Starting phenix.real_space_refine on Wed Dec 13 04:10:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/12_2023/3jc6_6534.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/12_2023/3jc6_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_6534/12_2023/3jc6_6534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/12_2023/3jc6_6534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/12_2023/3jc6_6534.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc6_6534/12_2023/3jc6_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 13.57, per 1000 atoms: 0.57 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: 10.02 Conformation dependent library (CDL) restraints added in 3.9 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: 2.67 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: 6.68 Time building geometry restraints manager: 10.65 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.030 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 65.150 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.520 ------------------------------------------------------------------------------- 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 : 2.663 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 outliers start: 23 outliers final: 10 residues processed: 1163 average time/residue: 0.4529 time to fit residues: 747.5611 Evaluate side-chains 644 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 634 time to evaluate : 3.054 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2105 time to fit residues: 8.2385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 169 optimal weight: 10.0000 chunk 263 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN ** 2 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 259 GLN 6 139 GLN 7 89 GLN E 22 HIS E 26 GLN E 243 GLN E 286 GLN E 382 HIS ** E 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 ASN E 604 ASN B 22 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24159 Z= 0.288 Angle : 1.022 13.690 32674 Z= 0.525 Chirality : 0.053 0.371 3740 Planarity : 0.006 0.064 4183 Dihedral : 6.612 72.312 3212 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.64 % Favored : 90.32 % Rotamer: Outliers : 4.37 % Allowed : 18.66 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.73 % Twisted Proline : 0.80 % 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: -2.60 (0.14), residues: 2883 helix: -1.33 (0.14), residues: 1027 sheet: -2.03 (0.22), residues: 384 loop : -1.89 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 74 HIS 0.007 0.001 HIS E 231 PHE 0.028 0.002 PHE A 115 TYR 0.035 0.002 TYR A 2 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 844 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 728 time to evaluate : 2.979 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 outliers start: 116 outliers final: 62 residues processed: 793 average time/residue: 0.3802 time to fit residues: 456.0392 Evaluate side-chains 638 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 576 time to evaluate : 2.849 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.2245 time to fit residues: 29.3757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 261 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 46 GLN 3 210 HIS ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 386 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** ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 HIS E 360 HIS ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24159 Z= 0.244 Angle : 0.939 13.751 32674 Z= 0.480 Chirality : 0.050 0.322 3740 Planarity : 0.005 0.062 4183 Dihedral : 6.182 56.540 3212 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.43 % Favored : 89.73 % Rotamer: Outliers : 3.24 % Allowed : 21.56 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.69 % Twisted Proline : 0.00 % 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: -2.04 (0.15), residues: 2883 helix: -0.49 (0.15), residues: 1036 sheet: -1.78 (0.24), residues: 384 loop : -1.86 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 6 356 HIS 0.011 0.001 HIS 4 354 PHE 0.020 0.002 PHE A 115 TYR 0.025 0.002 TYR 7 203 ARG 0.007 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 738 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 652 time to evaluate : 3.026 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 outliers start: 86 outliers final: 33 residues processed: 706 average time/residue: 0.4100 time to fit residues: 444.7507 Evaluate side-chains 597 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 564 time to evaluate : 2.881 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2759 time to fit residues: 20.1560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 260 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 264 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 333 GLN 3 177 ASN 3 239 ASN 4 386 HIS 4 387 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 13 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24159 Z= 0.308 Angle : 0.945 14.095 32674 Z= 0.480 Chirality : 0.051 0.314 3740 Planarity : 0.005 0.059 4183 Dihedral : 6.019 40.262 3212 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.71 % Favored : 89.46 % Rotamer: Outliers : 4.03 % Allowed : 23.71 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.76 % 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: -1.95 (0.15), residues: 2883 helix: -0.17 (0.16), residues: 1029 sheet: -1.87 (0.25), residues: 389 loop : -1.97 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 111 HIS 0.010 0.001 HIS 2 290 PHE 0.030 0.002 PHE 2 300 TYR 0.033 0.002 TYR 4 264 ARG 0.010 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 712 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 605 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 outliers start: 107 outliers final: 63 residues processed: 672 average time/residue: 0.3708 time to fit residues: 381.3248 Evaluate side-chains 601 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 538 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.2526 time to fit residues: 33.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 233 optimal weight: 0.0170 chunk 159 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 239 ASN 4 247 ASN 4 266 GLN 4 386 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** 5 253 GLN 6 182 GLN 6 362 GLN ** 6 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN E 604 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24159 Z= 0.256 Angle : 0.913 15.244 32674 Z= 0.462 Chirality : 0.049 0.264 3740 Planarity : 0.005 0.071 4183 Dihedral : 5.841 39.385 3212 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.89 % Favored : 89.28 % Rotamer: Outliers : 3.32 % Allowed : 25.22 % Favored : 71.47 % 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: -1.83 (0.15), residues: 2883 helix: 0.04 (0.16), residues: 1040 sheet: -1.84 (0.25), residues: 384 loop : -2.00 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 111 HIS 0.008 0.001 HIS D 186 PHE 0.019 0.002 PHE 6 122 TYR 0.021 0.002 TYR E 579 ARG 0.009 0.001 ARG E 494 *********************** 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 674 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 586 time to evaluate : 3.034 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 outliers start: 88 outliers final: 37 residues processed: 649 average time/residue: 0.3682 time to fit residues: 366.0434 Evaluate side-chains 568 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 531 time to evaluate : 3.149 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2560 time to fit residues: 20.8218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 94 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 177 ASN 4 386 HIS ** 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** 6 173 GLN 7 107 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN E 531 GLN E 604 ASN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24159 Z= 0.256 Angle : 0.909 13.364 32674 Z= 0.460 Chirality : 0.049 0.269 3740 Planarity : 0.005 0.069 4183 Dihedral : 5.748 39.925 3212 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.92 % Favored : 89.32 % Rotamer: Outliers : 2.41 % Allowed : 26.76 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 4.87 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.79 (0.15), residues: 2883 helix: 0.17 (0.16), residues: 1036 sheet: -1.87 (0.25), residues: 396 loop : -2.03 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 111 HIS 0.007 0.001 HIS B 167 PHE 0.018 0.002 PHE A 115 TYR 0.021 0.002 TYR E 579 ARG 0.012 0.001 ARG E 494 *********************** 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 625 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 560 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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