Starting phenix.real_space_refine on Tue Sep 24 15:26:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/09_2024/6tas_10426.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/09_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_10426/09_2024/6tas_10426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/09_2024/6tas_10426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/09_2024/6tas_10426.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tas_10426/09_2024/6tas_10426.cif" } 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. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.57, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 2.05 Conformation dependent library (CDL) restraints added in 1.2 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: 0.93 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: 1.74 Time building geometry restraints manager: 2.41 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: 0.00 - 2.55: 11513 2.55 - 5.09: 249 5.09 - 7.64: 32 7.64 - 10.19: 3 10.19 - 12.73: 1 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 3.120 nonbonded pdb=" OD1 ASP A 163 " pdb=" N GLU A 164 " model vdw 2.095 3.120 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 3.120 nonbonded pdb=" NH1 ARG E 56 " pdb=" OD2 ASP F 144 " model vdw 2.264 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.240 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.590 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- 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 : 0.796 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: 1.0496 time to fit residues: 162.2099 Evaluate side-chains 102 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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: 4.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 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 162 HIS B 99 GLN B 137 GLN B 186 HIS B 204 ASN C 197 GLN D 44 ASN D 127 GLN D 135 ASN D 137 GLN D 156 GLN D 162 HIS E 99 GLN 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: 0.7241 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8754 Z= 0.312 Angle : 0.620 7.979 11798 Z= 0.348 Chirality : 0.042 0.197 1236 Planarity : 0.004 0.032 1536 Dihedral : 4.796 30.993 1129 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.95 % Allowed : 17.90 % Favored : 79.15 % 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: -0.08 (0.26), residues: 1028 helix: 0.22 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.22 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 108 HIS 0.010 0.001 HIS E 203 PHE 0.031 0.003 PHE F 133 TYR 0.020 0.003 TYR B 126 ARG 0.002 0.000 ARG D 56 *********************** 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: 27 poor density : 119 time to evaluate : 1.037 Fit side-chains REVERT: A 48 CYS cc_start: 0.7950 (t) cc_final: 0.7486 (m) REVERT: A 77 ILE cc_start: 0.8357 (pt) cc_final: 0.8130 (pp) REVERT: A 120 SER cc_start: 0.7425 (m) cc_final: 0.7003 (p) REVERT: A 141 ASP cc_start: 0.7565 (m-30) cc_final: 0.7211 (m-30) REVERT: B 102 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.6927 (tmm-80) REVERT: B 134 GLN cc_start: 0.7825 (tp40) cc_final: 0.7185 (tm-30) REVERT: C 77 ILE cc_start: 0.9166 (pt) cc_final: 0.8951 (pp) REVERT: C 130 MET cc_start: 0.7761 (mmm) cc_final: 0.7364 (tpp) REVERT: C 135 ASN cc_start: 0.8731 (p0) cc_final: 0.8398 (p0) REVERT: C 137 GLN cc_start: 0.8564 (tt0) cc_final: 0.8274 (tt0) REVERT: C 141 ASP cc_start: 0.8089 (m-30) cc_final: 0.7751 (m-30) REVERT: C 196 GLU cc_start: 0.7415 (tt0) cc_final: 0.6855 (tt0) REVERT: C 202 GLU cc_start: 0.8254 (tt0) cc_final: 0.7465 (tp30) REVERT: D 48 CYS cc_start: 0.8022 (t) cc_final: 0.7473 (m) REVERT: D 80 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7704 (tm-30) REVERT: D 131 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: D 137 GLN cc_start: 0.8385 (pt0) cc_final: 0.8184 (pt0) REVERT: D 141 ASP cc_start: 0.7759 (m-30) cc_final: 0.7238 (m-30) REVERT: E 44 ASN cc_start: 0.9268 (p0) cc_final: 0.8893 (p0) REVERT: E 46 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7996 (p) REVERT: E 134 GLN cc_start: 0.7617 (tp40) cc_final: 0.7100 (tm-30) REVERT: F 79 ASP cc_start: 0.8496 (t0) cc_final: 0.8295 (t0) REVERT: F 130 MET cc_start: 0.7627 (mmm) cc_final: 0.7184 (tpp) REVERT: F 169 ASP cc_start: 0.7124 (t0) cc_final: 0.6859 (t0) REVERT: F 181 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7784 (ttpp) REVERT: F 202 GLU cc_start: 0.8305 (tt0) cc_final: 0.7851 (tp30) outliers start: 27 outliers final: 14 residues processed: 134 average time/residue: 0.9232 time to fit residues: 134.2395 Evaluate side-chains 123 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 236 THR 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 184 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 46 SER 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: 8.9990 chunk 75 optimal weight: 0.0010 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.7192 ------------------------------------------------------------------------------- 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 197 GLN D 44 ASN D 135 ASN F 137 GLN F 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8754 Z= 0.252 Angle : 0.540 6.538 11798 Z= 0.307 Chirality : 0.040 0.200 1236 Planarity : 0.004 0.031 1536 Dihedral : 4.476 16.436 1126 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.48 % Allowed : 19.65 % Favored : 75.87 % 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: 0.32 (0.27), residues: 1028 helix: 0.82 (0.23), residues: 538 sheet: None (None), residues: 0 loop : -0.39 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 98 HIS 0.010 0.001 HIS B 203 PHE 0.020 0.002 PHE F 133 TYR 0.016 0.002 TYR B 126 ARG 0.002 0.000 ARG D 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 151 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 0.993 Fit side-chains REVERT: A 48 CYS cc_start: 0.7819 (t) cc_final: 0.7418 (m) REVERT: A 77 ILE cc_start: 0.8312 (pt) cc_final: 0.8085 (pp) REVERT: A 80 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 120 SER cc_start: 0.7659 (m) cc_final: 0.7400 (p) REVERT: A 141 ASP cc_start: 0.7661 (m-30) cc_final: 0.7267 (m-30) REVERT: A 192 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7356 (tttt) REVERT: B 44 ASN cc_start: 0.9114 (p0) cc_final: 0.8912 (p0) REVERT: B 102 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.6976 (tmm-80) REVERT: B 134 GLN cc_start: 0.7953 (tp40) cc_final: 0.7280 (tm-30) REVERT: C 77 ILE cc_start: 0.9103 (pt) cc_final: 0.8893 (pp) REVERT: C 93 MET cc_start: 0.6913 (tpp) cc_final: 0.6692 (tmm) REVERT: C 130 MET cc_start: 0.7718 (mmm) cc_final: 0.7317 (tpp) REVERT: C 137 GLN cc_start: 0.8585 (tt0) cc_final: 0.8305 (tt0) REVERT: C 141 ASP cc_start: 0.8064 (m-30) cc_final: 0.7708 (m-30) REVERT: C 196 GLU cc_start: 0.7446 (tt0) cc_final: 0.6881 (tt0) REVERT: C 202 GLU cc_start: 0.8261 (tt0) cc_final: 0.7505 (tp30) REVERT: D 48 CYS cc_start: 0.7916 (t) cc_final: 0.7296 (m) REVERT: D 80 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7539 (tm-30) REVERT: D 131 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: D 141 ASP cc_start: 0.7489 (m-30) cc_final: 0.6989 (m-30) REVERT: E 44 ASN cc_start: 0.9295 (p0) cc_final: 0.8931 (p0) REVERT: E 134 GLN cc_start: 0.7650 (tp40) cc_final: 0.6974 (tm-30) REVERT: F 74 VAL cc_start: 0.6707 (t) cc_final: 0.6442 (t) REVERT: F 130 MET cc_start: 0.7553 (mmm) cc_final: 0.7116 (tpp) REVERT: F 169 ASP cc_start: 0.7251 (t0) cc_final: 0.6950 (t0) REVERT: F 202 GLU cc_start: 0.8309 (tt0) cc_final: 0.7826 (tp30) outliers start: 41 outliers final: 16 residues processed: 140 average time/residue: 0.8953 time to fit residues: 136.2727 Evaluate side-chains 121 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 B residue 96 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 131 GLU 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 118 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 115 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: 0.1980 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 0.0020 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- 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 A 176 ASN B 186 HIS B 203 HIS C 197 GLN E 203 HIS F 197 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8754 Z= 0.150 Angle : 0.467 5.623 11798 Z= 0.263 Chirality : 0.036 0.151 1236 Planarity : 0.003 0.028 1536 Dihedral : 4.102 17.720 1126 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.82 % Allowed : 21.40 % Favored : 74.78 % 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: 0.76 (0.27), residues: 1028 helix: 1.40 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.42 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 98 HIS 0.008 0.001 HIS B 203 PHE 0.024 0.001 PHE H 237 TYR 0.009 0.001 TYR C 126 ARG 0.002 0.000 ARG A 116 *********************** 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 146 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 0.991 Fit side-chains REVERT: A 48 CYS cc_start: 0.7786 (t) cc_final: 0.7461 (m) REVERT: A 77 ILE cc_start: 0.8164 (pt) cc_final: 0.7945 (pp) REVERT: A 80 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 120 SER cc_start: 0.7513 (m) cc_final: 0.7284 (p) REVERT: A 141 ASP cc_start: 0.7549 (m-30) cc_final: 0.7113 (m-30) REVERT: B 44 ASN cc_start: 0.9172 (p0) cc_final: 0.8927 (p0) REVERT: B 102 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6693 (tmm-80) REVERT: B 134 GLN cc_start: 0.7931 (tp40) cc_final: 0.7343 (tm-30) REVERT: C 77 ILE cc_start: 0.8989 (pt) cc_final: 0.8774 (pp) REVERT: C 130 MET cc_start: 0.7679 (mmm) cc_final: 0.7307 (tpp) REVERT: C 137 GLN cc_start: 0.8556 (tt0) cc_final: 0.8260 (tt0) REVERT: C 141 ASP cc_start: 0.8022 (m-30) cc_final: 0.7678 (m-30) REVERT: C 196 GLU cc_start: 0.7242 (tt0) cc_final: 0.6993 (tp30) REVERT: C 202 GLU cc_start: 0.8224 (tt0) cc_final: 0.7465 (tp30) REVERT: G 231 SER cc_start: 0.6609 (t) cc_final: 0.6367 (p) REVERT: D 48 CYS cc_start: 0.7781 (t) cc_final: 0.7275 (m) REVERT: D 80 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7538 (tm-30) REVERT: D 141 ASP cc_start: 0.7452 (m-30) cc_final: 0.6968 (m-30) REVERT: E 42 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6918 (mtpt) REVERT: E 44 ASN cc_start: 0.9346 (p0) cc_final: 0.9075 (p0) REVERT: E 134 GLN cc_start: 0.7663 (tp40) cc_final: 0.7072 (tm-30) REVERT: F 74 VAL cc_start: 0.6463 (t) cc_final: 0.6185 (t) REVERT: F 130 MET cc_start: 0.7383 (mmm) cc_final: 0.6982 (tpp) REVERT: F 169 ASP cc_start: 0.7232 (t0) cc_final: 0.6900 (t0) REVERT: F 202 GLU cc_start: 0.8295 (tt0) cc_final: 0.7802 (tp30) outliers start: 35 outliers final: 13 residues processed: 137 average time/residue: 0.9645 time to fit residues: 142.6615 Evaluate side-chains 116 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 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 C residue 200 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 118 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 195 LEU 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: 1.9990 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 0.0970 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 87 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 162 HIS B 186 HIS B 203 HIS C 58 HIS D 156 GLN E 203 HIS F 197 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8754 Z= 0.112 Angle : 0.450 6.475 11798 Z= 0.249 Chirality : 0.035 0.124 1236 Planarity : 0.003 0.026 1536 Dihedral : 3.723 15.646 1126 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.28 % Allowed : 22.27 % Favored : 74.45 % 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: 0.97 (0.27), residues: 1028 helix: 1.58 (0.24), residues: 526 sheet: None (None), residues: 0 loop : -0.33 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 97 HIS 0.006 0.001 HIS E 203 PHE 0.016 0.001 PHE H 237 TYR 0.006 0.001 TYR A 126 ARG 0.005 0.000 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 132 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 0.991 Fit side-chains REVERT: A 77 ILE cc_start: 0.8031 (pt) cc_final: 0.7814 (pp) REVERT: A 120 SER cc_start: 0.7373 (m) cc_final: 0.7137 (p) REVERT: A 141 ASP cc_start: 0.7390 (m-30) cc_final: 0.6983 (m-30) REVERT: B 44 ASN cc_start: 0.9161 (p0) cc_final: 0.8911 (p0) REVERT: B 102 ARG cc_start: 0.7181 (ttm-80) cc_final: 0.6632 (tmm-80) REVERT: B 134 GLN cc_start: 0.7889 (tp40) cc_final: 0.7376 (tm-30) REVERT: C 77 ILE cc_start: 0.8870 (pt) cc_final: 0.8662 (pp) REVERT: C 130 MET cc_start: 0.7592 (mmm) cc_final: 0.7234 (tpp) REVERT: C 137 GLN cc_start: 0.8510 (tt0) cc_final: 0.8213 (tt0) REVERT: C 141 ASP cc_start: 0.7975 (m-30) cc_final: 0.7630 (m-30) REVERT: C 202 GLU cc_start: 0.8275 (tt0) cc_final: 0.7468 (tp30) REVERT: D 48 CYS cc_start: 0.7721 (t) cc_final: 0.7306 (m) REVERT: D 80 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 137 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7345 (pp30) REVERT: E 42 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7004 (mtpt) REVERT: E 44 ASN cc_start: 0.9337 (p0) cc_final: 0.9112 (p0) REVERT: E 134 GLN cc_start: 0.7668 (tp40) cc_final: 0.7109 (tm-30) REVERT: F 74 VAL cc_start: 0.6290 (t) cc_final: 0.6026 (t) REVERT: F 79 ASP cc_start: 0.8402 (t0) cc_final: 0.8176 (t0) REVERT: F 130 MET cc_start: 0.7320 (mmm) cc_final: 0.6921 (tpp) REVERT: F 169 ASP cc_start: 0.7309 (t0) cc_final: 0.6956 (t0) REVERT: F 202 GLU cc_start: 0.8233 (tt0) cc_final: 0.7764 (tp30) outliers start: 30 outliers final: 15 residues processed: 125 average time/residue: 1.0080 time to fit residues: 135.7523 Evaluate side-chains 112 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 172 PHE Chi-restraints excluded: chain C residue 115 ILE 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 42 LYS Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 200 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 137 GLN A 156 GLN B 186 HIS ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 8754 Z= 0.358 Angle : 0.598 7.165 11798 Z= 0.332 Chirality : 0.041 0.128 1236 Planarity : 0.004 0.031 1536 Dihedral : 4.440 18.328 1126 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.68 % Allowed : 20.63 % Favored : 73.69 % 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: 1.27 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -0.62 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 98 HIS 0.007 0.001 HIS E 203 PHE 0.029 0.003 PHE D 132 TYR 0.023 0.003 TYR B 126 ARG 0.002 0.000 ARG G 247 *********************** 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 164 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 112 time to evaluate : 0.968 Fit side-chains REVERT: A 48 CYS cc_start: 0.7461 (m) cc_final: 0.7167 (t) REVERT: A 77 ILE cc_start: 0.8255 (pt) cc_final: 0.8009 (pp) REVERT: A 141 ASP cc_start: 0.7648 (m-30) cc_final: 0.7231 (m-30) REVERT: B 44 ASN cc_start: 0.9173 (p0) cc_final: 0.8874 (p0) REVERT: B 102 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.6991 (tmm-80) REVERT: B 134 GLN cc_start: 0.8137 (tp40) cc_final: 0.7265 (tm-30) REVERT: C 77 ILE cc_start: 0.9048 (pt) cc_final: 0.8806 (pp) REVERT: C 130 MET cc_start: 0.7495 (mmm) cc_final: 0.7258 (tpp) REVERT: C 137 GLN cc_start: 0.8660 (tt0) cc_final: 0.8286 (tt0) REVERT: C 141 ASP cc_start: 0.8052 (m-30) cc_final: 0.7683 (m-30) REVERT: C 196 GLU cc_start: 0.7506 (tt0) cc_final: 0.7189 (tp30) REVERT: C 202 GLU cc_start: 0.8275 (tt0) cc_final: 0.7521 (tp30) REVERT: D 48 CYS cc_start: 0.8045 (t) cc_final: 0.7317 (m) REVERT: D 80 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7599 (tm-30) REVERT: E 44 ASN cc_start: 0.9384 (p0) cc_final: 0.9080 (p0) REVERT: E 118 HIS cc_start: 0.6899 (OUTLIER) cc_final: 0.6683 (m170) REVERT: E 134 GLN cc_start: 0.8140 (tp40) cc_final: 0.7055 (tm-30) REVERT: E 135 ASN cc_start: 0.8101 (m-40) cc_final: 0.7819 (m-40) REVERT: F 130 MET cc_start: 0.7469 (mmm) cc_final: 0.7093 (tpp) REVERT: F 137 GLN cc_start: 0.8363 (tp40) cc_final: 0.7478 (tp40) REVERT: F 169 ASP cc_start: 0.7250 (t0) cc_final: 0.6929 (t0) REVERT: F 202 GLU cc_start: 0.8329 (tt0) cc_final: 0.7758 (tp30) outliers start: 52 outliers final: 28 residues processed: 151 average time/residue: 0.9434 time to fit residues: 153.8735 Evaluate side-chains 136 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 114 LEU 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 46 SER 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 C residue 200 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 THR 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 93 MET 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 172 PHE Chi-restraints excluded: chain F residue 86 ILE 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: 5.9990 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 E 137 GLN E 203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3081 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= 0.150 Angle : 0.485 8.482 11798 Z= 0.267 Chirality : 0.036 0.132 1236 Planarity : 0.003 0.028 1536 Dihedral : 3.977 18.895 1126 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.38 % Allowed : 23.14 % Favored : 73.47 % 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: 0.86 (0.28), residues: 1028 helix: 1.60 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 504 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 0.017 0.001 PHE A 64 TYR 0.009 0.001 TYR C 126 ARG 0.002 0.000 ARG C 199 *********************** 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 132 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.017 Fit side-chains REVERT: A 48 CYS cc_start: 0.7396 (m) cc_final: 0.7194 (t) REVERT: A 77 ILE cc_start: 0.8148 (pt) cc_final: 0.7912 (pp) REVERT: A 141 ASP cc_start: 0.7368 (m-30) cc_final: 0.6979 (m-30) REVERT: B 44 ASN cc_start: 0.9193 (p0) cc_final: 0.8880 (p0) REVERT: B 102 ARG cc_start: 0.7201 (ttm-80) cc_final: 0.6677 (tmm-80) REVERT: B 134 GLN cc_start: 0.8090 (tp40) cc_final: 0.7335 (tm-30) REVERT: C 77 ILE cc_start: 0.8877 (pt) cc_final: 0.8656 (pp) REVERT: C 130 MET cc_start: 0.7405 (mmm) cc_final: 0.7129 (tpp) REVERT: C 137 GLN cc_start: 0.8582 (tt0) cc_final: 0.8215 (tt0) REVERT: C 141 ASP cc_start: 0.7978 (m-30) cc_final: 0.7612 (m-30) REVERT: C 196 GLU cc_start: 0.6887 (tt0) cc_final: 0.6368 (tt0) REVERT: C 202 GLU cc_start: 0.8227 (tt0) cc_final: 0.7465 (tp30) REVERT: G 231 SER cc_start: 0.6479 (t) cc_final: 0.6220 (p) REVERT: D 48 CYS cc_start: 0.7872 (t) cc_final: 0.7262 (m) REVERT: D 80 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 137 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7363 (pp30) REVERT: E 44 ASN cc_start: 0.9387 (p0) cc_final: 0.9137 (p0) REVERT: E 118 HIS cc_start: 0.6610 (OUTLIER) cc_final: 0.6328 (m170) REVERT: E 134 GLN cc_start: 0.8180 (tp40) cc_final: 0.7222 (tm-30) REVERT: F 74 VAL cc_start: 0.6623 (t) cc_final: 0.6370 (t) REVERT: F 130 MET cc_start: 0.7356 (mmm) cc_final: 0.6904 (tpp) REVERT: F 137 GLN cc_start: 0.8285 (tp40) cc_final: 0.7495 (tp40) REVERT: F 202 GLU cc_start: 0.8264 (tt0) cc_final: 0.7744 (tp30) outliers start: 31 outliers final: 18 residues processed: 125 average time/residue: 1.0548 time to fit residues: 142.0208 Evaluate side-chains 119 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 122 THR 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 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 172 PHE Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 195 LEU 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: 0.2980 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 E 203 HIS H 248 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8754 Z= 0.173 Angle : 0.492 6.319 11798 Z= 0.270 Chirality : 0.037 0.295 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.894 16.888 1126 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.82 % Allowed : 23.25 % Favored : 72.93 % 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: 0.89 (0.28), residues: 1028 helix: 1.64 (0.24), residues: 526 sheet: None (None), residues: 0 loop : -0.53 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 97 HIS 0.007 0.001 HIS E 203 PHE 0.012 0.001 PHE A 64 TYR 0.011 0.001 TYR E 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 140 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 0.919 Fit side-chains REVERT: A 48 CYS cc_start: 0.7441 (m) cc_final: 0.7222 (t) REVERT: A 77 ILE cc_start: 0.8083 (pt) cc_final: 0.7839 (pp) REVERT: A 141 ASP cc_start: 0.7625 (m-30) cc_final: 0.7243 (m-30) REVERT: B 44 ASN cc_start: 0.9203 (p0) cc_final: 0.8894 (p0) REVERT: B 102 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.6866 (tmm-80) REVERT: B 134 GLN cc_start: 0.8079 (tp40) cc_final: 0.7365 (tm-30) REVERT: C 77 ILE cc_start: 0.8854 (pt) cc_final: 0.8633 (pp) REVERT: C 130 MET cc_start: 0.7417 (mmm) cc_final: 0.7146 (tpp) REVERT: C 137 GLN cc_start: 0.8601 (tt0) cc_final: 0.8232 (tt0) REVERT: C 141 ASP cc_start: 0.7977 (m-30) cc_final: 0.7607 (m-30) REVERT: C 196 GLU cc_start: 0.7108 (tt0) cc_final: 0.6557 (tt0) REVERT: C 202 GLU cc_start: 0.8249 (tt0) cc_final: 0.7458 (tp30) REVERT: G 231 SER cc_start: 0.6453 (t) cc_final: 0.6199 (p) REVERT: D 48 CYS cc_start: 0.7911 (t) cc_final: 0.7258 (m) REVERT: D 80 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7413 (tm-30) REVERT: D 137 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7484 (pp30) REVERT: E 44 ASN cc_start: 0.9389 (p0) cc_final: 0.9129 (p0) REVERT: E 118 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.6363 (m170) REVERT: E 134 GLN cc_start: 0.8232 (tp40) cc_final: 0.7223 (tm-30) REVERT: F 74 VAL cc_start: 0.6817 (t) cc_final: 0.6554 (t) REVERT: F 130 MET cc_start: 0.7375 (mmm) cc_final: 0.6914 (tpp) REVERT: F 137 GLN cc_start: 0.8313 (tp40) cc_final: 0.7508 (tp40) REVERT: F 202 GLU cc_start: 0.8314 (tt0) cc_final: 0.7800 (tp30) outliers start: 35 outliers final: 20 residues processed: 130 average time/residue: 1.0003 time to fit residues: 140.3747 Evaluate side-chains 125 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 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 96 THR 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 D residue 184 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 172 PHE Chi-restraints excluded: chain E residue 183 ILE 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: 2.9990 chunk 54 optimal weight: 0.0020 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- 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 156 GLN E 203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8754 Z= 0.185 Angle : 0.498 6.077 11798 Z= 0.274 Chirality : 0.036 0.121 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.883 18.377 1126 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.71 % Allowed : 23.47 % Favored : 72.82 % 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: 0.90 (0.28), residues: 1028 helix: 1.69 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.56 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 97 HIS 0.006 0.001 HIS E 203 PHE 0.012 0.001 PHE A 64 TYR 0.012 0.001 TYR B 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 132 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 0.940 Fit side-chains REVERT: A 77 ILE cc_start: 0.8087 (pt) cc_final: 0.7853 (pp) REVERT: B 44 ASN cc_start: 0.9202 (p0) cc_final: 0.8899 (p0) REVERT: B 102 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6802 (tmm-80) REVERT: B 134 GLN cc_start: 0.8079 (tp40) cc_final: 0.7374 (tm-30) REVERT: C 77 ILE cc_start: 0.8844 (pt) cc_final: 0.8619 (pp) REVERT: C 130 MET cc_start: 0.7420 (mmm) cc_final: 0.7145 (tpp) REVERT: C 137 GLN cc_start: 0.8611 (tt0) cc_final: 0.8249 (tt0) REVERT: C 141 ASP cc_start: 0.7951 (m-30) cc_final: 0.7569 (m-30) REVERT: C 196 GLU cc_start: 0.7166 (tt0) cc_final: 0.6919 (tp30) REVERT: C 202 GLU cc_start: 0.8247 (tt0) cc_final: 0.7497 (tp30) REVERT: G 231 SER cc_start: 0.6436 (t) cc_final: 0.6179 (p) REVERT: D 48 CYS cc_start: 0.7931 (t) cc_final: 0.7264 (m) REVERT: D 80 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7412 (tm-30) REVERT: D 137 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7519 (pp30) REVERT: E 44 ASN cc_start: 0.9399 (p0) cc_final: 0.9135 (p0) REVERT: E 118 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.6355 (m170) REVERT: E 134 GLN cc_start: 0.8146 (tp40) cc_final: 0.7161 (tm-30) REVERT: F 74 VAL cc_start: 0.6818 (t) cc_final: 0.6555 (t) REVERT: F 130 MET cc_start: 0.7385 (mmm) cc_final: 0.6910 (tpp) REVERT: F 137 GLN cc_start: 0.8333 (tp40) cc_final: 0.7504 (tp40) REVERT: F 202 GLU cc_start: 0.8318 (tt0) cc_final: 0.7800 (tp30) outliers start: 34 outliers final: 21 residues processed: 123 average time/residue: 0.8909 time to fit residues: 119.2357 Evaluate side-chains 120 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 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 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 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 183 ILE 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 122 THR 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 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 172 PHE Chi-restraints excluded: chain E residue 183 ILE 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: 0.7980 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 186 HIS B 203 HIS ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8754 Z= 0.276 Angle : 0.568 7.684 11798 Z= 0.314 Chirality : 0.040 0.362 1236 Planarity : 0.004 0.028 1536 Dihedral : 4.189 17.911 1126 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.06 % Allowed : 24.24 % Favored : 72.71 % 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: 0.72 (0.28), residues: 1028 helix: 1.53 (0.24), residues: 524 sheet: None (None), residues: 0 loop : -0.65 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 97 HIS 0.007 0.001 HIS E 203 PHE 0.018 0.002 PHE D 133 TYR 0.017 0.002 TYR B 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 129 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.952 Fit side-chains REVERT: A 77 ILE cc_start: 0.8175 (pt) cc_final: 0.7920 (pp) REVERT: B 44 ASN cc_start: 0.9191 (p0) cc_final: 0.8882 (p0) REVERT: B 102 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.6981 (tmm-80) REVERT: B 134 GLN cc_start: 0.8084 (tp40) cc_final: 0.7338 (tm-30) REVERT: C 77 ILE cc_start: 0.8883 (pt) cc_final: 0.8639 (pp) REVERT: C 130 MET cc_start: 0.7506 (mmm) cc_final: 0.7234 (tpp) REVERT: C 137 GLN cc_start: 0.8663 (tt0) cc_final: 0.8268 (tt0) REVERT: C 141 ASP cc_start: 0.7957 (m-30) cc_final: 0.7569 (m-30) REVERT: C 196 GLU cc_start: 0.7430 (tt0) cc_final: 0.7118 (tp30) REVERT: C 202 GLU cc_start: 0.8247 (tt0) cc_final: 0.7517 (tp30) REVERT: G 231 SER cc_start: 0.6452 (t) cc_final: 0.6192 (p) REVERT: G 246 ASP cc_start: 0.6095 (t70) cc_final: 0.5833 (t70) REVERT: D 48 CYS cc_start: 0.8054 (t) cc_final: 0.7300 (m) REVERT: D 80 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7510 (tm-30) REVERT: E 44 ASN cc_start: 0.9413 (p0) cc_final: 0.9071 (p0) REVERT: E 118 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.6435 (m170) REVERT: E 134 GLN cc_start: 0.8357 (tp40) cc_final: 0.7227 (tm-30) REVERT: E 135 ASN cc_start: 0.7982 (m-40) cc_final: 0.7755 (m-40) REVERT: F 74 VAL cc_start: 0.6895 (t) cc_final: 0.6634 (t) REVERT: F 130 MET cc_start: 0.7435 (mmm) cc_final: 0.6997 (tpp) REVERT: F 137 GLN cc_start: 0.8407 (tp40) cc_final: 0.7562 (tp40) REVERT: F 202 GLU cc_start: 0.8332 (tt0) cc_final: 0.7779 (tp30) outliers start: 28 outliers final: 20 residues processed: 122 average time/residue: 0.8972 time to fit residues: 118.8852 Evaluate side-chains 121 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 106 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 183 ILE 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 122 THR 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 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 172 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 22 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 69 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 156 GLN B 186 HIS B 203 HIS E 203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.137143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.123819 restraints weight = 14742.497| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.40 r_work: 0.3736 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8754 Z= 0.124 Angle : 0.465 6.353 11798 Z= 0.256 Chirality : 0.034 0.125 1236 Planarity : 0.003 0.027 1536 Dihedral : 3.612 18.039 1126 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.07 % Allowed : 25.44 % Favored : 72.49 % 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: 1.08 (0.28), residues: 1028 helix: 1.94 (0.24), residues: 514 sheet: None (None), residues: 0 loop : -0.56 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 98 HIS 0.007 0.001 HIS E 203 PHE 0.017 0.001 PHE A 64 TYR 0.007 0.001 TYR C 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: 2912.32 seconds wall clock time: 51 minutes 34.78 seconds (3094.78 seconds total)