Starting phenix.real_space_refine on Tue Mar 19 08:37:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/03_2024/3jc6_6534.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/03_2024/3jc6_6534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/03_2024/3jc6_6534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/03_2024/3jc6_6534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/03_2024/3jc6_6534.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/03_2024/3jc6_6534.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 99 5.16 5 C 15099 2.51 5 N 4077 2.21 5 O 4456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 224": "NH1" <-> "NH2" Residue "2 TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 319": "NH1" <-> "NH2" Residue "2 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 383": "NH1" <-> "NH2" Residue "2 ARG 387": "NH1" <-> "NH2" Residue "2 TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 459": "NH1" <-> "NH2" Residue "3 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 108": "NH1" <-> "NH2" Residue "3 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 137": "OD1" <-> "OD2" Residue "3 ARG 208": "NH1" <-> "NH2" Residue "3 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 224": "NH1" <-> "NH2" Residue "3 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 291": "NH1" <-> "NH2" Residue "3 TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 178": "NH1" <-> "NH2" Residue "4 ARG 234": "NH1" <-> "NH2" Residue "4 TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 388": "NH1" <-> "NH2" Residue "4 ARG 428": "NH1" <-> "NH2" Residue "4 ARG 449": "NH1" <-> "NH2" Residue "4 ARG 451": "NH1" <-> "NH2" Residue "5 ARG 51": "NH1" <-> "NH2" Residue "5 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 152": "OD1" <-> "OD2" Residue "5 TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 112": "NH1" <-> "NH2" Residue "6 PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 ARG 176": "NH1" <-> "NH2" Residue "6 ARG 186": "NH1" <-> "NH2" Residue "6 ARG 190": "NH1" <-> "NH2" Residue "6 ARG 275": "NH1" <-> "NH2" Residue "6 ARG 277": "NH1" <-> "NH2" Residue "6 ARG 280": "NH1" <-> "NH2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 375": "NH1" <-> "NH2" Residue "6 ARG 382": "NH1" <-> "NH2" Residue "7 ASP 101": "OD1" <-> "OD2" Residue "7 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 152": "NH1" <-> "NH2" Residue "7 ARG 157": "NH1" <-> "NH2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 216": "NH1" <-> "NH2" Residue "7 TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 303": "NH1" <-> "NH2" Residue "7 PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 226": "NH1" <-> "NH2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 398": "NH1" <-> "NH2" Residue "E TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E ARG 472": "NH1" <-> "NH2" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 547": "NH1" <-> "NH2" Residue "E TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 587": "NH1" <-> "NH2" Residue "E TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 634": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23732 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1911 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 10, 'PTRANS': 11, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "3" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2130 Classifications: {'peptide': 269} Link IDs: {'CIS': 12, 'PTRANS': 16, 'TRANS': 240} Chain breaks: 2 Chain: "4" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2203 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 19, 'PTRANS': 11, 'TRANS': 244} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2028 Classifications: {'peptide': 254} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 231} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2049 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 237} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "7" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2611 Classifications: {'peptide': 325} Link IDs: {'CIS': 15, 'PTRANS': 16, 'TRANS': 293} Chain breaks: 2 Chain: "E" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4482 Classifications: {'peptide': 553} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 516} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1820 Classifications: {'peptide': 221} Link IDs: {'CIS': 12, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 2 Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'CIS': 6, 'PTRANS': 9, 'TRANS': 165} Chain breaks: 1 Chain: "A" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1696 Classifications: {'peptide': 208} Link IDs: {'CIS': 13, 'PTRANS': 3, 'TRANS': 191} Chain: "C" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1288 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 145} Chain breaks: 3 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: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11961 SG CYS 7 262 77.075 177.885 81.548 1.00167.77 S ATOM 12175 SG CYS 7 289 76.706 178.847 84.926 1.00194.98 S Time building chain proxies: 12.46, per 1000 atoms: 0.53 Number of scatterers: 23732 At special positions: 0 Unit cell: (169.68, 215.13, 111.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 99 16.00 O 4456 8.00 N 4077 7.00 C 15099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " 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=0, symmetry=0 Time building additional restraints: 9.44 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 71001 " pdb="ZN ZN 71001 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 71001 " - pdb=" SG CYS 7 289 " 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 27 sheets defined 39.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain '2' and resid 202 through 216 removed outlier: 3.894A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE 2 207 " --> pdb=" O VAL 2 203 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER 2 213 " --> pdb=" O ARG 2 209 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 237 Processing helix chain '2' and resid 245 through 253 Processing helix chain '2' and resid 253 through 261 removed outlier: 3.919A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.998A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 3.523A pdb=" N ASN 2 313 " --> pdb=" O ARG 2 310 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 397 removed outlier: 3.601A pdb=" N VAL 2 397 " --> pdb=" O PRO 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 413 through 415 No H-bonds generated for 'chain '2' and resid 413 through 415' Processing helix chain '3' and resid 19 through 32 removed outlier: 3.594A pdb=" N GLU 3 30 " --> pdb=" O ARG 3 26 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) Processing helix chain '3' and resid 38 through 55 removed outlier: 3.646A pdb=" N ASN 3 49 " --> pdb=" O ILE 3 45 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 101 No H-bonds generated for 'chain '3' and resid 99 through 101' Processing helix chain '3' and resid 102 through 107 removed outlier: 4.144A pdb=" N PHE 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 removed outlier: 3.568A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE 3 114 " --> pdb=" O PHE 3 110 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 121 through 135 removed outlier: 3.551A pdb=" N SER 3 135 " --> pdb=" O ASP 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 261 through 265 removed outlier: 3.537A pdb=" N ALA 3 265 " --> pdb=" O PRO 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 279 through 283 Processing helix chain '4' and resid 189 through 196 Processing helix chain '4' and resid 226 through 237 removed outlier: 3.791A pdb=" N LEU 4 230 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.766A pdb=" N TYR 4 258 " --> pdb=" O THR 4 254 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 3.660A pdb=" N VAL 4 268 " --> pdb=" O TYR 4 264 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) Processing helix chain '4' and resid 294 through 299 removed outlier: 3.571A pdb=" N THR 4 298 " --> pdb=" O ASP 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 420 through 424 Processing helix chain '5' and resid 22 through 37 removed outlier: 3.519A pdb=" N SER 5 30 " --> pdb=" O GLU 5 26 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU 5 37 " --> pdb=" O ASN 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 56 removed outlier: 4.053A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 Processing helix chain '5' and resid 72 through 80 removed outlier: 4.165A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 102 Proline residue: 5 88 - end of helix removed outlier: 3.622A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 279 through 283 Processing helix chain '6' and resid 106 through 121 removed outlier: 3.647A pdb=" N LYS 6 110 " --> pdb=" O VAL 6 106 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 144 Processing helix chain '6' and resid 155 through 161 removed outlier: 3.870A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 170 removed outlier: 4.039A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE 6 170 " --> pdb=" O LEU 6 166 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 176 Processing helix chain '6' and resid 177 through 193 removed outlier: 3.820A pdb=" N LYS 6 191 " --> pdb=" O ARG 6 187 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 25 removed outlier: 3.757A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.818A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL 7 70 " --> pdb=" O MET 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 92 removed outlier: 3.530A pdb=" N GLN 7 89 " --> pdb=" O ILE 7 85 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN 7 90 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 7 91 " --> pdb=" O GLN 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 110 removed outlier: 3.771A pdb=" N GLN 7 107 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 115 Processing helix chain '7' and resid 119 through 125 removed outlier: 4.026A pdb=" N ASN 7 123 " --> pdb=" O ARG 7 119 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 158 removed outlier: 3.599A pdb=" N LEU 7 143 " --> pdb=" O LEU 7 139 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 220 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain 'E' and resid 7 through 18 Processing helix chain 'E' and resid 35 through 52 removed outlier: 3.780A pdb=" N LEU E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 4.203A pdb=" N ARG E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 removed outlier: 3.521A pdb=" N PHE E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.929A pdb=" N ILE E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 130 through 135' Processing helix chain 'E' and resid 152 through 157 removed outlier: 3.621A pdb=" N LYS E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 240 removed outlier: 3.945A pdb=" N VAL E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.611A pdb=" N GLN E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 290 through 301 removed outlier: 4.643A pdb=" N LEU E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 340 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.701A pdb=" N LYS E 347 " --> pdb=" O TYR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 367 removed outlier: 3.752A pdb=" N LYS E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS E 360 " --> pdb=" O LYS E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 375 removed outlier: 3.574A pdb=" N GLU E 375 " --> pdb=" O SER E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.670A pdb=" N MET E 380 " --> pdb=" O TRP E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 387 Processing helix chain 'E' and resid 390 through 396 Processing helix chain 'E' and resid 397 through 400 Processing helix chain 'E' and resid 421 through 434 removed outlier: 3.662A pdb=" N VAL E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU E 433 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 434 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 483 removed outlier: 3.945A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA E 483 " --> pdb=" O LEU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 515 removed outlier: 3.572A pdb=" N LEU E 498 " --> pdb=" O ARG E 494 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 501 " --> pdb=" O GLN E 497 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 508 " --> pdb=" O ARG E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 540 Processing helix chain 'E' and resid 541 through 557 removed outlier: 3.636A pdb=" N ALA E 557 " --> pdb=" O ILE E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 614 removed outlier: 3.589A pdb=" N ILE E 612 " --> pdb=" O ALA E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 646 removed outlier: 4.484A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 80 through 105 removed outlier: 4.026A pdb=" N ARG D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 164 removed outlier: 3.641A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 198 Processing helix chain 'D' and resid 279 through 288 removed outlier: 5.006A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.867A pdb=" N GLN B 17 " --> pdb=" O PRO B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.782A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 4.029A pdb=" N ARG B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.220A pdb=" N PHE B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 140 through 160 removed outlier: 3.653A pdb=" N ARG B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 199 removed outlier: 3.536A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 4.207A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 22 removed outlier: 4.021A pdb=" N ASN A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 61 removed outlier: 4.008A pdb=" N GLN A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 104 removed outlier: 4.091A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.614A pdb=" N TYR A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 4.034A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 removed outlier: 3.575A pdb=" N VAL C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.705A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 104 through 116 removed outlier: 4.395A pdb=" N LYS C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.970A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.743A pdb=" N LEU C 169 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 192 removed outlier: 3.549A pdb=" N PHE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 331 through 333 removed outlier: 3.535A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 2 383 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 331 through 333 removed outlier: 3.535A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 2 383 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '3' and resid 179 through 180 removed outlier: 7.140A pdb=" N ASP 3 275 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 210 through 213 Processing sheet with id= E, first strand: chain '4' and resid 332 through 335 removed outlier: 6.610A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS 4 398 " --> pdb=" O ARG 4 334 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '4' and resid 339 through 342 Processing sheet with id= G, first strand: chain '4' and resid 344 through 345 Processing sheet with id= H, first strand: chain '4' and resid 365 through 366 removed outlier: 6.903A pdb=" N ILE 4 365 " --> pdb=" O THR 6 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain '4' and resid 435 through 436 Processing sheet with id= J, first strand: chain '4' and resid 439 through 442 Processing sheet with id= K, first strand: chain '5' and resid 60 through 63 removed outlier: 6.245A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '5' and resid 298 through 301 removed outlier: 8.912A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL 5 292 " --> pdb=" O GLY 5 164 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN 5 334 " --> pdb=" O THR 5 293 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '5' and resid 190 through 193 removed outlier: 6.898A pdb=" N SER 5 247 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N MET 5 182 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N HIS 5 245 " --> pdb=" O MET 5 182 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '6' and resid 150 through 154 removed outlier: 3.675A pdb=" N SER 6 266 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE 6 153 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '6' and resid 273 through 274 Processing sheet with id= P, first strand: chain '6' and resid 454 through 456 removed outlier: 6.330A pdb=" N ASP 6 378 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA 6 456 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE 6 380 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY 6 292 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 404 through 405 Processing sheet with id= R, first strand: chain '7' and resid 77 through 81 Processing sheet with id= S, first strand: chain '7' and resid 252 through 253 removed outlier: 6.777A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '7' and resid 252 through 253 removed outlier: 3.587A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '7' and resid 269 through 270 removed outlier: 3.857A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 119 through 123 removed outlier: 6.944A pdb=" N LEU E 81 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU E 123 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU E 83 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL E 28 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 58 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 188 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 191 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 318 through 321 removed outlier: 5.507A pdb=" N THR E 412 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE E 419 " --> pdb=" O THR E 412 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY E 414 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 569 through 571 removed outlier: 3.993A pdb=" N LEU E 569 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 582 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 227 through 228 removed outlier: 4.020A pdb=" N MET D 277 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 69 through 72 Processing sheet with id= AA, first strand: chain 'C' and resid 15 through 19 removed outlier: 3.607A pdb=" N LEU C 44 " --> pdb=" O CYS C 18 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2247 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: 6.89 Time building geometry restraints manager: 10.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4109 1.32 - 1.45: 6553 1.45 - 1.58: 13334 1.58 - 1.71: 7 1.71 - 1.84: 156 Bond restraints: 24159 Sorted by residual: bond pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta sigma weight residual 1.540 1.620 -0.079 1.36e-02 5.41e+03 3.41e+01 bond pdb=" CA ILE 3 122 " pdb=" CB ILE 3 122 " ideal model delta sigma weight residual 1.537 1.560 -0.024 5.00e-03 4.00e+04 2.23e+01 bond pdb=" N MET C 191 " pdb=" CA MET C 191 " ideal model delta sigma weight residual 1.458 1.518 -0.060 1.27e-02 6.20e+03 2.20e+01 bond pdb=" CA VAL 3 139 " pdb=" CB VAL 3 139 " ideal model delta sigma weight residual 1.537 1.592 -0.055 1.29e-02 6.01e+03 1.82e+01 bond pdb=" N PRO 3 232 " pdb=" CD PRO 3 232 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 ... (remaining 24154 not shown) Histogram of bond angle deviations from ideal: 96.27 - 105.09: 428 105.09 - 113.91: 13783 113.91 - 122.73: 14891 122.73 - 131.55: 3518 131.55 - 140.36: 54 Bond angle restraints: 32674 Sorted by residual: angle pdb=" C THR 5 325 " pdb=" N PRO 5 326 " pdb=" CA PRO 5 326 " ideal model delta sigma weight residual 119.83 140.36 -20.53 1.08e+00 8.57e-01 3.62e+02 angle pdb=" C GLU 4 378 " pdb=" N PRO 4 379 " pdb=" CA PRO 4 379 " ideal model delta sigma weight residual 119.56 134.51 -14.95 1.02e+00 9.61e-01 2.15e+02 angle pdb=" C CYS 6 333 " pdb=" N PRO 6 334 " pdb=" CA PRO 6 334 " ideal model delta sigma weight residual 119.84 136.20 -16.36 1.25e+00 6.40e-01 1.71e+02 angle pdb=" N LEU 7 94 " pdb=" CA LEU 7 94 " pdb=" C LEU 7 94 " ideal model delta sigma weight residual 111.36 123.86 -12.50 1.09e+00 8.42e-01 1.31e+02 angle pdb=" C MET 6 373 " pdb=" N PRO 6 374 " pdb=" CA PRO 6 374 " ideal model delta sigma weight residual 119.90 129.28 -9.38 1.02e+00 9.61e-01 8.46e+01 ... (remaining 32669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.96: 14292 26.96 - 53.93: 437 53.93 - 80.89: 40 80.89 - 107.86: 9 107.86 - 134.82: 1 Dihedral angle restraints: 14779 sinusoidal: 6075 harmonic: 8704 Sorted by residual: dihedral pdb=" CA ASN 4 377 " pdb=" C ASN 4 377 " pdb=" N GLU 4 378 " pdb=" CA GLU 4 378 " ideal model delta harmonic sigma weight residual -180.00 -45.18 -134.82 0 5.00e+00 4.00e-02 7.27e+02 dihedral pdb=" CA ASN A 104 " pdb=" C ASN A 104 " pdb=" N ASN A 105 " pdb=" CA ASN A 105 " ideal model delta harmonic sigma weight residual 180.00 122.45 57.55 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA VAL 7 257 " pdb=" C VAL 7 257 " pdb=" N ILE 7 258 " pdb=" CA ILE 7 258 " ideal model delta harmonic sigma weight residual 0.00 43.85 -43.85 0 5.00e+00 4.00e-02 7.69e+01 ... (remaining 14776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3028 0.072 - 0.144: 616 0.144 - 0.216: 86 0.216 - 0.288: 8 0.288 - 0.361: 2 Chirality restraints: 3740 Sorted by residual: chirality pdb=" CA GLN A 206 " pdb=" N GLN A 206 " pdb=" C GLN A 206 " pdb=" CB GLN A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE 7 258 " pdb=" CA ILE 7 258 " pdb=" CG1 ILE 7 258 " pdb=" CG2 ILE 7 258 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ARG 4 373 " pdb=" N ARG 4 373 " pdb=" C ARG 4 373 " pdb=" CB ARG 4 373 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 3737 not shown) Planarity restraints: 4183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE 2 331 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO 2 332 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO 2 332 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO 2 332 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 122 " -0.046 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO 3 123 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO 3 123 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO 3 123 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 3 193 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO 3 194 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO 3 194 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 3 194 " 0.037 5.00e-02 4.00e+02 ... (remaining 4180 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 16 1.94 - 2.68: 978 2.68 - 3.42: 34855 3.42 - 4.16: 54699 4.16 - 4.90: 94522 Nonbonded interactions: 185070 Sorted by model distance: nonbonded pdb=" CG LYS D 137 " pdb=" NH1 ARG D 141 " model vdw 1.203 3.520 nonbonded pdb=" ND2 ASN E 345 " pdb=" CZ2 TRP E 551 " model vdw 1.551 3.420 nonbonded pdb=" O LYS C 83 " pdb=" OD1 ASN C 86 " model vdw 1.554 3.040 nonbonded pdb=" CG1 VAL A 165 " pdb=" CD2 LEU A 205 " model vdw 1.619 3.880 nonbonded pdb=" OE2 GLU B 187 " pdb=" CG2 ILE C 176 " model vdw 1.653 3.460 ... (remaining 185065 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 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.960 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 63.620 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.009 0.079 24159 Z= 0.571 Angle : 1.540 20.535 32674 Z= 0.988 Chirality : 0.058 0.361 3740 Planarity : 0.006 0.072 4183 Dihedral : 12.912 134.823 9106 Min Nonbonded Distance : 1.203 Molprobity Statistics. All-atom Clashscore : 39.73 Ramachandran Plot: Outliers : 1.14 % Allowed : 9.82 % Favored : 89.04 % Rotamer: Outliers : 0.87 % Allowed : 6.63 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.37 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -3.87 (0.13), residues: 2883 helix: -3.14 (0.11), residues: 982 sheet: -2.24 (0.21), residues: 377 loop : -2.22 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 111 HIS 0.010 0.002 HIS C 138 PHE 0.026 0.003 PHE 6 454 TYR 0.024 0.002 TYR E 325 ARG 0.007 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1144 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8193 (ttm-80) REVERT: 2 246 TYR cc_start: 0.7766 (t80) cc_final: 0.7545 (t80) REVERT: 2 263 CYS cc_start: 0.8077 (m) cc_final: 0.7395 (p) REVERT: 2 265 GLU cc_start: 0.8928 (tp30) cc_final: 0.8423 (tt0) REVERT: 2 277 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7771 (mt-10) REVERT: 2 283 TYR cc_start: 0.6191 (m-10) cc_final: 0.5645 (m-10) REVERT: 2 292 GLU cc_start: 0.8562 (tp30) cc_final: 0.7745 (tm-30) REVERT: 2 308 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8910 (mp0) REVERT: 2 319 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7410 (mtm180) REVERT: 2 352 PHE cc_start: 0.7932 (t80) cc_final: 0.7492 (t80) REVERT: 2 402 LEU cc_start: 0.7982 (mp) cc_final: 0.7521 (tt) REVERT: 2 423 GLU cc_start: 0.8410 (mp0) cc_final: 0.8187 (mp0) REVERT: 2 447 PHE cc_start: 0.8471 (m-10) cc_final: 0.8239 (m-10) REVERT: 3 23 ASP cc_start: 0.8869 (m-30) cc_final: 0.8649 (t0) REVERT: 3 105 GLU cc_start: 0.8936 (mp0) cc_final: 0.8566 (mp0) REVERT: 3 171 LEU cc_start: 0.7959 (tt) cc_final: 0.7736 (tp) REVERT: 3 178 LYS cc_start: 0.8626 (mttm) cc_final: 0.8138 (mtpt) REVERT: 3 193 ARG cc_start: 0.8550 (ttm170) cc_final: 0.8266 (ttm-80) REVERT: 3 212 ARG cc_start: 0.7995 (tpp80) cc_final: 0.6992 (mmm-85) REVERT: 3 213 ASP cc_start: 0.9251 (t0) cc_final: 0.9010 (t0) REVERT: 3 261 MET cc_start: 0.8114 (mmm) cc_final: 0.7477 (mmm) REVERT: 3 272 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.7967 (ttt90) REVERT: 3 275 ASP cc_start: 0.8331 (p0) cc_final: 0.8114 (p0) REVERT: 3 287 LYS cc_start: 0.8490 (pttm) cc_final: 0.8221 (ptmm) REVERT: 4 185 VAL cc_start: 0.8264 (t) cc_final: 0.7955 (m) REVERT: 4 190 CYS cc_start: 0.7838 (m) cc_final: 0.7631 (p) REVERT: 4 229 GLN cc_start: 0.8276 (mt0) cc_final: 0.7865 (mt0) REVERT: 4 232 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8591 (tm-30) REVERT: 4 267 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8647 (mm-30) REVERT: 4 303 VAL cc_start: 0.8946 (t) cc_final: 0.8640 (m) REVERT: 4 326 ILE cc_start: 0.8811 (mt) cc_final: 0.8544 (pt) REVERT: 4 372 GLU cc_start: 0.7375 (mp0) cc_final: 0.7063 (mt-10) REVERT: 4 382 MET cc_start: 0.7498 (tpp) cc_final: 0.7271 (tpt) REVERT: 5 33 ASN cc_start: 0.8479 (m-40) cc_final: 0.8096 (t0) REVERT: 5 37 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8327 (mp0) REVERT: 5 46 TYR cc_start: 0.7457 (m-10) cc_final: 0.7179 (m-10) REVERT: 5 57 LYS cc_start: 0.8786 (mttt) cc_final: 0.8527 (mtmm) REVERT: 5 77 LYS cc_start: 0.8596 (tptt) cc_final: 0.8321 (tppt) REVERT: 5 78 LYS cc_start: 0.8798 (ptpt) cc_final: 0.8191 (ptpp) REVERT: 5 96 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7720 (tm-30) REVERT: 5 165 ILE cc_start: 0.8663 (mt) cc_final: 0.8358 (pt) REVERT: 5 175 ARG cc_start: 0.8977 (mtp180) cc_final: 0.8195 (mtp85) REVERT: 5 181 ILE cc_start: 0.8818 (mt) cc_final: 0.8567 (mm) REVERT: 5 257 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8555 (ttpt) REVERT: 5 275 THR cc_start: 0.8743 (m) cc_final: 0.8419 (p) REVERT: 5 287 ILE cc_start: 0.8783 (mp) cc_final: 0.8511 (tp) REVERT: 6 139 GLN cc_start: 0.9555 (tp-100) cc_final: 0.9174 (tp-100) REVERT: 6 147 ASP cc_start: 0.5227 (m-30) cc_final: 0.3724 (t0) REVERT: 6 153 ILE cc_start: 0.7946 (pp) cc_final: 0.7420 (pp) REVERT: 6 168 MET cc_start: 0.8782 (mmt) cc_final: 0.8456 (mmp) REVERT: 6 174 TYR cc_start: 0.8436 (t80) cc_final: 0.7952 (t80) REVERT: 6 176 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8181 (ttt-90) REVERT: 6 191 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8166 (ttmm) REVERT: 6 269 ASN cc_start: 0.8846 (t0) cc_final: 0.8277 (t0) REVERT: 6 276 ILE cc_start: 0.8500 (pp) cc_final: 0.8191 (pt) REVERT: 6 283 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8755 (mmmm) REVERT: 6 303 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7598 (mt-10) REVERT: 6 355 ASP cc_start: 0.7964 (m-30) cc_final: 0.7548 (m-30) REVERT: 6 382 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7925 (ttt180) REVERT: 6 420 THR cc_start: 0.7364 (p) cc_final: 0.6937 (p) REVERT: 6 457 CYS cc_start: 0.9105 (p) cc_final: 0.8861 (p) REVERT: 7 15 ASN cc_start: 0.9082 (t0) cc_final: 0.8755 (t0) REVERT: 7 20 GLU cc_start: 0.9274 (tt0) cc_final: 0.8890 (tp30) REVERT: 7 73 ARG cc_start: 0.8370 (mtm110) cc_final: 0.7922 (ttp80) REVERT: 7 88 TYR cc_start: 0.8402 (t80) cc_final: 0.7890 (t80) REVERT: 7 122 ASP cc_start: 0.9038 (t0) cc_final: 0.8721 (m-30) REVERT: 7 194 PRO cc_start: 0.7249 (Cg_endo) cc_final: 0.6777 (Cg_exo) REVERT: 7 203 TYR cc_start: 0.8613 (m-10) cc_final: 0.8378 (m-10) REVERT: 7 245 ILE cc_start: 0.7541 (mm) cc_final: 0.7068 (mm) REVERT: 7 252 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8302 (mmtt) REVERT: 7 256 GLU cc_start: 0.8795 (tp30) cc_final: 0.8371 (mp0) REVERT: 7 294 THR cc_start: 0.8114 (m) cc_final: 0.7719 (p) REVERT: 7 313 CYS cc_start: 0.8753 (p) cc_final: 0.8405 (m) REVERT: 7 321 GLN cc_start: 0.8577 (mt0) cc_final: 0.8157 (mp10) REVERT: 7 370 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7260 (mp) REVERT: 7 373 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8322 (mt-10) REVERT: E 72 SER cc_start: 0.8872 (t) cc_final: 0.8553 (p) REVERT: E 151 THR cc_start: 0.8176 (p) cc_final: 0.7959 (p) REVERT: E 241 TYR cc_start: 0.8077 (t80) cc_final: 0.7656 (t80) REVERT: E 264 GLU cc_start: 0.8305 (mp0) cc_final: 0.8054 (mp0) REVERT: E 294 LEU cc_start: 0.9342 (mt) cc_final: 0.9024 (mm) REVERT: E 311 LYS cc_start: 0.7563 (mmmt) cc_final: 0.6465 (mmtm) REVERT: E 325 TYR cc_start: 0.7635 (m-80) cc_final: 0.7305 (m-80) REVERT: E 339 TYR cc_start: 0.9094 (t80) cc_final: 0.8833 (t80) REVERT: E 349 SER cc_start: 0.9084 (m) cc_final: 0.8484 (t) REVERT: E 387 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8301 (mm-30) REVERT: E 407 ASP cc_start: 0.8657 (m-30) cc_final: 0.8006 (m-30) REVERT: E 413 LEU cc_start: 0.6326 (tp) cc_final: 0.6078 (tp) REVERT: E 420 SER cc_start: 0.9109 (m) cc_final: 0.8643 (p) REVERT: E 429 THR cc_start: 0.8547 (p) cc_final: 0.8345 (m) REVERT: E 485 ASP cc_start: 0.8776 (m-30) cc_final: 0.8076 (p0) REVERT: E 487 ARG cc_start: 0.8821 (ptp-170) cc_final: 0.8511 (ptp90) REVERT: E 498 LEU cc_start: 0.8838 (mt) cc_final: 0.8589 (tt) REVERT: E 519 ILE cc_start: 0.7767 (mp) cc_final: 0.7374 (tp) REVERT: E 541 ASN cc_start: 0.8918 (t0) cc_final: 0.8612 (t0) REVERT: E 628 SER cc_start: 0.9007 (p) cc_final: 0.8585 (t) REVERT: D 58 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9101 (mt0) REVERT: D 64 MET cc_start: 0.9357 (mmm) cc_final: 0.9093 (mtm) REVERT: D 76 LEU cc_start: 0.9184 (tp) cc_final: 0.8804 (tp) REVERT: D 84 MET cc_start: 0.8017 (ttm) cc_final: 0.7740 (tmm) REVERT: D 85 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8789 (tptp) REVERT: D 93 MET cc_start: 0.8626 (mmp) cc_final: 0.8415 (tmm) REVERT: D 160 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8818 (tm-30) REVERT: D 218 MET cc_start: 0.8718 (mtp) cc_final: 0.8475 (mtp) REVERT: D 222 PRO cc_start: 0.7837 (Cg_endo) cc_final: 0.7568 (Cg_exo) REVERT: D 230 ILE cc_start: 0.9395 (pt) cc_final: 0.8934 (pt) REVERT: D 290 LYS cc_start: 0.8933 (mttp) cc_final: 0.8473 (mmmt) REVERT: B 81 GLN cc_start: 0.9014 (tt0) cc_final: 0.8450 (pp30) REVERT: B 87 ILE cc_start: 0.8305 (tp) cc_final: 0.7989 (mt) REVERT: B 91 GLN cc_start: 0.8260 (pm20) cc_final: 0.7896 (tm-30) REVERT: B 100 ARG cc_start: 0.8497 (ptp-170) cc_final: 0.8062 (mtm110) REVERT: B 104 TYR cc_start: 0.8572 (t80) cc_final: 0.7865 (t80) REVERT: B 174 SER cc_start: 0.8799 (t) cc_final: 0.8332 (p) REVERT: A 1 MET cc_start: 0.7589 (ptp) cc_final: 0.7101 (ptp) REVERT: A 2 TYR cc_start: 0.6825 (t80) cc_final: 0.5871 (t80) REVERT: A 4 ASP cc_start: 0.8883 (p0) cc_final: 0.8641 (p0) REVERT: A 27 VAL cc_start: 0.8394 (p) cc_final: 0.7918 (p) REVERT: A 32 TYR cc_start: 0.8661 (t80) cc_final: 0.8381 (t80) REVERT: A 35 ASP cc_start: 0.8973 (p0) cc_final: 0.8671 (p0) REVERT: A 70 CYS cc_start: 0.9069 (m) cc_final: 0.8857 (t) REVERT: A 73 PHE cc_start: 0.8791 (t80) cc_final: 0.8424 (t80) REVERT: A 91 ARG cc_start: 0.8489 (ttt90) cc_final: 0.8159 (tpp80) REVERT: A 115 PHE cc_start: 0.6593 (m-80) cc_final: 0.6289 (m-80) REVERT: A 128 GLN cc_start: 0.9038 (tt0) cc_final: 0.8608 (mt0) REVERT: A 129 GLU cc_start: 0.9435 (tt0) cc_final: 0.9008 (mt-10) REVERT: A 133 GLU cc_start: 0.9574 (tt0) cc_final: 0.9371 (mt-10) REVERT: A 137 LEU cc_start: 0.8952 (tt) cc_final: 0.8722 (tt) REVERT: A 151 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8142 (tt) REVERT: A 183 LEU cc_start: 0.8407 (mm) cc_final: 0.7187 (mm) REVERT: A 197 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8114 (mt-10) REVERT: C 19 LYS cc_start: 0.9060 (pttp) cc_final: 0.8637 (pptt) REVERT: C 48 LEU cc_start: 0.9489 (tp) cc_final: 0.9235 (tt) REVERT: C 126 GLU cc_start: 0.9158 (tp30) cc_final: 0.8906 (mm-30) REVERT: C 176 ILE cc_start: 0.8807 (pp) cc_final: 0.8404 (mt) REVERT: C 179 LYS cc_start: 0.9149 (mtpt) cc_final: 0.8909 (mtmt) REVERT: C 188 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8305 (tppt) outliers start: 23 outliers final: 10 residues processed: 1163 average time/residue: 0.4396 time to fit residues: 726.7422 Evaluate side-chains 694 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 682 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 GLN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 263 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 52 ASN 3 177 ASN 4 184 ASN ** 4 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 287 ASN ** 4 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 259 GLN ** 5 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 GLN 7 19 ASN 7 89 GLN E 22 HIS E 26 GLN E 243 GLN E 286 GLN E 360 HIS E 382 HIS ** E 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 GLN ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 ASN E 604 ASN B 22 ASN B 146 GLN B 179 ASN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24159 Z= 0.324 Angle : 1.007 13.748 32674 Z= 0.520 Chirality : 0.053 0.479 3740 Planarity : 0.006 0.064 4183 Dihedral : 7.028 75.902 3234 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.88 % Favored : 90.08 % Rotamer: Outliers : 4.37 % Allowed : 17.68 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.73 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.14), residues: 2883 helix: -1.41 (0.14), residues: 1025 sheet: -2.23 (0.22), residues: 396 loop : -1.88 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 74 HIS 0.009 0.001 HIS 4 386 PHE 0.022 0.002 PHE 4 197 TYR 0.024 0.002 TYR E 288 ARG 0.010 0.001 ARG 4 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 750 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8171 (ttm-80) REVERT: 2 263 CYS cc_start: 0.7972 (m) cc_final: 0.7167 (p) REVERT: 2 265 GLU cc_start: 0.8766 (tp30) cc_final: 0.8400 (tt0) REVERT: 2 277 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7780 (mt-10) REVERT: 2 292 GLU cc_start: 0.8310 (tp30) cc_final: 0.7833 (tm-30) REVERT: 2 300 PHE cc_start: 0.7554 (t80) cc_final: 0.7209 (t80) REVERT: 2 382 TYR cc_start: 0.8986 (m-80) cc_final: 0.8661 (m-80) REVERT: 2 384 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8349 (p0) REVERT: 2 402 LEU cc_start: 0.8025 (mp) cc_final: 0.7527 (tt) REVERT: 3 178 LYS cc_start: 0.8530 (mttm) cc_final: 0.8077 (mtpt) REVERT: 3 193 ARG cc_start: 0.8627 (ttm170) cc_final: 0.8408 (ttm-80) REVERT: 3 212 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7463 (mmm-85) REVERT: 3 213 ASP cc_start: 0.9273 (t0) cc_final: 0.9012 (m-30) REVERT: 3 261 MET cc_start: 0.7998 (mmm) cc_final: 0.7595 (mmm) REVERT: 4 180 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7034 (pt) REVERT: 4 185 VAL cc_start: 0.8291 (t) cc_final: 0.7913 (m) REVERT: 4 197 PHE cc_start: 0.7444 (t80) cc_final: 0.7243 (t80) REVERT: 4 244 ASP cc_start: 0.6767 (t0) cc_final: 0.6441 (t0) REVERT: 4 264 TYR cc_start: 0.8818 (m-10) cc_final: 0.8517 (m-10) REVERT: 4 421 ASP cc_start: 0.9292 (m-30) cc_final: 0.9031 (t0) REVERT: 5 57 LYS cc_start: 0.8831 (mttt) cc_final: 0.8624 (mtmm) REVERT: 5 77 LYS cc_start: 0.8554 (tptt) cc_final: 0.8224 (tppt) REVERT: 5 82 GLU cc_start: 0.8516 (pm20) cc_final: 0.7957 (pm20) REVERT: 5 96 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7421 (tm-30) REVERT: 5 99 LYS cc_start: 0.7963 (mmtp) cc_final: 0.7670 (mptt) REVERT: 5 152 ASP cc_start: 0.8959 (t0) cc_final: 0.8344 (p0) REVERT: 5 175 ARG cc_start: 0.8851 (mtp180) cc_final: 0.8182 (mtp85) REVERT: 5 249 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8411 (mmtm) REVERT: 5 257 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8512 (ttpt) REVERT: 5 275 THR cc_start: 0.8642 (m) cc_final: 0.8355 (p) REVERT: 5 287 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8636 (tp) REVERT: 6 147 ASP cc_start: 0.5412 (m-30) cc_final: 0.3796 (t0) REVERT: 6 168 MET cc_start: 0.8977 (mmt) cc_final: 0.8652 (mmp) REVERT: 6 172 GLU cc_start: 0.9000 (mp0) cc_final: 0.8560 (mp0) REVERT: 6 269 ASN cc_start: 0.8520 (t0) cc_final: 0.7730 (t0) REVERT: 6 355 ASP cc_start: 0.7742 (m-30) cc_final: 0.7392 (m-30) REVERT: 6 382 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7900 (ttt180) REVERT: 6 457 CYS cc_start: 0.9045 (p) cc_final: 0.8773 (p) REVERT: 7 20 GLU cc_start: 0.9227 (tt0) cc_final: 0.8931 (tp30) REVERT: 7 64 MET cc_start: 0.7970 (mmm) cc_final: 0.7698 (mmm) REVERT: 7 203 TYR cc_start: 0.8563 (m-80) cc_final: 0.8081 (m-10) REVERT: 7 252 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8491 (mmmt) REVERT: 7 321 GLN cc_start: 0.8558 (mt0) cc_final: 0.8159 (mp-120) REVERT: E 62 PHE cc_start: 0.8507 (t80) cc_final: 0.8175 (t80) REVERT: E 241 TYR cc_start: 0.8065 (t80) cc_final: 0.7782 (t80) REVERT: E 264 GLU cc_start: 0.8453 (mp0) cc_final: 0.8096 (mp0) REVERT: E 297 ASP cc_start: 0.9086 (m-30) cc_final: 0.8781 (t0) REVERT: E 298 GLU cc_start: 0.8622 (mp0) cc_final: 0.8378 (mp0) REVERT: E 349 SER cc_start: 0.9143 (m) cc_final: 0.8511 (t) REVERT: E 386 ARG cc_start: 0.8749 (mmp80) cc_final: 0.8545 (mmm160) REVERT: E 420 SER cc_start: 0.9101 (m) cc_final: 0.8787 (p) REVERT: E 426 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8300 (tp30) REVERT: E 471 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8418 (mmtm) REVERT: E 485 ASP cc_start: 0.8898 (m-30) cc_final: 0.8042 (p0) REVERT: E 487 ARG cc_start: 0.8756 (ptp-170) cc_final: 0.8511 (ptp90) REVERT: E 498 LEU cc_start: 0.8699 (mt) cc_final: 0.8377 (tp) REVERT: E 628 SER cc_start: 0.8941 (p) cc_final: 0.8547 (t) REVERT: E 629 ILE cc_start: 0.8978 (tt) cc_final: 0.8613 (mp) REVERT: D 58 GLN cc_start: 0.9400 (mm-40) cc_final: 0.9111 (mt0) REVERT: D 70 GLU cc_start: 0.9584 (tp30) cc_final: 0.9158 (tm-30) REVERT: D 93 MET cc_start: 0.8582 (mmp) cc_final: 0.8340 (tmm) REVERT: D 96 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8701 (pp30) REVERT: B 26 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8699 (mtpp) REVERT: B 104 TYR cc_start: 0.8393 (t80) cc_final: 0.8156 (t80) REVERT: B 174 SER cc_start: 0.8938 (t) cc_final: 0.8604 (p) REVERT: A 1 MET cc_start: 0.7428 (ptp) cc_final: 0.6998 (ptp) REVERT: A 2 TYR cc_start: 0.6605 (t80) cc_final: 0.5877 (t80) REVERT: A 35 ASP cc_start: 0.9051 (p0) cc_final: 0.8826 (p0) REVERT: A 91 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8123 (tpp80) REVERT: A 105 ASN cc_start: 0.6349 (m-40) cc_final: 0.6118 (t0) REVERT: A 115 PHE cc_start: 0.6507 (m-80) cc_final: 0.6267 (m-80) REVERT: A 128 GLN cc_start: 0.9089 (tt0) cc_final: 0.8682 (tm-30) REVERT: A 129 GLU cc_start: 0.9463 (tt0) cc_final: 0.9063 (mt-10) REVERT: A 176 THR cc_start: 0.9288 (m) cc_final: 0.9041 (p) REVERT: A 197 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7856 (pt0) REVERT: C 48 LEU cc_start: 0.9456 (tp) cc_final: 0.9140 (tt) REVERT: C 126 GLU cc_start: 0.9010 (tp30) cc_final: 0.8805 (mm-30) REVERT: C 179 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8844 (mtmt) REVERT: C 188 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8062 (tppt) outliers start: 116 outliers final: 62 residues processed: 820 average time/residue: 0.3804 time to fit residues: 468.6862 Evaluate side-chains 676 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 610 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 273 LEU Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 384 ASN Chi-restraints excluded: chain 3 residue 306 MET Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 282 SER Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 163 SER Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 287 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 107 THR Chi-restraints excluded: chain 6 residue 121 ASP Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 278 ASP Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 111 ASN Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 GLN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 332 SER Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 333 GLN 2 454 ASN 3 29 GLN 3 210 HIS ** 4 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 259 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN A 90 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24159 Z= 0.250 Angle : 0.934 13.663 32674 Z= 0.477 Chirality : 0.050 0.422 3740 Planarity : 0.005 0.060 4183 Dihedral : 6.447 59.223 3223 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.54 % Favored : 89.66 % Rotamer: Outliers : 5.01 % Allowed : 20.96 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.69 % Twisted Proline : 0.80 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 2883 helix: -0.56 (0.15), residues: 1024 sheet: -1.93 (0.24), residues: 387 loop : -1.87 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 224 HIS 0.010 0.001 HIS A 125 PHE 0.018 0.002 PHE E 116 TYR 0.022 0.002 TYR 4 460 ARG 0.008 0.001 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 667 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8116 (ttm-80) REVERT: 2 263 CYS cc_start: 0.7945 (m) cc_final: 0.6995 (p) REVERT: 2 265 GLU cc_start: 0.8725 (tp30) cc_final: 0.8427 (tt0) REVERT: 2 267 MET cc_start: 0.7832 (ttp) cc_final: 0.7565 (ttp) REVERT: 2 277 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7753 (mt-10) REVERT: 2 292 GLU cc_start: 0.8412 (tp30) cc_final: 0.7950 (tm-30) REVERT: 2 402 LEU cc_start: 0.7922 (mp) cc_final: 0.7388 (tt) REVERT: 2 444 PHE cc_start: 0.8286 (m-80) cc_final: 0.7845 (m-80) REVERT: 3 38 TYR cc_start: 0.7914 (m-10) cc_final: 0.7702 (m-10) REVERT: 3 120 TYR cc_start: 0.8769 (m-10) cc_final: 0.8544 (m-10) REVERT: 3 178 LYS cc_start: 0.8473 (mttm) cc_final: 0.8032 (mtpt) REVERT: 3 193 ARG cc_start: 0.8511 (ttm170) cc_final: 0.8301 (ttm-80) REVERT: 3 212 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7629 (ttp80) REVERT: 3 230 ILE cc_start: 0.7551 (pt) cc_final: 0.7254 (tp) REVERT: 3 237 GLU cc_start: 0.8365 (pm20) cc_final: 0.8090 (pm20) REVERT: 3 250 PHE cc_start: 0.8833 (m-80) cc_final: 0.8551 (m-80) REVERT: 3 261 MET cc_start: 0.7920 (mmm) cc_final: 0.7467 (mmm) REVERT: 3 290 ASP cc_start: 0.9060 (p0) cc_final: 0.8460 (m-30) REVERT: 4 180 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7101 (pt) REVERT: 4 185 VAL cc_start: 0.8600 (t) cc_final: 0.8262 (m) REVERT: 4 244 ASP cc_start: 0.6900 (t0) cc_final: 0.6564 (t0) REVERT: 4 272 MET cc_start: 0.8097 (ttm) cc_final: 0.7816 (mtm) REVERT: 4 346 PHE cc_start: 0.8184 (t80) cc_final: 0.7393 (t80) REVERT: 4 356 MET cc_start: 0.8749 (tpp) cc_final: 0.8288 (ttm) REVERT: 4 371 CYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6296 (t) REVERT: 4 417 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6478 (pt) REVERT: 5 37 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8162 (mp0) REVERT: 5 57 LYS cc_start: 0.8811 (mttt) cc_final: 0.8601 (mtmm) REVERT: 5 82 GLU cc_start: 0.8456 (pm20) cc_final: 0.7818 (pm20) REVERT: 5 91 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7842 (mt-10) REVERT: 5 96 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7373 (tm-30) REVERT: 5 99 LYS cc_start: 0.7836 (mmtp) cc_final: 0.7566 (mptt) REVERT: 5 152 ASP cc_start: 0.8891 (t0) cc_final: 0.8594 (t0) REVERT: 5 158 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8424 (mtmm) REVERT: 5 175 ARG cc_start: 0.8802 (mtp180) cc_final: 0.8146 (mtp85) REVERT: 5 249 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8322 (mmtm) REVERT: 5 257 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8379 (ttpt) REVERT: 5 270 MET cc_start: 0.8189 (mmp) cc_final: 0.7773 (tpt) REVERT: 5 287 ILE cc_start: 0.8917 (mp) cc_final: 0.8647 (tp) REVERT: 5 334 GLN cc_start: 0.7979 (tt0) cc_final: 0.7324 (tm-30) REVERT: 6 122 PHE cc_start: 0.8173 (p90) cc_final: 0.7967 (p90) REVERT: 6 147 ASP cc_start: 0.5400 (m-30) cc_final: 0.3842 (t0) REVERT: 6 168 MET cc_start: 0.8958 (mmt) cc_final: 0.8517 (mmm) REVERT: 6 172 GLU cc_start: 0.9111 (mp0) cc_final: 0.8630 (mp0) REVERT: 6 280 ARG cc_start: 0.8445 (mmt-90) cc_final: 0.8035 (mmp80) REVERT: 6 283 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8930 (mppt) REVERT: 6 303 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7586 (mt-10) REVERT: 6 378 ASP cc_start: 0.8365 (t0) cc_final: 0.8092 (t0) REVERT: 6 381 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7763 (tt) REVERT: 7 20 GLU cc_start: 0.9205 (tt0) cc_final: 0.8867 (tp30) REVERT: 7 153 MET cc_start: 0.4519 (mmp) cc_final: 0.3604 (mmt) REVERT: 7 203 TYR cc_start: 0.8574 (m-80) cc_final: 0.8191 (m-10) REVERT: 7 225 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8408 (pp) REVERT: 7 244 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7658 (tp) REVERT: 7 252 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8469 (mmmt) REVERT: 7 270 PHE cc_start: 0.7688 (m-80) cc_final: 0.7377 (m-80) REVERT: 7 276 ARG cc_start: 0.8537 (tpp-160) cc_final: 0.8268 (tpp-160) REVERT: 7 321 GLN cc_start: 0.8520 (mt0) cc_final: 0.8161 (mp-120) REVERT: E 51 LYS cc_start: 0.8769 (tppt) cc_final: 0.8317 (tppt) REVERT: E 57 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: E 62 PHE cc_start: 0.8652 (t80) cc_final: 0.8364 (t80) REVERT: E 124 ASP cc_start: 0.7576 (t0) cc_final: 0.7239 (t0) REVERT: E 241 TYR cc_start: 0.8041 (t80) cc_final: 0.7837 (t80) REVERT: E 264 GLU cc_start: 0.8379 (mp0) cc_final: 0.8063 (mp0) REVERT: E 297 ASP cc_start: 0.9098 (m-30) cc_final: 0.8733 (t0) REVERT: E 298 GLU cc_start: 0.8478 (mp0) cc_final: 0.8272 (mp0) REVERT: E 349 SER cc_start: 0.9180 (m) cc_final: 0.8542 (t) REVERT: E 402 GLN cc_start: 0.8997 (tp40) cc_final: 0.8457 (tm-30) REVERT: E 471 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8344 (mmtm) REVERT: E 476 ASN cc_start: 0.8704 (t0) cc_final: 0.8404 (t0) REVERT: E 485 ASP cc_start: 0.8928 (m-30) cc_final: 0.8071 (p0) REVERT: E 497 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: E 628 SER cc_start: 0.8907 (p) cc_final: 0.8563 (t) REVERT: E 629 ILE cc_start: 0.9011 (tt) cc_final: 0.8691 (mp) REVERT: D 58 GLN cc_start: 0.9408 (mm-40) cc_final: 0.9106 (mt0) REVERT: D 60 PHE cc_start: 0.9268 (t80) cc_final: 0.9051 (t80) REVERT: D 85 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8841 (ptpp) REVERT: D 92 SER cc_start: 0.9225 (t) cc_final: 0.8886 (p) REVERT: D 137 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8584 (tttt) REVERT: D 202 MET cc_start: 0.8303 (tpp) cc_final: 0.7732 (tpp) REVERT: D 216 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7773 (p) REVERT: D 226 LYS cc_start: 0.9059 (tppt) cc_final: 0.8640 (tppp) REVERT: D 257 THR cc_start: 0.6388 (p) cc_final: 0.5905 (p) REVERT: B 23 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8932 (mt-10) REVERT: B 91 GLN cc_start: 0.8291 (pm20) cc_final: 0.8033 (tm-30) REVERT: B 103 GLN cc_start: 0.8862 (pp30) cc_final: 0.8637 (pp30) REVERT: B 104 TYR cc_start: 0.8360 (t80) cc_final: 0.8088 (t80) REVERT: B 132 ASP cc_start: 0.8539 (p0) cc_final: 0.8050 (p0) REVERT: B 133 ASP cc_start: 0.8177 (t0) cc_final: 0.7900 (t0) REVERT: B 167 HIS cc_start: 0.8446 (t70) cc_final: 0.8157 (t-170) REVERT: B 174 SER cc_start: 0.8929 (t) cc_final: 0.8653 (p) REVERT: A 1 MET cc_start: 0.7448 (ptp) cc_final: 0.6801 (ptp) REVERT: A 2 TYR cc_start: 0.6562 (t80) cc_final: 0.5859 (t80) REVERT: A 34 GLU cc_start: 0.9083 (pp20) cc_final: 0.8542 (tp30) REVERT: A 80 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9191 (mm-30) REVERT: A 87 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9199 (mm) REVERT: A 91 ARG cc_start: 0.8470 (ttt90) cc_final: 0.8122 (tpp80) REVERT: A 114 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6142 (p) REVERT: A 115 PHE cc_start: 0.6461 (m-80) cc_final: 0.6094 (m-80) REVERT: A 128 GLN cc_start: 0.9134 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 129 GLU cc_start: 0.9590 (tt0) cc_final: 0.9090 (mt-10) REVERT: A 182 ASN cc_start: 0.8872 (t0) cc_final: 0.8510 (t0) REVERT: A 204 TYR cc_start: 0.8451 (m-80) cc_final: 0.8224 (m-80) REVERT: C 179 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8832 (mtmt) REVERT: C 188 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8046 (tppt) outliers start: 133 outliers final: 68 residues processed: 748 average time/residue: 0.3713 time to fit residues: 420.7622 Evaluate side-chains 671 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 592 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 384 ASN Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 190 SER Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 306 MET Chi-restraints excluded: chain 4 residue 180 ILE Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 262 LEU Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 428 ARG Chi-restraints excluded: chain 5 residue 163 SER Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 328 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 121 ASP Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 288 LEU Chi-restraints excluded: chain 6 residue 368 ILE Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 111 ASN Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 GLN Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 497 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 79 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 260 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 280 optimal weight: 0.0670 chunk 138 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 46 GLN 3 175 HIS 3 239 ASN ** 4 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 259 GLN 7 112 HIS E 243 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24159 Z= 0.266 Angle : 0.908 13.927 32674 Z= 0.460 Chirality : 0.049 0.277 3740 Planarity : 0.005 0.058 4183 Dihedral : 6.122 54.620 3223 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.82 % Favored : 89.42 % Rotamer: Outliers : 5.77 % Allowed : 22.69 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.76 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2883 helix: -0.14 (0.16), residues: 1032 sheet: -1.89 (0.25), residues: 382 loop : -1.89 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 111 HIS 0.008 0.001 HIS 4 354 PHE 0.023 0.002 PHE 2 300 TYR 0.028 0.002 TYR 4 264 ARG 0.009 0.001 ARG E 494 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 643 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8049 (ttm-80) REVERT: 2 263 CYS cc_start: 0.7450 (m) cc_final: 0.6598 (p) REVERT: 2 265 GLU cc_start: 0.8732 (tp30) cc_final: 0.8471 (tt0) REVERT: 2 277 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7824 (mt-10) REVERT: 2 292 GLU cc_start: 0.8411 (tp30) cc_final: 0.7883 (tm-30) REVERT: 2 300 PHE cc_start: 0.7549 (t80) cc_final: 0.7245 (t80) REVERT: 2 402 LEU cc_start: 0.7935 (mp) cc_final: 0.7394 (tt) REVERT: 3 39 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8186 (mtp-110) REVERT: 3 178 LYS cc_start: 0.8469 (mttm) cc_final: 0.8003 (mtpt) REVERT: 3 193 ARG cc_start: 0.8512 (ttm170) cc_final: 0.8206 (ttm-80) REVERT: 3 212 ARG cc_start: 0.7998 (tpp80) cc_final: 0.7667 (ttp80) REVERT: 3 250 PHE cc_start: 0.8835 (m-80) cc_final: 0.8252 (m-80) REVERT: 3 261 MET cc_start: 0.7897 (mmm) cc_final: 0.7465 (mmm) REVERT: 3 290 ASP cc_start: 0.9064 (p0) cc_final: 0.8392 (m-30) REVERT: 4 181 TRP cc_start: 0.4622 (t-100) cc_final: 0.4149 (t-100) REVERT: 4 185 VAL cc_start: 0.8531 (t) cc_final: 0.8273 (m) REVERT: 4 244 ASP cc_start: 0.6979 (t0) cc_final: 0.6710 (t70) REVERT: 4 346 PHE cc_start: 0.8156 (t80) cc_final: 0.7371 (t80) REVERT: 4 371 CYS cc_start: 0.6679 (OUTLIER) cc_final: 0.5700 (t) REVERT: 5 29 LYS cc_start: 0.8427 (mmtp) cc_final: 0.7891 (tmmt) REVERT: 5 57 LYS cc_start: 0.8780 (mttt) cc_final: 0.8578 (mtmm) REVERT: 5 91 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7990 (mt-10) REVERT: 5 96 GLN cc_start: 0.8484 (mm-40) cc_final: 0.7460 (tm-30) REVERT: 5 99 LYS cc_start: 0.7844 (mmtp) cc_final: 0.7543 (mptt) REVERT: 5 152 ASP cc_start: 0.8938 (t0) cc_final: 0.8497 (p0) REVERT: 5 158 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8400 (mtmm) REVERT: 5 175 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8197 (mtp85) REVERT: 5 249 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8298 (mmtm) REVERT: 5 256 LEU cc_start: 0.8608 (mp) cc_final: 0.8318 (mp) REVERT: 5 257 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8320 (ttpt) REVERT: 5 287 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8659 (tp) REVERT: 5 334 GLN cc_start: 0.7977 (tt0) cc_final: 0.7334 (tm-30) REVERT: 6 143 MET cc_start: 0.8474 (tpt) cc_final: 0.8108 (tpt) REVERT: 6 147 ASP cc_start: 0.5378 (m-30) cc_final: 0.3816 (t0) REVERT: 6 154 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7836 (t0) REVERT: 6 168 MET cc_start: 0.8970 (mmt) cc_final: 0.8500 (mmm) REVERT: 6 172 GLU cc_start: 0.9135 (mp0) cc_final: 0.8620 (mp0) REVERT: 6 180 PHE cc_start: 0.7865 (m-80) cc_final: 0.7479 (m-80) REVERT: 6 269 ASN cc_start: 0.8564 (m110) cc_final: 0.8340 (t0) REVERT: 6 280 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.8057 (mmp80) REVERT: 6 283 LYS cc_start: 0.9265 (mmmt) cc_final: 0.8965 (mppt) REVERT: 6 378 ASP cc_start: 0.8180 (t0) cc_final: 0.7902 (t0) REVERT: 6 381 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7872 (tt) REVERT: 7 20 GLU cc_start: 0.9186 (tt0) cc_final: 0.8877 (tp30) REVERT: 7 203 TYR cc_start: 0.8608 (m-80) cc_final: 0.8227 (m-10) REVERT: 7 225 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8528 (pp) REVERT: 7 244 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7682 (tp) REVERT: 7 252 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8609 (mmmt) REVERT: 7 270 PHE cc_start: 0.7551 (m-80) cc_final: 0.7336 (m-80) REVERT: 7 276 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.8349 (tpp-160) REVERT: 7 321 GLN cc_start: 0.8420 (mt0) cc_final: 0.8053 (mp10) REVERT: 7 347 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.7683 (p0) REVERT: E 51 LYS cc_start: 0.8458 (tppt) cc_final: 0.8237 (tppt) REVERT: E 72 SER cc_start: 0.8842 (t) cc_final: 0.8519 (p) REVERT: E 124 ASP cc_start: 0.7661 (t0) cc_final: 0.7161 (t0) REVERT: E 297 ASP cc_start: 0.9100 (m-30) cc_final: 0.8695 (t0) REVERT: E 349 SER cc_start: 0.9233 (m) cc_final: 0.8590 (t) REVERT: E 402 GLN cc_start: 0.8887 (tp40) cc_final: 0.8417 (tm-30) REVERT: E 476 ASN cc_start: 0.8752 (t0) cc_final: 0.8405 (t0) REVERT: E 485 ASP cc_start: 0.9041 (m-30) cc_final: 0.8094 (p0) REVERT: E 497 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: E 498 LEU cc_start: 0.8768 (mt) cc_final: 0.8413 (tt) REVERT: E 537 ASP cc_start: 0.9059 (p0) cc_final: 0.8825 (t0) REVERT: E 605 PHE cc_start: 0.8765 (m-80) cc_final: 0.8252 (m-80) REVERT: E 628 SER cc_start: 0.8889 (p) cc_final: 0.8597 (t) REVERT: E 629 ILE cc_start: 0.9046 (tt) cc_final: 0.8735 (mp) REVERT: D 58 GLN cc_start: 0.9413 (mm-40) cc_final: 0.9002 (mt0) REVERT: D 60 PHE cc_start: 0.9295 (t80) cc_final: 0.8997 (t80) REVERT: D 64 MET cc_start: 0.9288 (mmm) cc_final: 0.9019 (ttm) REVERT: D 85 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8748 (pttm) REVERT: D 202 MET cc_start: 0.8197 (tpp) cc_final: 0.7666 (tpp) REVERT: D 213 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7470 (tm-30) REVERT: D 226 LYS cc_start: 0.9089 (tppt) cc_final: 0.8821 (tppt) REVERT: D 257 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.6103 (p) REVERT: B 23 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8931 (mt-10) REVERT: B 80 LYS cc_start: 0.9138 (tptp) cc_final: 0.8820 (tptt) REVERT: B 91 GLN cc_start: 0.8371 (pm20) cc_final: 0.8057 (tm-30) REVERT: B 103 GLN cc_start: 0.8932 (pp30) cc_final: 0.8677 (pp30) REVERT: B 104 TYR cc_start: 0.8432 (t80) cc_final: 0.7974 (t80) REVERT: B 167 HIS cc_start: 0.8437 (t70) cc_final: 0.8208 (t-170) REVERT: B 174 SER cc_start: 0.8916 (t) cc_final: 0.8621 (p) REVERT: A 1 MET cc_start: 0.7487 (ptp) cc_final: 0.6782 (ptp) REVERT: A 2 TYR cc_start: 0.6592 (t80) cc_final: 0.5885 (t80) REVERT: A 32 TYR cc_start: 0.8715 (t80) cc_final: 0.8402 (t80) REVERT: A 34 GLU cc_start: 0.9074 (pp20) cc_final: 0.8659 (tp30) REVERT: A 87 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9161 (mm) REVERT: A 91 ARG cc_start: 0.8476 (ttt90) cc_final: 0.8082 (tpp80) REVERT: A 115 PHE cc_start: 0.6486 (m-80) cc_final: 0.6265 (m-80) REVERT: A 182 ASN cc_start: 0.8835 (t0) cc_final: 0.8555 (t0) REVERT: A 204 TYR cc_start: 0.8640 (m-80) cc_final: 0.8353 (m-80) REVERT: C 110 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8892 (mttp) REVERT: C 115 PHE cc_start: 0.8611 (m-80) cc_final: 0.8308 (m-80) outliers start: 153 outliers final: 95 residues processed: 737 average time/residue: 0.3660 time to fit residues: 409.2747 Evaluate side-chains 693 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 587 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 273 LEU Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 290 HIS Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 384 ASN Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 3 residue 40 ASP Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 190 SER Chi-restraints excluded: chain 3 residue 259 GLN Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 306 MET Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 282 SER Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 334 ARG Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 428 ARG Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 163 SER Chi-restraints excluded: chain 5 residue 170 SER Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 287 ILE Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 107 THR Chi-restraints excluded: chain 6 residue 121 ASP Chi-restraints excluded: chain 6 residue 154 ASP Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 288 LEU Chi-restraints excluded: chain 6 residue 364 ASN Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 380 ILE Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 449 THR Chi-restraints excluded: chain 7 residue 16 ASN Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 111 ASN Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 292 ASN Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 347 ASP Chi-restraints excluded: chain 7 residue 349 VAL Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 373 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 497 GLN Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 110 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 233 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 193 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 251 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 239 ASN ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 155 HIS 5 253 GLN 6 182 GLN 6 362 GLN 7 19 ASN E 13 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 186 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 24159 Z= 0.410 Angle : 0.969 13.366 32674 Z= 0.493 Chirality : 0.052 0.288 3740 Planarity : 0.006 0.082 4183 Dihedral : 6.099 42.649 3216 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.89 % Favored : 88.28 % Rotamer: Outliers : 7.99 % Allowed : 22.47 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.83 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.15), residues: 2883 helix: -0.20 (0.16), residues: 1045 sheet: -2.03 (0.24), residues: 403 loop : -2.06 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 111 HIS 0.009 0.002 HIS D 186 PHE 0.030 0.003 PHE 5 90 TYR 0.038 0.003 TYR 4 264 ARG 0.008 0.001 ARG E 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 610 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8169 (ttm-80) REVERT: 2 263 CYS cc_start: 0.7648 (m) cc_final: 0.6622 (p) REVERT: 2 267 MET cc_start: 0.7783 (ttp) cc_final: 0.7548 (ttp) REVERT: 2 277 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7864 (mt-10) REVERT: 2 292 GLU cc_start: 0.8390 (tp30) cc_final: 0.7819 (tm-30) REVERT: 2 384 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8486 (p0) REVERT: 2 390 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8001 (tt) REVERT: 2 402 LEU cc_start: 0.7892 (mp) cc_final: 0.7357 (tt) REVERT: 2 457 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8209 (mmmt) REVERT: 3 39 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.8105 (mtm110) REVERT: 3 136 MET cc_start: 0.7738 (tpt) cc_final: 0.7487 (tpt) REVERT: 3 171 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8128 (mp) REVERT: 3 174 GLN cc_start: 0.8936 (mp10) cc_final: 0.8699 (pm20) REVERT: 3 178 LYS cc_start: 0.8604 (mttm) cc_final: 0.8128 (mtpt) REVERT: 3 193 ARG cc_start: 0.8542 (ttm170) cc_final: 0.8218 (ttm-80) REVERT: 3 212 ARG cc_start: 0.7946 (tpp80) cc_final: 0.7686 (ttp80) REVERT: 3 261 MET cc_start: 0.7901 (mmm) cc_final: 0.7448 (mmm) REVERT: 4 181 TRP cc_start: 0.4322 (t-100) cc_final: 0.4116 (t-100) REVERT: 4 185 VAL cc_start: 0.8582 (t) cc_final: 0.8299 (m) REVERT: 4 225 TYR cc_start: 0.4748 (t80) cc_final: 0.4545 (t80) REVERT: 4 244 ASP cc_start: 0.7207 (t0) cc_final: 0.6727 (t70) REVERT: 4 347 PHE cc_start: 0.9089 (m-80) cc_final: 0.8725 (m-80) REVERT: 4 371 CYS cc_start: 0.6449 (OUTLIER) cc_final: 0.6083 (t) REVERT: 4 386 HIS cc_start: 0.9303 (m-70) cc_final: 0.9076 (m-70) REVERT: 4 417 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7163 (pt) REVERT: 5 29 LYS cc_start: 0.8521 (mmtp) cc_final: 0.8006 (tmmt) REVERT: 5 37 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8160 (mp0) REVERT: 5 57 LYS cc_start: 0.8798 (mttt) cc_final: 0.8590 (mtmm) REVERT: 5 74 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8748 (p0) REVERT: 5 82 GLU cc_start: 0.8626 (pm20) cc_final: 0.8136 (pm20) REVERT: 5 96 GLN cc_start: 0.8709 (mm-40) cc_final: 0.7949 (tm-30) REVERT: 5 99 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7707 (mptt) REVERT: 5 152 ASP cc_start: 0.9010 (t0) cc_final: 0.8431 (p0) REVERT: 5 155 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6361 (p-80) REVERT: 5 158 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8424 (mtmm) REVERT: 5 161 ARG cc_start: 0.8307 (ttt-90) cc_final: 0.7913 (ttt-90) REVERT: 5 175 ARG cc_start: 0.8997 (mtp180) cc_final: 0.8704 (mtp85) REVERT: 5 179 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7184 (pp) REVERT: 5 205 VAL cc_start: 0.7952 (t) cc_final: 0.7601 (m) REVERT: 5 249 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8373 (mmtm) REVERT: 5 255 PHE cc_start: 0.8774 (m-80) cc_final: 0.8453 (m-80) REVERT: 5 257 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8244 (ttpt) REVERT: 5 287 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8718 (tp) REVERT: 5 331 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8064 (pp) REVERT: 5 334 GLN cc_start: 0.8117 (tt0) cc_final: 0.7271 (tm-30) REVERT: 6 143 MET cc_start: 0.8496 (tpt) cc_final: 0.8274 (tpt) REVERT: 6 147 ASP cc_start: 0.5358 (m-30) cc_final: 0.3767 (t0) REVERT: 6 168 MET cc_start: 0.9068 (mmt) cc_final: 0.8804 (mmp) REVERT: 6 172 GLU cc_start: 0.9205 (mp0) cc_final: 0.8810 (mp0) REVERT: 6 283 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8966 (mppt) REVERT: 6 378 ASP cc_start: 0.8279 (t0) cc_final: 0.8040 (t0) REVERT: 6 381 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7892 (tt) REVERT: 7 203 TYR cc_start: 0.8624 (m-80) cc_final: 0.8191 (m-10) REVERT: 7 225 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8687 (pp) REVERT: 7 231 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8629 (mmmt) REVERT: 7 244 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7782 (tp) REVERT: 7 252 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8547 (mmmt) REVERT: 7 276 ARG cc_start: 0.8608 (tpp-160) cc_final: 0.8316 (tpp-160) REVERT: 7 287 GLU cc_start: 0.8282 (tp30) cc_final: 0.7970 (tp30) REVERT: 7 292 ASN cc_start: 0.5203 (OUTLIER) cc_final: 0.4818 (p0) REVERT: 7 321 GLN cc_start: 0.8339 (mt0) cc_final: 0.8060 (mp10) REVERT: E 51 LYS cc_start: 0.8653 (tppt) cc_final: 0.8391 (tppt) REVERT: E 124 ASP cc_start: 0.7752 (t0) cc_final: 0.7350 (t70) REVERT: E 241 TYR cc_start: 0.8018 (t80) cc_final: 0.7709 (t80) REVERT: E 297 ASP cc_start: 0.9140 (m-30) cc_final: 0.8710 (t0) REVERT: E 314 ASP cc_start: 0.7206 (m-30) cc_final: 0.6993 (m-30) REVERT: E 402 GLN cc_start: 0.8850 (tp40) cc_final: 0.8363 (tm-30) REVERT: E 413 LEU cc_start: 0.7169 (tp) cc_final: 0.6907 (tp) REVERT: E 416 ARG cc_start: 0.8553 (mtt90) cc_final: 0.8320 (mtm-85) REVERT: E 485 ASP cc_start: 0.8984 (m-30) cc_final: 0.8036 (p0) REVERT: E 497 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: E 498 LEU cc_start: 0.8825 (mt) cc_final: 0.8456 (tp) REVERT: E 506 ILE cc_start: 0.9311 (mm) cc_final: 0.9110 (tt) REVERT: E 537 ASP cc_start: 0.9163 (p0) cc_final: 0.8919 (t0) REVERT: E 605 PHE cc_start: 0.8859 (m-80) cc_final: 0.8351 (m-80) REVERT: E 611 GLN cc_start: 0.6776 (pp30) cc_final: 0.6481 (pp30) REVERT: E 629 ILE cc_start: 0.9039 (tt) cc_final: 0.8739 (mp) REVERT: D 58 GLN cc_start: 0.9328 (mm-40) cc_final: 0.9058 (mt0) REVERT: D 92 SER cc_start: 0.9196 (t) cc_final: 0.8623 (p) REVERT: D 108 MET cc_start: 0.5577 (tmm) cc_final: 0.5358 (ppp) REVERT: D 130 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8699 (tm-30) REVERT: D 201 TYR cc_start: 0.7139 (m-80) cc_final: 0.6807 (m-80) REVERT: D 202 MET cc_start: 0.8262 (tpp) cc_final: 0.7846 (tpp) REVERT: D 213 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7729 (tm-30) REVERT: D 257 THR cc_start: 0.7155 (OUTLIER) cc_final: 0.6588 (p) REVERT: D 273 SER cc_start: 0.8737 (m) cc_final: 0.8432 (p) REVERT: B 14 GLU cc_start: 0.9193 (pp20) cc_final: 0.8976 (pp20) REVERT: B 23 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9008 (mt-10) REVERT: B 63 MET cc_start: 0.7740 (mpp) cc_final: 0.7366 (mtt) REVERT: B 91 GLN cc_start: 0.8418 (pm20) cc_final: 0.8148 (tm-30) REVERT: B 103 GLN cc_start: 0.8955 (pp30) cc_final: 0.8660 (pp30) REVERT: B 104 TYR cc_start: 0.8632 (t80) cc_final: 0.8102 (t80) REVERT: B 132 ASP cc_start: 0.8700 (p0) cc_final: 0.8298 (p0) REVERT: B 133 ASP cc_start: 0.8445 (t0) cc_final: 0.8232 (t0) REVERT: B 174 SER cc_start: 0.8866 (t) cc_final: 0.8578 (p) REVERT: B 189 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7861 (mtt) REVERT: A 1 MET cc_start: 0.7495 (ptp) cc_final: 0.6989 (ptp) REVERT: A 2 TYR cc_start: 0.6940 (t80) cc_final: 0.6351 (t80) REVERT: A 32 TYR cc_start: 0.8700 (t80) cc_final: 0.8317 (t80) REVERT: A 34 GLU cc_start: 0.9239 (pp20) cc_final: 0.8931 (tp30) REVERT: A 87 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9252 (mm) REVERT: A 91 ARG cc_start: 0.8625 (ttt90) cc_final: 0.8285 (tpp80) REVERT: A 114 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.6113 (p) REVERT: A 115 PHE cc_start: 0.6480 (m-80) cc_final: 0.6020 (m-80) REVERT: A 182 ASN cc_start: 0.8851 (t0) cc_final: 0.8565 (t0) REVERT: A 202 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8482 (tt0) outliers start: 212 outliers final: 131 residues processed: 755 average time/residue: 0.3637 time to fit residues: 417.5435 Evaluate side-chains 715 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 564 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 203 VAL Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 220 ASP Chi-restraints excluded: chain 2 residue 273 LEU Chi-restraints excluded: chain 2 residue 274 VAL Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 290 HIS Chi-restraints excluded: chain 2 residue 304 TYR Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 384 ASN Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 2 residue 389 THR Chi-restraints excluded: chain 2 residue 390 LEU Chi-restraints excluded: chain 2 residue 413 ASP Chi-restraints excluded: chain 2 residue 432 ASN Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 3 residue 40 ASP Chi-restraints excluded: chain 3 residue 97 ILE Chi-restraints excluded: chain 3 residue 98 ILE Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 137 ASP Chi-restraints excluded: chain 3 residue 166 LEU Chi-restraints excluded: chain 3 residue 171 LEU Chi-restraints excluded: chain 3 residue 190 SER Chi-restraints excluded: chain 3 residue 197 ILE Chi-restraints excluded: chain 3 residue 209 PHE Chi-restraints excluded: chain 3 residue 239 ASN Chi-restraints excluded: chain 3 residue 259 GLN Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 306 MET Chi-restraints excluded: chain 4 residue 183 THR Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 247 ASN Chi-restraints excluded: chain 4 residue 262 LEU Chi-restraints excluded: chain 4 residue 282 SER Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 334 ARG Chi-restraints excluded: chain 4 residue 360 ILE Chi-restraints excluded: chain 4 residue 371 CYS Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 414 SER Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 423 LEU Chi-restraints excluded: chain 4 residue 428 ARG Chi-restraints excluded: chain 4 residue 452 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 74 ASP Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 103 ILE Chi-restraints excluded: chain 5 residue 155 HIS Chi-restraints excluded: chain 5 residue 163 SER Chi-restraints excluded: chain 5 residue 170 SER Chi-restraints excluded: chain 5 residue 179 LEU Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 207 LEU Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 287 ILE Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 328 ILE Chi-restraints excluded: chain 5 residue 331 LEU Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 105 ASP Chi-restraints excluded: chain 6 residue 107 THR Chi-restraints excluded: chain 6 residue 121 ASP Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 272 THR Chi-restraints excluded: chain 6 residue 278 ASP Chi-restraints excluded: chain 6 residue 288 LEU Chi-restraints excluded: chain 6 residue 364 ASN Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 381 LEU Chi-restraints excluded: chain 7 residue 16 ASN Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 111 ASN Chi-restraints excluded: chain 7 residue 114 THR Chi-restraints excluded: chain 7 residue 116 LEU Chi-restraints excluded: chain 7 residue 147 ARG Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 260 TYR Chi-restraints excluded: chain 7 residue 292 ASN Chi-restraints excluded: chain 7 residue 312 GLU Chi-restraints excluded: chain 7 residue 339 LEU Chi-restraints excluded: chain 7 residue 347 ASP Chi-restraints excluded: chain 7 residue 352 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 497 GLN Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 555 CYS Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 184 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 94 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 280 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 269 ASN 7 107 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 604 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24159 Z= 0.270 Angle : 0.918 13.930 32674 Z= 0.464 Chirality : 0.049 0.278 3740 Planarity : 0.005 0.075 4183 Dihedral : 5.869 40.820 3214 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.58 % Favored : 88.66 % Rotamer: Outliers : 6.71 % Allowed : 25.14 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.91 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.15), residues: 2883 helix: 0.05 (0.16), residues: 1048 sheet: -1.95 (0.25), residues: 383 loop : -1.96 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 111 HIS 0.027 0.001 HIS 5 155 PHE 0.026 0.002 PHE 4 300 TYR 0.027 0.002 TYR 4 264 ARG 0.007 0.001 ARG 2 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 606 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable