 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1474 helix: 1.65 (0.19), residues: 773 sheet: 0.77 (0.50), residues: 109 loop : -0.95 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 72 HIS 0.006 0.001 HIS d 23 PHE 0.018 0.001 PHE O 325 TYR 0.019 0.001 TYR a 83 ARG 0.009 0.000 ARG d 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8821 (mmt) cc_final: 0.8278 (mmt) REVERT: M 179 GLU cc_start: 0.8730 (tt0) cc_final: 0.8448 (mm-30) REVERT: M 227 GLN cc_start: 0.9166 (mp10) cc_final: 0.8864 (pm20) REVERT: M 259 TYR cc_start: 0.9480 (t80) cc_final: 0.9129 (t80) REVERT: O 229 GLN cc_start: 0.8648 (mp10) cc_final: 0.8389 (mp10) REVERT: O 237 TYR cc_start: 0.7956 (m-80) cc_final: 0.7543 (m-80) REVERT: U 35 ASP cc_start: 0.7907 (p0) cc_final: 0.6784 (p0) REVERT: U 37 GLN cc_start: 0.9138 (mp-120) cc_final: 0.8561 (mp10) REVERT: U 355 ASP cc_start: 0.8630 (p0) cc_final: 0.8113 (p0) REVERT: V 86 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8423 (tm-30) REVERT: V 89 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8841 (tptt) REVERT: a 7 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8472 (tt) REVERT: a 11 CYS cc_start: 0.9408 (m) cc_final: 0.8900 (m) REVERT: a 35 ASN cc_start: 0.9386 (m110) cc_final: 0.9098 (m110) REVERT: a 57 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8498 (tt0) REVERT: a 180 MET cc_start: 0.9113 (mmm) cc_final: 0.8824 (mpp) REVERT: b 204 MET cc_start: 0.8633 (mmm) cc_final: 0.7946 (mmm) REVERT: b 340 TYR cc_start: 0.7554 (t80) cc_final: 0.7313 (t80) REVERT: c 315 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.5988 (tp) REVERT: d 9 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8314 (tmm160) outliers start: 26 outliers final: 22 residues processed: 164 average time/residue: 0.2393 time to fit residues: 59.3446 Evaluate side-chains 165 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 35 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 354 CYS Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 119 HIS ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14619 Z= 0.187 Angle : 0.640 12.501 20112 Z= 0.336 Chirality : 0.040 0.205 2206 Planarity : 0.004 0.061 2263 Dihedral : 21.843 151.792 2641 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.87 % Allowed : 16.78 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1474 helix: 1.69 (0.19), residues: 773 sheet: 0.81 (0.51), residues: 107 loop : -0.83 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 72 HIS 0.005 0.001 HIS a 223 PHE 0.014 0.001 PHE U 351 TYR 0.020 0.001 TYR a 83 ARG 0.008 0.000 ARG d 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 124 MET cc_start: 0.8807 (mmt) cc_final: 0.8315 (mmt) REVERT: M 179 GLU cc_start: 0.8709 (tt0) cc_final: 0.8418 (mm-30) REVERT: M 227 GLN cc_start: 0.9156 (mp10) cc_final: 0.8847 (pm20) REVERT: M 259 TYR cc_start: 0.9479 (t80) cc_final: 0.9120 (t80) REVERT: O 229 GLN cc_start: 0.8627 (mp10) cc_final: 0.8411 (mp10) REVERT: O 237 TYR cc_start: 0.8150 (m-80) cc_final: 0.7760 (m-80) REVERT: U 35 ASP cc_start: 0.8045 (p0) cc_final: 0.7026 (p0) REVERT: U 37 GLN cc_start: 0.9195 (mp-120) cc_final: 0.8622 (mp10) REVERT: U 346 LYS cc_start: 0.8241 (tppt) cc_final: 0.7945 (tptp) REVERT: U 355 ASP cc_start: 0.8603 (p0) cc_final: 0.8065 (p0) REVERT: V 86 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8341 (tm-30) REVERT: V 89 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8768 (tptt) REVERT: a 7 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8432 (tt) REVERT: a 11 CYS cc_start: 0.9400 (m) cc_final: 0.8856 (m) REVERT: a 35 ASN cc_start: 0.9376 (m110) cc_final: 0.9084 (m110) REVERT: a 57 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8461 (tt0) REVERT: a 116 ASN cc_start: 0.9014 (t0) cc_final: 0.8810 (t0) REVERT: b 204 MET cc_start: 0.8609 (mmm) cc_final: 0.7919 (mmm) REVERT: c 315 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6164 (tp) outliers start: 25 outliers final: 21 residues processed: 167 average time/residue: 0.2484 time to fit residues: 61.9093 Evaluate side-chains 167 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 129 ASN Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 283 VAL Chi-restraints excluded: chain O residue 221 CYS Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 194 ILE Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 174 MET Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 354 CYS Chi-restraints excluded: chain b residue 365 VAL Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 216 HIS Chi-restraints excluded: chain c residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 125 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 119 HIS ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 268 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 = 0.3957 r_free = 0.3957 target = 0.081378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.060038 restraints weight = 67323.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.061466 restraints weight = 32707.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.062256 restraints weight = 21549.504| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14619 Z= 0.187 Angle : 0.644 14.343 20112 Z= 0.336 Chirality : 0.040 0.199 2206 Planarity : 0.004 0.060 2263 Dihedral : 21.808 152.129 2641 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.87 % Allowed : 17.08 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1474 helix: 1.65 (0.19), residues: 772 sheet: 1.10 (0.51), residues: 102 loop : -0.77 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 72 HIS 0.004 0.001 HIS c 261 PHE 0.013 0.001 PHE U 351 TYR 0.018 0.001 TYR a 83 ARG 0.011 0.000 ARG V 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.00 seconds wall clock time: 50 minutes 13.40 seconds (3013.40 seconds total)