Starting phenix.real_space_refine on Thu Jan 18 10:34:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/01_2024/6tas_10426.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/01_2024/6tas_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_10426/01_2024/6tas_10426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/01_2024/6tas_10426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/01_2024/6tas_10426.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/01_2024/6tas_10426.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 5.10, per 1000 atoms: 0.60 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: 2.90 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: 0.63 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: 2.15 Time building geometry restraints manager: 3.16 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.150 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.340 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.380 ------------------------------------------------------------------------------- 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 % Allowed : 6.55 % Favored : 93.34 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 108 HIS 0.018 0.001 HIS D 118 PHE 0.017 0.001 PHE B 191 TYR 0.016 0.002 TYR A 126 ARG 0.003 0.000 ARG G 233 *********************** 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 : 0.928 Fit side-chains REVERT: B 44 ASN cc_start: 0.9079 (p0) cc_final: 0.8767 (p0) REVERT: B 71 TYR cc_start: 0.7119 (t80) cc_final: 0.6669 (t80) REVERT: B 102 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7460 (tmm-80) REVERT: B 134 GLN cc_start: 0.7733 (tp40) cc_final: 0.7175 (tm130) REVERT: C 77 ILE cc_start: 0.9147 (pt) cc_final: 0.8944 (pp) REVERT: C 137 GLN cc_start: 0.8352 (tt0) cc_final: 0.8149 (tt0) REVERT: C 141 ASP cc_start: 0.8107 (m-30) cc_final: 0.7781 (m-30) REVERT: C 188 VAL cc_start: 0.6506 (OUTLIER) cc_final: 0.6304 (p) REVERT: C 196 GLU cc_start: 0.7474 (tt0) cc_final: 0.6961 (tt0) REVERT: C 202 GLU cc_start: 0.8285 (tt0) cc_final: 0.7408 (tp30) REVERT: D 80 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8039 (tm-30) REVERT: D 86 ILE cc_start: 0.8198 (tp) cc_final: 0.7995 (tp) REVERT: D 141 ASP cc_start: 0.7822 (m-30) cc_final: 0.7366 (m-30) REVERT: E 134 GLN cc_start: 0.7578 (tp40) cc_final: 0.7079 (tt0) REVERT: F 79 ASP cc_start: 0.8332 (t0) cc_final: 0.8043 (t0) REVERT: F 80 GLU cc_start: 0.8443 (pp20) cc_final: 0.8035 (tm-30) REVERT: F 102 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8316 (ttm170) REVERT: F 202 GLU cc_start: 0.8394 (tt0) cc_final: 0.7865 (tp30) outliers start: 1 outliers final: 1 residues processed: 144 average time/residue: 1.0497 time to fit residues: 162.1215 Evaluate side-chains 102 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 VAL 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: 2.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 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: 4.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 99 GLN B 137 GLN B 186 HIS B 204 ASN C 197 GLN D 44 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 162 HIS E 99 GLN E 135 ASN E 137 GLN ** E 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN F 197 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8754 Z= 0.196 Angle : 0.536 6.706 11798 Z= 0.301 Chirality : 0.038 0.175 1236 Planarity : 0.004 0.026 1536 Dihedral : 4.472 33.087 1129 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.84 % Allowed : 15.83 % Favored : 81.33 % 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: 0.07 (0.26), residues: 1028 helix: 0.35 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.15 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 108 HIS 0.009 0.001 HIS E 203 PHE 0.023 0.002 PHE H 237 TYR 0.011 0.002 TYR B 126 ARG 0.002 0.000 ARG H 226 *********************** 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 146 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.979 Fit side-chains REVERT: A 77 ILE cc_start: 0.8232 (pt) cc_final: 0.8011 (pp) REVERT: A 120 SER cc_start: 0.6911 (m) cc_final: 0.6528 (p) REVERT: A 141 ASP cc_start: 0.7535 (m-30) cc_final: 0.7195 (m-30) REVERT: B 102 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6782 (tmm-80) REVERT: B 134 GLN cc_start: 0.7723 (tp40) cc_final: 0.7183 (tm-30) REVERT: C 77 ILE cc_start: 0.9142 (pt) cc_final: 0.8922 (pp) REVERT: C 130 MET cc_start: 0.7722 (mmm) cc_final: 0.7327 (tpp) REVERT: C 135 ASN cc_start: 0.8682 (p0) cc_final: 0.8399 (p0) REVERT: C 141 ASP cc_start: 0.8090 (m-30) cc_final: 0.7731 (m-30) REVERT: C 196 GLU cc_start: 0.7376 (tt0) cc_final: 0.6813 (tt0) REVERT: C 202 GLU cc_start: 0.8246 (tt0) cc_final: 0.7440 (tp30) REVERT: D 80 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7613 (tm-30) REVERT: D 131 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: D 141 ASP cc_start: 0.7636 (m-30) cc_final: 0.7105 (m-30) REVERT: E 44 ASN cc_start: 0.9208 (p0) cc_final: 0.8879 (p0) REVERT: E 134 GLN cc_start: 0.7384 (tp40) cc_final: 0.6941 (tm-30) REVERT: F 135 ASN cc_start: 0.8682 (p0) cc_final: 0.8480 (p0) REVERT: F 169 ASP cc_start: 0.7025 (t0) cc_final: 0.6793 (t0) REVERT: F 181 LYS cc_start: 0.8299 (tmmt) cc_final: 0.7825 (ttpp) REVERT: F 202 GLU cc_start: 0.8254 (tt0) cc_final: 0.7802 (tp30) outliers start: 26 outliers final: 12 residues processed: 135 average time/residue: 0.9879 time to fit residues: 144.7426 Evaluate side-chains 123 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain G residue 237 PHE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 115 ILE 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: 0.9980 chunk 75 optimal weight: 0.0170 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.6024 ------------------------------------------------------------------------------- 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** B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 197 GLN D 44 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** E 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8754 Z= 0.242 Angle : 0.528 6.434 11798 Z= 0.298 Chirality : 0.039 0.192 1236 Planarity : 0.004 0.028 1536 Dihedral : 4.321 15.924 1126 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.82 % Allowed : 19.87 % Favored : 76.31 % 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: 0.35 (0.27), residues: 1028 helix: 0.82 (0.23), residues: 540 sheet: None (None), residues: 0 loop : -0.35 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 98 HIS 0.009 0.001 HIS B 203 PHE 0.020 0.002 PHE F 133 TYR 0.016 0.002 TYR B 126 ARG 0.004 0.000 ARG F 116 *********************** 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 139 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 0.928 Fit side-chains REVERT: A 77 ILE cc_start: 0.8238 (pt) cc_final: 0.8008 (pp) REVERT: A 80 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 120 SER cc_start: 0.7503 (m) cc_final: 0.7200 (p) REVERT: A 137 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7898 (pp30) REVERT: A 141 ASP cc_start: 0.7565 (m-30) cc_final: 0.7177 (m-30) REVERT: B 44 ASN cc_start: 0.8986 (p0) cc_final: 0.8745 (p0) REVERT: B 102 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.6811 (tmm-80) REVERT: B 134 GLN cc_start: 0.7908 (tp40) cc_final: 0.7362 (tm-30) REVERT: C 56 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7564 (ttt90) REVERT: C 77 ILE cc_start: 0.9120 (pt) cc_final: 0.8916 (pp) REVERT: C 130 MET cc_start: 0.7729 (mmm) cc_final: 0.7382 (tpp) REVERT: C 135 ASN cc_start: 0.8719 (p0) cc_final: 0.8439 (p0) REVERT: C 141 ASP cc_start: 0.8101 (m-30) cc_final: 0.7759 (m-30) REVERT: C 196 GLU cc_start: 0.7370 (tt0) cc_final: 0.6805 (tt0) REVERT: C 202 GLU cc_start: 0.8251 (tt0) cc_final: 0.7502 (tp30) REVERT: D 80 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7517 (tm-30) REVERT: D 131 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: D 137 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7550 (pp30) REVERT: D 141 ASP cc_start: 0.7480 (m-30) cc_final: 0.7015 (m-30) REVERT: E 44 ASN cc_start: 0.9187 (p0) cc_final: 0.8869 (p0) REVERT: E 134 GLN cc_start: 0.7578 (tp40) cc_final: 0.7006 (tm-30) REVERT: F 135 ASN cc_start: 0.8720 (p0) cc_final: 0.8484 (p0) REVERT: F 169 ASP cc_start: 0.7220 (t0) cc_final: 0.6925 (t0) REVERT: F 202 GLU cc_start: 0.8252 (tt0) cc_final: 0.7781 (tp30) outliers start: 35 outliers final: 13 residues processed: 125 average time/residue: 0.9366 time to fit residues: 126.9265 Evaluate side-chains 113 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 200 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.0570 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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** B 186 HIS B 203 HIS C 197 GLN D 44 ASN D 127 GLN D 135 ASN E 203 HIS F 197 GLN H 248 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8754 Z= 0.114 Angle : 0.433 5.230 11798 Z= 0.242 Chirality : 0.035 0.154 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.839 15.252 1126 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.95 % Allowed : 20.63 % Favored : 76.42 % 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: 0.94 (0.27), residues: 1028 helix: 1.47 (0.24), residues: 526 sheet: None (None), residues: 0 loop : -0.24 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 108 HIS 0.009 0.001 HIS B 203 PHE 0.025 0.001 PHE H 237 TYR 0.006 0.001 TYR C 126 ARG 0.003 0.000 ARG H 247 *********************** 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 134 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.915 Fit side-chains REVERT: A 77 ILE cc_start: 0.8049 (pt) cc_final: 0.7839 (pp) REVERT: A 120 SER cc_start: 0.7433 (m) cc_final: 0.7158 (p) REVERT: A 141 ASP cc_start: 0.7491 (m-30) cc_final: 0.7083 (m-30) REVERT: A 192 LYS cc_start: 0.7326 (ttmt) cc_final: 0.7103 (tttt) REVERT: B 44 ASN cc_start: 0.9123 (p0) cc_final: 0.8761 (p0) REVERT: B 102 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6647 (tmm-80) REVERT: B 134 GLN cc_start: 0.7900 (tp40) cc_final: 0.7402 (tm-30) REVERT: C 56 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.5971 (ttm110) REVERT: C 77 ILE cc_start: 0.8953 (pt) cc_final: 0.8752 (pp) REVERT: C 130 MET cc_start: 0.7651 (mmm) cc_final: 0.7314 (tpp) REVERT: C 135 ASN cc_start: 0.8652 (p0) cc_final: 0.8432 (p0) REVERT: C 141 ASP cc_start: 0.8030 (m-30) cc_final: 0.7678 (m-30) REVERT: C 202 GLU cc_start: 0.8227 (tt0) cc_final: 0.7499 (tp30) REVERT: D 80 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7416 (tm-30) REVERT: E 44 ASN cc_start: 0.9221 (p0) cc_final: 0.8890 (p0) REVERT: E 134 GLN cc_start: 0.7573 (tp40) cc_final: 0.7077 (tm-30) REVERT: F 56 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7592 (ttm110) REVERT: F 130 MET cc_start: 0.7428 (mmm) cc_final: 0.6973 (tpp) REVERT: F 137 GLN cc_start: 0.8427 (tt0) cc_final: 0.7685 (tp40) REVERT: F 169 ASP cc_start: 0.7221 (t0) cc_final: 0.6872 (t0) REVERT: F 202 GLU cc_start: 0.8239 (tt0) cc_final: 0.7749 (tp30) outliers start: 27 outliers final: 8 residues processed: 126 average time/residue: 1.1648 time to fit residues: 156.9992 Evaluate side-chains 107 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 118 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 86 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN F 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8754 Z= 0.389 Angle : 0.612 6.290 11798 Z= 0.344 Chirality : 0.042 0.141 1236 Planarity : 0.004 0.032 1536 Dihedral : 4.584 17.607 1126 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.35 % Allowed : 21.07 % Favored : 73.58 % 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: 0.42 (0.27), residues: 1028 helix: 1.17 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -0.65 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 98 HIS 0.009 0.001 HIS E 203 PHE 0.031 0.003 PHE D 132 TYR 0.025 0.003 TYR B 126 ARG 0.002 0.001 ARG F 116 *********************** 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 160 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 111 time to evaluate : 0.998 Fit side-chains REVERT: A 77 ILE cc_start: 0.8340 (pt) cc_final: 0.8097 (pp) REVERT: A 120 SER cc_start: 0.7786 (m) cc_final: 0.7584 (p) REVERT: A 141 ASP cc_start: 0.7708 (m-30) cc_final: 0.7282 (m-30) REVERT: A 192 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7530 (tttt) REVERT: B 44 ASN cc_start: 0.9122 (p0) cc_final: 0.8782 (p0) REVERT: B 102 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.6980 (tmm-80) REVERT: B 134 GLN cc_start: 0.7983 (tp40) cc_final: 0.7278 (tm-30) REVERT: C 56 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6265 (ttm110) REVERT: C 77 ILE cc_start: 0.9092 (pt) cc_final: 0.8855 (pp) REVERT: C 130 MET cc_start: 0.7468 (mmm) cc_final: 0.7225 (tpp) REVERT: C 141 ASP cc_start: 0.8068 (m-30) cc_final: 0.7699 (m-30) REVERT: C 196 GLU cc_start: 0.7621 (tt0) cc_final: 0.7083 (tt0) REVERT: C 202 GLU cc_start: 0.8247 (tt0) cc_final: 0.7520 (tp30) REVERT: D 48 CYS cc_start: 0.8283 (t) cc_final: 0.7057 (m) REVERT: D 80 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7695 (tm-30) REVERT: D 102 ARG cc_start: 0.8758 (ttm110) cc_final: 0.8506 (ttm-80) REVERT: D 137 GLN cc_start: 0.8194 (pp30) cc_final: 0.7864 (pt0) REVERT: D 141 ASP cc_start: 0.7594 (m-30) cc_final: 0.7120 (m-30) REVERT: E 44 ASN cc_start: 0.9251 (p0) cc_final: 0.8830 (p0) REVERT: E 134 GLN cc_start: 0.7858 (tp40) cc_final: 0.6867 (tm130) REVERT: F 130 MET cc_start: 0.7623 (mmm) cc_final: 0.7136 (tpp) REVERT: F 137 GLN cc_start: 0.8612 (tt0) cc_final: 0.7934 (tp40) REVERT: F 169 ASP cc_start: 0.7309 (t0) cc_final: 0.6994 (t0) REVERT: F 202 GLU cc_start: 0.8327 (tt0) cc_final: 0.7787 (tp30) outliers start: 49 outliers final: 26 residues processed: 145 average time/residue: 0.9218 time to fit residues: 145.1943 Evaluate side-chains 136 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 166 THR 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: 2.9990 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 0.0870 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.8762 ------------------------------------------------------------------------------- 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 186 HIS B 203 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS F 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8754 Z= 0.130 Angle : 0.469 8.168 11798 Z= 0.261 Chirality : 0.035 0.114 1236 Planarity : 0.003 0.028 1536 Dihedral : 4.023 18.105 1126 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.60 % Allowed : 23.25 % Favored : 73.14 % 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: 1.60 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -0.54 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 98 HIS 0.006 0.001 HIS E 203 PHE 0.016 0.001 PHE A 64 TYR 0.009 0.001 TYR C 126 ARG 0.002 0.000 ARG E 185 *********************** 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 131 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 1.055 Fit side-chains REVERT: A 77 ILE cc_start: 0.8124 (pt) cc_final: 0.7896 (pp) REVERT: A 120 SER cc_start: 0.7432 (m) cc_final: 0.7200 (p) REVERT: A 141 ASP cc_start: 0.7444 (m-30) cc_final: 0.7063 (m-30) REVERT: B 44 ASN cc_start: 0.9174 (p0) cc_final: 0.8761 (p0) REVERT: B 102 ARG cc_start: 0.7215 (ttm-80) cc_final: 0.6681 (tmm-80) REVERT: B 134 GLN cc_start: 0.7949 (tp40) cc_final: 0.7305 (tm-30) REVERT: C 77 ILE cc_start: 0.8961 (pt) cc_final: 0.8749 (pp) REVERT: C 130 MET cc_start: 0.7461 (mmm) cc_final: 0.7177 (tpp) REVERT: C 135 ASN cc_start: 0.8704 (p0) cc_final: 0.8423 (p0) REVERT: C 141 ASP cc_start: 0.7981 (m-30) cc_final: 0.7596 (m-30) REVERT: C 196 GLU cc_start: 0.7249 (tt0) cc_final: 0.6768 (tt0) REVERT: C 202 GLU cc_start: 0.8211 (tt0) cc_final: 0.7485 (tp30) REVERT: D 80 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7470 (tm-30) REVERT: D 137 GLN cc_start: 0.8055 (pp30) cc_final: 0.7640 (pt0) REVERT: E 44 ASN cc_start: 0.9306 (p0) cc_final: 0.9031 (p0) REVERT: E 134 GLN cc_start: 0.7840 (tp40) cc_final: 0.7112 (tt0) REVERT: F 130 MET cc_start: 0.7390 (mmm) cc_final: 0.6933 (tpp) REVERT: F 137 GLN cc_start: 0.8464 (tt0) cc_final: 0.7773 (tp40) REVERT: F 202 GLU cc_start: 0.8242 (tt0) cc_final: 0.7752 (tp30) outliers start: 33 outliers final: 17 residues processed: 124 average time/residue: 0.8897 time to fit residues: 120.1575 Evaluate side-chains 109 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 195 LEU 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: 3.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 135 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** 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: 0.7261 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8754 Z= 0.312 Angle : 0.564 8.433 11798 Z= 0.312 Chirality : 0.040 0.295 1236 Planarity : 0.004 0.029 1536 Dihedral : 4.345 17.586 1126 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.04 % Allowed : 23.69 % Favored : 72.27 % 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: 0.55 (0.28), residues: 1028 helix: 1.38 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -0.72 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 98 HIS 0.007 0.001 HIS E 203 PHE 0.024 0.002 PHE D 132 TYR 0.019 0.002 TYR B 126 ARG 0.004 0.000 ARG D 102 *********************** 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 137 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 0.862 Fit side-chains REVERT: A 77 ILE cc_start: 0.8238 (pt) cc_final: 0.7992 (pp) REVERT: A 141 ASP cc_start: 0.7645 (m-30) cc_final: 0.7241 (m-30) REVERT: B 44 ASN cc_start: 0.9147 (p0) cc_final: 0.8753 (p0) REVERT: B 102 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.6984 (tmm-80) REVERT: B 134 GLN cc_start: 0.7993 (tp40) cc_final: 0.7318 (tm-30) REVERT: C 77 ILE cc_start: 0.9005 (pt) cc_final: 0.8757 (pp) REVERT: C 130 MET cc_start: 0.7526 (mmm) cc_final: 0.7257 (tpp) REVERT: C 141 ASP cc_start: 0.8029 (m-30) cc_final: 0.7643 (m-30) REVERT: C 196 GLU cc_start: 0.7478 (tt0) cc_final: 0.6909 (tt0) REVERT: C 202 GLU cc_start: 0.8240 (tt0) cc_final: 0.7524 (tp30) REVERT: D 80 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 131 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7077 (tt0) REVERT: D 137 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: E 44 ASN cc_start: 0.9294 (p0) cc_final: 0.8873 (p0) REVERT: E 134 GLN cc_start: 0.7994 (tp40) cc_final: 0.6897 (tm-30) REVERT: E 135 ASN cc_start: 0.7789 (m-40) cc_final: 0.7488 (m-40) REVERT: F 130 MET cc_start: 0.7547 (mmm) cc_final: 0.7070 (tpp) REVERT: F 137 GLN cc_start: 0.8552 (tt0) cc_final: 0.7846 (tp40) REVERT: F 202 GLU cc_start: 0.8277 (tt0) cc_final: 0.7720 (tp30) outliers start: 37 outliers final: 20 residues processed: 124 average time/residue: 0.8705 time to fit residues: 117.7789 Evaluate side-chains 120 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ** 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: 0.7197 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8754 Z= 0.174 Angle : 0.486 8.302 11798 Z= 0.269 Chirality : 0.036 0.120 1236 Planarity : 0.003 0.028 1536 Dihedral : 4.051 17.701 1126 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.93 % Allowed : 23.91 % Favored : 72.16 % 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: 0.77 (0.28), residues: 1028 helix: 1.60 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -0.65 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 97 HIS 0.006 0.001 HIS E 203 PHE 0.017 0.001 PHE H 237 TYR 0.011 0.001 TYR B 126 ARG 0.004 0.000 ARG D 102 *********************** 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 134 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 0.979 Fit side-chains REVERT: A 77 ILE cc_start: 0.8159 (pt) cc_final: 0.7919 (pp) REVERT: A 141 ASP cc_start: 0.7629 (m-30) cc_final: 0.7252 (m-30) REVERT: B 44 ASN cc_start: 0.9178 (p0) cc_final: 0.8750 (p0) REVERT: B 102 ARG cc_start: 0.7371 (ttm-80) cc_final: 0.6838 (tmm-80) REVERT: B 134 GLN cc_start: 0.7983 (tp40) cc_final: 0.7361 (tm-30) REVERT: C 77 ILE cc_start: 0.8937 (pt) cc_final: 0.8709 (pp) REVERT: C 130 MET cc_start: 0.7487 (mmm) cc_final: 0.7221 (tpp) REVERT: C 141 ASP cc_start: 0.7971 (m-30) cc_final: 0.7583 (m-30) REVERT: C 196 GLU cc_start: 0.7387 (tt0) cc_final: 0.6852 (tt0) REVERT: C 202 GLU cc_start: 0.8209 (tt0) cc_final: 0.7504 (tp30) REVERT: D 80 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7508 (tm-30) REVERT: E 44 ASN cc_start: 0.9334 (p0) cc_final: 0.9040 (p0) REVERT: E 134 GLN cc_start: 0.8100 (tp40) cc_final: 0.7011 (tm-30) REVERT: F 130 MET cc_start: 0.7477 (mmm) cc_final: 0.6997 (tpp) REVERT: F 137 GLN cc_start: 0.8505 (tt0) cc_final: 0.7803 (tp40) REVERT: F 202 GLU cc_start: 0.8217 (tt0) cc_final: 0.7682 (tp30) outliers start: 36 outliers final: 21 residues processed: 126 average time/residue: 0.8980 time to fit residues: 122.9594 Evaluate side-chains 119 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 195 LEU 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: 0.0070 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 135 ASN B 186 HIS B 203 HIS D 137 GLN D 176 ASN E 203 HIS F 197 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3292 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= 0.128 Angle : 0.465 11.380 11798 Z= 0.252 Chirality : 0.036 0.347 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.668 16.374 1126 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.62 % Allowed : 25.55 % Favored : 71.83 % 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: 0.94 (0.28), residues: 1028 helix: 1.70 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.52 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 98 HIS 0.006 0.001 HIS E 203 PHE 0.020 0.001 PHE H 237 TYR 0.007 0.001 TYR C 126 ARG 0.004 0.000 ARG D 102 *********************** 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 124 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.876 Fit side-chains REVERT: A 77 ILE cc_start: 0.8016 (pt) cc_final: 0.7785 (pp) REVERT: A 137 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6514 (pp30) REVERT: B 44 ASN cc_start: 0.9199 (p0) cc_final: 0.8800 (p0) REVERT: B 102 ARG cc_start: 0.7176 (ttm-80) cc_final: 0.6644 (tmm-80) REVERT: B 134 GLN cc_start: 0.7912 (tp40) cc_final: 0.7373 (tm-30) REVERT: C 77 ILE cc_start: 0.8778 (pt) cc_final: 0.8565 (pp) REVERT: C 130 MET cc_start: 0.7380 (mmm) cc_final: 0.7098 (tpp) REVERT: C 141 ASP cc_start: 0.7925 (m-30) cc_final: 0.7523 (m-30) REVERT: C 196 GLU cc_start: 0.6960 (tt0) cc_final: 0.6494 (tt0) REVERT: C 201 ILE cc_start: 0.7204 (tp) cc_final: 0.6903 (OUTLIER) REVERT: C 202 GLU cc_start: 0.8213 (tt0) cc_final: 0.7472 (tp30) REVERT: D 80 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7320 (tm-30) REVERT: D 137 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: E 44 ASN cc_start: 0.9346 (p0) cc_final: 0.9064 (p0) REVERT: E 134 GLN cc_start: 0.8038 (tp40) cc_final: 0.6995 (tm130) REVERT: F 130 MET cc_start: 0.7418 (mmm) cc_final: 0.6935 (tpp) REVERT: F 137 GLN cc_start: 0.8482 (tt0) cc_final: 0.7833 (tp40) REVERT: F 202 GLU cc_start: 0.8170 (tt0) cc_final: 0.7630 (tp30) outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 0.9890 time to fit residues: 129.3959 Evaluate side-chains 116 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 61 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- 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 137 GLN E 203 HIS F 197 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3279 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 : 0.485 10.288 11798 Z= 0.264 Chirality : 0.035 0.122 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.688 15.996 1126 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.95 % Allowed : 25.44 % Favored : 71.62 % 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: 0.93 (0.28), residues: 1028 helix: 1.62 (0.24), residues: 538 sheet: None (None), residues: 0 loop : -0.51 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 98 HIS 0.007 0.001 HIS E 203 PHE 0.018 0.001 PHE A 172 TYR 0.010 0.001 TYR E 126 ARG 0.004 0.000 ARG D 102 ********************** 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 130 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ILE cc_start: 0.8035 (pt) cc_final: 0.7800 (pp) REVERT: B 44 ASN cc_start: 0.9195 (p0) cc_final: 0.8814 (p0) REVERT: B 102 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6666 (tmm-80) REVERT: B 134 GLN cc_start: 0.7920 (tp40) cc_final: 0.7355 (tm-30) REVERT: C 77 ILE cc_start: 0.8826 (pt) cc_final: 0.8608 (pp) REVERT: C 130 MET cc_start: 0.7405 (mmm) cc_final: 0.7136 (tpp) REVERT: C 141 ASP cc_start: 0.7952 (m-30) cc_final: 0.7547 (m-30) REVERT: C 196 GLU cc_start: 0.7247 (tt0) cc_final: 0.6643 (tt0) REVERT: C 202 GLU cc_start: 0.8215 (tt0) cc_final: 0.7486 (tp30) REVERT: D 80 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7344 (tm-30) REVERT: E 44 ASN cc_start: 0.9345 (p0) cc_final: 0.9056 (p0) REVERT: E 134 GLN cc_start: 0.8068 (tp40) cc_final: 0.7000 (tm130) REVERT: F 130 MET cc_start: 0.7365 (mmm) cc_final: 0.6902 (tpp) REVERT: F 202 GLU cc_start: 0.8183 (tt0) cc_final: 0.7644 (tp30) outliers start: 27 outliers final: 21 residues processed: 124 average time/residue: 0.9912 time to fit residues: 132.8101 Evaluate side-chains 120 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 137 GLN F 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.128999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.115547 restraints weight = 14802.095| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.44 r_work: 0.3619 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8754 Z= 0.278 Angle : 0.559 9.425 11798 Z= 0.307 Chirality : 0.039 0.352 1236 Planarity : 0.004 0.028 1536 Dihedral : 4.048 16.100 1126 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.06 % Allowed : 25.11 % Favored : 71.83 % 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: 0.75 (0.28), residues: 1028 helix: 1.53 (0.24), residues: 534 sheet: None (None), residues: 0 loop : -0.65 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 97 HIS 0.008 0.001 HIS E 140 PHE 0.025 0.002 PHE A 172 TYR 0.017 0.002 TYR E 126 ARG 0.004 0.000 ARG D 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2859.14 seconds wall clock time: 51 minutes 44.26 seconds (3104.26 seconds total)