Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 19:40:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/07_2023/6tas_10426.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/07_2023/6tas_10426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/07_2023/6tas_10426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/07_2023/6tas_10426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/07_2023/6tas_10426.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/07_2023/6tas_10426.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.013 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 2 6.06 5 S 24 5.16 5 C 5412 2.51 5 N 1508 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E ARG 199": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F ARG 180": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 8552 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "C" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1356 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain: "G" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 233 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "D" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "E" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "F" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1356 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain: "H" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 233 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" 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 4073 SG CYS G 227 66.952 25.150 72.746 1.00119.70 S ATOM 4098 SG CYS G 230 67.250 28.326 70.975 1.00110.74 S ATOM 4180 SG CYS G 240 63.716 27.219 71.933 1.00141.84 S ATOM 8348 SG CYS H 227 68.651 25.134 58.063 1.00119.70 S ATOM 8373 SG CYS H 230 68.384 28.313 59.924 1.00110.74 S ATOM 8455 SG CYS H 240 71.913 27.194 58.968 1.00141.84 S Time building chain proxies: 4.57, per 1000 atoms: 0.53 Number of scatterers: 8552 At special positions: 0 Unit cell: (136.843, 65.394, 131.999, 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 2 29.99 S 24 16.00 O 1606 8.00 N 1508 7.00 C 5412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 235 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 227 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 230 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 240 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 235 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 230 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 240 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 227 " Number of angles added : 6 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 63.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 57 through 75 removed outlier: 3.673A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.555A pdb=" N LYS A 84 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 87 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.737A pdb=" N THR A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 101 " --> pdb=" O TRP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.764A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.740A pdb=" N ILE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 153 Processing helix chain 'A' and resid 154 through 157 removed outlier: 3.971A pdb=" N LEU A 157 " --> pdb=" O LEU A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.518A pdb=" N LYS A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.685A pdb=" N GLU A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 76 removed outlier: 3.519A pdb=" N GLY B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.536A pdb=" N LEU B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 removed outlier: 4.554A pdb=" N SER B 87 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.522A pdb=" N THR B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 124 through 133 removed outlier: 4.292A pdb=" N ILE B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 153 removed outlier: 3.622A pdb=" N PHE B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.530A pdb=" N PHE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.563A pdb=" N ARG B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 181' Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.927A pdb=" N VAL B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 205 removed outlier: 4.104A pdb=" N LEU B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 75 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.885A pdb=" N ILE C 86 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER C 87 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 88 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 101 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.809A pdb=" N ILE C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.609A pdb=" N PHE C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 176 through 181 removed outlier: 3.520A pdb=" N ARG C 180 " --> pdb=" O ASN C 176 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 181' Processing helix chain 'C' and resid 190 through 204 removed outlier: 3.969A pdb=" N LEU C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN C 204 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 245 Processing helix chain 'D' and resid 57 through 75 removed outlier: 3.674A pdb=" N VAL D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 75 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 removed outlier: 3.554A pdb=" N LYS D 84 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER D 87 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.738A pdb=" N THR D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 101 " --> pdb=" O TRP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.764A pdb=" N ALA D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 112 " --> pdb=" O TRP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 132 removed outlier: 3.738A pdb=" N ILE D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 153 Processing helix chain 'D' and resid 154 through 157 removed outlier: 3.971A pdb=" N LEU D 157 " --> pdb=" O LEU D 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 157' Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 176 through 181 removed outlier: 3.518A pdb=" N LYS D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 203 removed outlier: 3.685A pdb=" N GLU D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 76 removed outlier: 3.520A pdb=" N GLY E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.535A pdb=" N LEU E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 89 removed outlier: 4.554A pdb=" N SER E 87 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.523A pdb=" N THR E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 124 through 133 removed outlier: 4.291A pdb=" N ILE E 128 " --> pdb=" O PRO E 124 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 133 " --> pdb=" O TYR E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 153 removed outlier: 3.621A pdb=" N PHE E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 removed outlier: 3.530A pdb=" N PHE E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 181 removed outlier: 3.563A pdb=" N ARG E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 181' Processing helix chain 'E' and resid 184 through 188 removed outlier: 3.927A pdb=" N VAL E 188 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 205 removed outlier: 4.104A pdb=" N LEU E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU E 195 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU E 196 " --> pdb=" O LYS E 192 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.884A pdb=" N ILE F 86 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER F 87 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 88 " --> pdb=" O GLY F 85 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE F 90 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 101 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 124 through 133 removed outlier: 3.809A pdb=" N ILE F 128 " --> pdb=" O PRO F 124 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE F 133 " --> pdb=" O TYR F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 155 removed outlier: 3.609A pdb=" N PHE F 146 " --> pdb=" O PRO F 142 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 176 through 181 removed outlier: 3.521A pdb=" N ARG F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 181 " --> pdb=" O ILE F 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 176 through 181' Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.814A pdb=" N LEU F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 245 343 hydrogen bonds defined for protein. 957 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: 1.80 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1450 1.31 - 1.43: 2492 1.43 - 1.56: 4776 1.56 - 1.69: 0 1.69 - 1.82: 36 Bond restraints: 8754 Sorted by residual: bond pdb=" C HIS F 189 " pdb=" O HIS F 189 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.26e-02 6.30e+03 1.89e+01 bond pdb=" C PRO D 121 " pdb=" O PRO D 121 " ideal model delta sigma weight residual 1.232 1.190 0.043 1.20e-02 6.94e+03 1.26e+01 bond pdb=" N HIS H 235 " pdb=" CA HIS H 235 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" N PHE A 133 " pdb=" CA PHE A 133 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.23e-02 6.61e+03 1.13e+01 bond pdb=" N CYS B 48 " pdb=" CA CYS B 48 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.34e-02 5.57e+03 1.09e+01 ... (remaining 8749 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.04: 198 107.04 - 113.79: 4806 113.79 - 120.53: 3825 120.53 - 127.28: 2855 127.28 - 134.02: 114 Bond angle restraints: 11798 Sorted by residual: angle pdb=" O HIS F 186 " pdb=" C HIS F 186 " pdb=" N SER F 187 " ideal model delta sigma weight residual 122.03 130.38 -8.35 1.04e+00 9.25e-01 6.45e+01 angle pdb=" CA HIS D 118 " pdb=" CB HIS D 118 " pdb=" CG HIS D 118 " ideal model delta sigma weight residual 113.80 120.42 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" N HIS H 235 " pdb=" CA HIS H 235 " pdb=" C HIS H 235 " ideal model delta sigma weight residual 107.88 116.05 -8.17 1.41e+00 5.03e-01 3.36e+01 angle pdb=" CB ARG G 233 " pdb=" CG ARG G 233 " pdb=" CD ARG G 233 " ideal model delta sigma weight residual 111.30 124.03 -12.73 2.30e+00 1.89e-01 3.06e+01 angle pdb=" CA HIS F 186 " pdb=" C HIS F 186 " pdb=" N SER F 187 " ideal model delta sigma weight residual 116.92 110.62 6.30 1.16e+00 7.43e-01 2.95e+01 ... (remaining 11793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 4318 14.88 - 29.76: 615 29.76 - 44.64: 188 44.64 - 59.52: 27 59.52 - 74.40: 6 Dihedral angle restraints: 5154 sinusoidal: 2146 harmonic: 3008 Sorted by residual: dihedral pdb=" C THR C 190 " pdb=" N THR C 190 " pdb=" CA THR C 190 " pdb=" CB THR C 190 " ideal model delta harmonic sigma weight residual -122.00 -134.93 12.93 0 2.50e+00 1.60e-01 2.67e+01 dihedral pdb=" C PHE A 133 " pdb=" N PHE A 133 " pdb=" CA PHE A 133 " pdb=" CB PHE A 133 " ideal model delta harmonic sigma weight residual -122.60 -134.25 11.65 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" N THR C 190 " pdb=" C THR C 190 " pdb=" CA THR C 190 " pdb=" CB THR C 190 " ideal model delta harmonic sigma weight residual 123.40 134.19 -10.79 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 5151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1129 0.083 - 0.165: 92 0.165 - 0.248: 8 0.248 - 0.330: 4 0.330 - 0.413: 3 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CA THR C 190 " pdb=" N THR C 190 " pdb=" C THR C 190 " pdb=" CB THR C 190 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA HIS F 189 " pdb=" N HIS F 189 " pdb=" C HIS F 189 " pdb=" CB HIS F 189 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA PHE A 133 " pdb=" N PHE A 133 " pdb=" C PHE A 133 " pdb=" CB PHE A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1233 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 186 " -0.019 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C HIS F 186 " 0.073 2.00e-02 2.50e+03 pdb=" O HIS F 186 " -0.029 2.00e-02 2.50e+03 pdb=" N SER F 187 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 232 " 0.018 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C PHE G 232 " -0.068 2.00e-02 2.50e+03 pdb=" O PHE G 232 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG G 233 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS G 230 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C CYS G 230 " 0.067 2.00e-02 2.50e+03 pdb=" O CYS G 230 " -0.025 2.00e-02 2.50e+03 pdb=" N SER G 231 " -0.023 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 71 2.66 - 3.22: 7804 3.22 - 3.78: 10856 3.78 - 4.34: 13552 4.34 - 4.90: 22148 Nonbonded interactions: 54431 Sorted by model distance: nonbonded pdb=" OD1 ASP D 163 " pdb=" N GLU D 164 " model vdw 2.094 2.520 nonbonded pdb=" OD1 ASP A 163 " pdb=" N GLU A 164 " model vdw 2.095 2.520 nonbonded pdb=" OE2 GLU F 164 " pdb=" CD2 PHE F 191 " model vdw 2.232 3.340 nonbonded pdb=" NH1 ARG B 56 " pdb=" OD2 ASP C 144 " model vdw 2.263 2.520 nonbonded pdb=" NH1 ARG E 56 " pdb=" OD2 ASP F 144 " model vdw 2.264 2.520 ... (remaining 54426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 41 through 204) selection = (chain 'C' and resid 41 through 204) selection = chain 'D' selection = (chain 'E' and resid 41 through 204) selection = (chain 'F' and resid 41 through 204) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.000 Extract box with map and model: 1.510 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.090 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 : 0.006 0.055 8754 Z= 0.404 Angle : 0.866 12.733 11798 Z= 0.593 Chirality : 0.055 0.413 1236 Planarity : 0.005 0.044 1536 Dihedral : 14.836 74.403 3214 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1028 helix: -1.54 (0.17), residues: 498 sheet: None (None), residues: 0 loop : 0.08 (0.29), residues: 530 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.008 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 144 average time/residue: 1.0846 time to fit residues: 167.3167 Evaluate side-chains 95 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1253 time to fit residues: 1.5722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 99 GLN B 135 ASN B 137 GLN B 186 HIS B 204 ASN C 197 GLN D 44 ASN D 127 GLN D 135 ASN D 162 HIS E 99 GLN E 135 ASN E 137 GLN E 203 HIS E 204 ASN F 197 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8754 Z= 0.166 Angle : 0.532 6.645 11798 Z= 0.297 Chirality : 0.038 0.179 1236 Planarity : 0.003 0.026 1536 Dihedral : 4.296 14.252 1126 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1028 helix: 0.40 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.12 (0.29), residues: 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.973 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 128 average time/residue: 0.9687 time to fit residues: 134.0185 Evaluate side-chains 106 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 5 average time/residue: 0.3846 time to fit residues: 3.6513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS D 44 ASN D 135 ASN E 134 GLN E 135 ASN F 135 ASN ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8754 Z= 0.275 Angle : 0.566 6.635 11798 Z= 0.319 Chirality : 0.040 0.202 1236 Planarity : 0.004 0.029 1536 Dihedral : 4.385 16.329 1126 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 1028 helix: 0.89 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -0.46 (0.29), residues: 494 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 103 time to evaluate : 1.053 Fit side-chains outliers start: 41 outliers final: 18 residues processed: 130 average time/residue: 0.9989 time to fit residues: 140.2845 Evaluate side-chains 108 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 9 residues processed: 9 average time/residue: 0.4228 time to fit residues: 5.7926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 0.0170 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 197 GLN H 248 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 8754 Z= 0.329 Angle : 0.580 6.344 11798 Z= 0.327 Chirality : 0.040 0.170 1236 Planarity : 0.004 0.032 1536 Dihedral : 4.584 18.417 1126 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 5.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.27), residues: 1028 helix: 1.11 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -0.61 (0.29), residues: 506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 0.989 Fit side-chains outliers start: 49 outliers final: 26 residues processed: 139 average time/residue: 0.9416 time to fit residues: 142.2188 Evaluate side-chains 123 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 13 residues processed: 13 average time/residue: 0.5181 time to fit residues: 8.9949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.0030 chunk 87 optimal weight: 8.9990 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8754 Z= 0.258 Angle : 0.546 6.357 11798 Z= 0.306 Chirality : 0.039 0.124 1236 Planarity : 0.004 0.031 1536 Dihedral : 4.462 17.886 1126 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 4.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 1028 helix: 1.24 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -0.63 (0.29), residues: 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 102 time to evaluate : 1.045 Fit side-chains outliers start: 42 outliers final: 23 residues processed: 137 average time/residue: 0.9069 time to fit residues: 135.1458 Evaluate side-chains 116 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.3494 time to fit residues: 3.9006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN F 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 8754 Z= 0.241 Angle : 0.541 6.355 11798 Z= 0.302 Chirality : 0.038 0.260 1236 Planarity : 0.004 0.030 1536 Dihedral : 4.370 18.246 1126 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 4.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.28), residues: 1028 helix: 1.28 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 1.076 Fit side-chains outliers start: 43 outliers final: 28 residues processed: 133 average time/residue: 0.9125 time to fit residues: 131.7788 Evaluate side-chains 123 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 6 average time/residue: 0.3122 time to fit residues: 3.6076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS B 203 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8754 Z= 0.200 Angle : 0.529 12.634 11798 Z= 0.288 Chirality : 0.037 0.115 1236 Planarity : 0.003 0.030 1536 Dihedral : 4.188 18.522 1126 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 4.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 1028 helix: 1.41 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 104 time to evaluate : 0.995 Fit side-chains outliers start: 42 outliers final: 29 residues processed: 138 average time/residue: 0.9456 time to fit residues: 141.3384 Evaluate side-chains 122 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.5732 time to fit residues: 5.1241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.0370 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 176 ASN B 134 GLN B 135 ASN B 186 HIS B 203 HIS D 137 GLN D 176 ASN F 197 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8754 Z= 0.191 Angle : 0.530 11.087 11798 Z= 0.289 Chirality : 0.037 0.306 1236 Planarity : 0.003 0.030 1536 Dihedral : 4.069 17.642 1126 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 4.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 1028 helix: 1.44 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.60 (0.30), residues: 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 95 time to evaluate : 3.452 Fit side-chains outliers start: 38 outliers final: 27 residues processed: 130 average time/residue: 0.9808 time to fit residues: 139.4468 Evaluate side-chains 122 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 0.5089 time to fit residues: 3.2039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 HIS B 203 HIS F 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8754 Z= 0.191 Angle : 0.532 10.447 11798 Z= 0.291 Chirality : 0.036 0.123 1236 Planarity : 0.003 0.030 1536 Dihedral : 4.017 17.226 1126 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 1028 helix: 1.44 (0.24), residues: 536 sheet: None (None), residues: 0 loop : -0.66 (0.30), residues: 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.052 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 132 average time/residue: 0.9927 time to fit residues: 141.9741 Evaluate side-chains 118 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 0.0702 time to fit residues: 1.5415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0570 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 61 optimal weight: 0.0040 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 186 HIS B 203 HIS D 137 GLN E 203 HIS F 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 8754 Z= 0.138 Angle : 0.506 10.261 11798 Z= 0.276 Chirality : 0.035 0.338 1236 Planarity : 0.003 0.031 1536 Dihedral : 3.670 16.557 1126 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 1028 helix: 1.44 (0.23), residues: 556 sheet: None (None), residues: 0 loop : -0.48 (0.31), residues: 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.992 Fit side-chains outliers start: 28 outliers final: 17 residues processed: 123 average time/residue: 0.9297 time to fit residues: 124.0720 Evaluate side-chains 107 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.0767 time to fit residues: 1.4791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.0370 chunk 57 optimal weight: 5.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 134 GLN B 186 HIS B 203 HIS ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS F 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.136483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.123073 restraints weight = 14725.986| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.42 r_work: 0.3718 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 8754 Z= 0.137 Angle : 0.490 9.972 11798 Z= 0.268 Chirality : 0.034 0.123 1236 Planarity : 0.003 0.029 1536 Dihedral : 3.511 16.316 1126 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.28), residues: 1028 helix: 1.63 (0.24), residues: 556 sheet: None (None), residues: 0 loop : -0.42 (0.31), residues: 472 =============================================================================== Job complete usr+sys time: 2817.03 seconds wall clock time: 50 minutes 58.12 seconds (3058.12 seconds total)