Starting phenix.real_space_refine on Thu Mar 14 14:47:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/03_2024/8i6o_35201.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/03_2024/8i6o_35201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/03_2024/8i6o_35201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/03_2024/8i6o_35201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/03_2024/8i6o_35201.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/03_2024/8i6o_35201.pdb" } resolution = 3.8 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= 0.047 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5876 2.51 5 N 1498 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "D TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 142": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9084 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2299 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2299 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1126 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 148} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 12, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Time building chain proxies: 5.06, per 1000 atoms: 0.56 Number of scatterers: 9084 At special positions: 0 Unit cell: (78.455, 81.77, 233.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1690 8.00 N 1498 7.00 C 5876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 61.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.735A pdb=" N HIS A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 84 removed outlier: 3.887A pdb=" N SER A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.407A pdb=" N TRP A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.673A pdb=" N GLU A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 234 removed outlier: 3.859A pdb=" N ARG A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 247 through 272 Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.891A pdb=" N GLY A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 Processing helix chain 'B' and resid 41 through 49 removed outlier: 4.117A pdb=" N LEU B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.554A pdb=" N GLN B 80 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 81 " --> pdb=" O ARG B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 81' Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.931A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.907A pdb=" N ILE B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 151 removed outlier: 4.036A pdb=" N ALA B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 186 removed outlier: 3.863A pdb=" N SER B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'C' and resid 36 through 54 Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.748A pdb=" N GLY C 67 " --> pdb=" O CYS C 63 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Proline residue: C 73 - end of helix Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 105 through 119 Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.989A pdb=" N GLN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 180 removed outlier: 4.019A pdb=" N GLU C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 233 removed outlier: 3.547A pdb=" N LEU C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 247 through 292 removed outlier: 3.786A pdb=" N VAL C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Proline residue: C 254 - end of helix removed outlier: 3.655A pdb=" N ASN C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 313 Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.938A pdb=" N ALA C 326 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 39 Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.696A pdb=" N ILE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 79 removed outlier: 3.576A pdb=" N ARG D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 108 Processing helix chain 'D' and resid 110 through 126 removed outlier: 3.710A pdb=" N GLU D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 151 removed outlier: 3.909A pdb=" N ALA D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 186 removed outlier: 4.077A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.650A pdb=" N ALA D 201 " --> pdb=" O ALA D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 98 removed outlier: 3.777A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.765A pdb=" N GLN E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.844A pdb=" N LEU E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 186 removed outlier: 3.992A pdb=" N ILE E 169 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 removed outlier: 4.068A pdb=" N ALA E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN E 198 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN E 199 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 removed outlier: 6.844A pdb=" N VAL A 158 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 127 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 160 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA A 125 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR A 162 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 21 removed outlier: 5.443A pdb=" N VAL B 7 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 4 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU B 60 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN B 6 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS B 58 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 83 removed outlier: 7.007A pdb=" N GLY B 82 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 211 removed outlier: 7.307A pdb=" N THR B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.504A pdb=" N GLN C 126 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 186 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 8 removed outlier: 3.927A pdb=" N GLU D 5 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 58 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL D 7 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER D 56 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.652A pdb=" N PHE D 32 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 219 " --> pdb=" O MET D 207 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.657A pdb=" N ASP D 162 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA D 161 " --> pdb=" O LEU D 191 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1512 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: 2.46 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2982 1.34 - 1.46: 1047 1.46 - 1.58: 5159 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 9226 Sorted by residual: bond pdb=" C ILE E 144 " pdb=" O ILE E 144 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.29e-02 6.01e+03 1.82e+00 bond pdb=" CA GLU D 163 " pdb=" CB GLU D 163 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.33e+00 bond pdb=" CG GLU C 114 " pdb=" CD GLU C 114 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" CD GLU C 114 " pdb=" OE1 GLU C 114 " ideal model delta sigma weight residual 1.249 1.228 0.021 1.90e-02 2.77e+03 1.18e+00 bond pdb=" N LYS D 130 " pdb=" CA LYS D 130 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.40e-01 ... (remaining 9221 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.96: 230 106.96 - 113.78: 5373 113.78 - 120.59: 3672 120.59 - 127.40: 3094 127.40 - 134.22: 83 Bond angle restraints: 12452 Sorted by residual: angle pdb=" N VAL C 319 " pdb=" CA VAL C 319 " pdb=" C VAL C 319 " ideal model delta sigma weight residual 111.62 108.52 3.10 7.90e-01 1.60e+00 1.54e+01 angle pdb=" N GLU C 114 " pdb=" CA GLU C 114 " pdb=" CB GLU C 114 " ideal model delta sigma weight residual 110.28 116.11 -5.83 1.55e+00 4.16e-01 1.41e+01 angle pdb=" C ARG C 113 " pdb=" N GLU C 114 " pdb=" CA GLU C 114 " ideal model delta sigma weight residual 120.31 115.50 4.81 1.52e+00 4.33e-01 1.00e+01 angle pdb=" CB LYS E 173 " pdb=" CG LYS E 173 " pdb=" CD LYS E 173 " ideal model delta sigma weight residual 111.30 118.02 -6.72 2.30e+00 1.89e-01 8.53e+00 angle pdb=" N GLY C 58 " pdb=" CA GLY C 58 " pdb=" C GLY C 58 " ideal model delta sigma weight residual 111.10 107.05 4.05 1.46e+00 4.69e-01 7.70e+00 ... (remaining 12447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4961 17.96 - 35.92: 561 35.92 - 53.88: 87 53.88 - 71.84: 21 71.84 - 89.81: 8 Dihedral angle restraints: 5638 sinusoidal: 2242 harmonic: 3396 Sorted by residual: dihedral pdb=" CA LEU C 316 " pdb=" C LEU C 316 " pdb=" N GLY C 317 " pdb=" CA GLY C 317 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO E 131 " pdb=" C PRO E 131 " pdb=" N GLU E 132 " pdb=" CA GLU E 132 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS B 19 " pdb=" C HIS B 19 " pdb=" N GLU B 20 " pdb=" CA GLU B 20 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 951 0.032 - 0.063: 347 0.063 - 0.095: 126 0.095 - 0.127: 53 0.127 - 0.158: 5 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CB ILE E 169 " pdb=" CA ILE E 169 " pdb=" CG1 ILE E 169 " pdb=" CG2 ILE E 169 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CG LEU E 183 " pdb=" CB LEU E 183 " pdb=" CD1 LEU E 183 " pdb=" CD2 LEU E 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA GLN E 172 " pdb=" N GLN E 172 " pdb=" C GLN E 172 " pdb=" CB GLN E 172 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1479 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 153 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 154 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 154 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 154 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 109 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 110 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 134 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO B 135 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.025 5.00e-02 4.00e+02 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 133 2.69 - 3.24: 9205 3.24 - 3.79: 13611 3.79 - 4.35: 16723 4.35 - 4.90: 26606 Nonbonded interactions: 66278 Sorted by model distance: nonbonded pdb=" O GLN E 151 " pdb=" OG SER E 154 " model vdw 2.135 2.440 nonbonded pdb=" OG SER C 105 " pdb=" OD1 ASN C 107 " model vdw 2.180 2.440 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG SER B 22 " model vdw 2.240 2.440 nonbonded pdb=" O ARG D 27 " pdb=" OG1 THR D 189 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASP A 101 " pdb=" OG1 THR A 104 " model vdw 2.262 2.440 ... (remaining 66273 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 11.770 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.440 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.003 0.035 9226 Z= 0.185 Angle : 0.664 9.289 12452 Z= 0.348 Chirality : 0.041 0.158 1482 Planarity : 0.004 0.054 1559 Dihedral : 15.305 89.805 3452 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.61 % Allowed : 1.84 % Favored : 97.54 % 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: 0.14 (0.25), residues: 1186 helix: 1.61 (0.21), residues: 696 sheet: -1.53 (0.67), residues: 66 loop : -2.34 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 90 HIS 0.007 0.001 HIS E 130 PHE 0.020 0.001 PHE E 155 TYR 0.014 0.001 TYR E 114 ARG 0.000 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8636 (m-30) cc_final: 0.8331 (m-30) REVERT: B 163 GLU cc_start: 0.8195 (tp30) cc_final: 0.7945 (tp30) REVERT: B 196 ASP cc_start: 0.8807 (t0) cc_final: 0.8122 (p0) REVERT: B 207 MET cc_start: 0.8162 (ptp) cc_final: 0.7544 (ptm) REVERT: B 209 THR cc_start: 0.8036 (m) cc_final: 0.7627 (t) REVERT: C 124 GLU cc_start: 0.8257 (pp20) cc_final: 0.8010 (pp20) REVERT: D 116 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8756 (pttm) REVERT: D 169 ASP cc_start: 0.8462 (t0) cc_final: 0.8214 (t0) REVERT: E 169 ILE cc_start: 0.8959 (tp) cc_final: 0.8754 (tp) outliers start: 6 outliers final: 6 residues processed: 171 average time/residue: 0.1938 time to fit residues: 46.7108 Evaluate side-chains 133 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 194 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9226 Z= 0.211 Angle : 0.627 8.217 12452 Z= 0.318 Chirality : 0.040 0.131 1482 Planarity : 0.004 0.046 1559 Dihedral : 6.155 57.838 1234 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.95 % Allowed : 13.01 % Favored : 85.04 % 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: 0.31 (0.25), residues: 1186 helix: 1.81 (0.21), residues: 705 sheet: -1.55 (0.66), residues: 64 loop : -2.48 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 318 HIS 0.007 0.001 HIS D 88 PHE 0.013 0.001 PHE E 155 TYR 0.011 0.001 TYR E 140 ARG 0.000 0.000 ARG E 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: B 207 MET cc_start: 0.8300 (ptp) cc_final: 0.7601 (ptm) REVERT: B 209 THR cc_start: 0.8092 (m) cc_final: 0.7701 (t) REVERT: C 103 LYS cc_start: 0.8095 (tppt) cc_final: 0.7780 (pttt) REVERT: C 167 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: C 258 MET cc_start: 0.7547 (ttp) cc_final: 0.7316 (ttm) REVERT: D 116 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8605 (pttm) REVERT: D 169 ASP cc_start: 0.8034 (t0) cc_final: 0.7643 (t0) REVERT: E 143 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6623 (t80) REVERT: E 169 ILE cc_start: 0.9013 (tp) cc_final: 0.8779 (tp) outliers start: 19 outliers final: 14 residues processed: 146 average time/residue: 0.1897 time to fit residues: 39.4372 Evaluate side-chains 141 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9226 Z= 0.260 Angle : 0.643 9.014 12452 Z= 0.325 Chirality : 0.040 0.155 1482 Planarity : 0.004 0.046 1559 Dihedral : 5.665 59.209 1226 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.07 % Allowed : 17.73 % Favored : 79.20 % 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: 0.29 (0.25), residues: 1186 helix: 1.76 (0.21), residues: 713 sheet: -1.67 (0.67), residues: 59 loop : -2.45 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 318 HIS 0.006 0.001 HIS D 88 PHE 0.015 0.001 PHE E 155 TYR 0.013 0.001 TYR E 114 ARG 0.000 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8446 (tt) REVERT: B 207 MET cc_start: 0.8394 (ptp) cc_final: 0.7793 (ptm) REVERT: B 209 THR cc_start: 0.8149 (m) cc_final: 0.7794 (t) REVERT: C 114 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: C 167 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: D 116 LYS cc_start: 0.8907 (ptpp) cc_final: 0.8607 (pttm) REVERT: D 169 ASP cc_start: 0.8228 (t0) cc_final: 0.7835 (t0) REVERT: E 97 ASP cc_start: 0.9208 (m-30) cc_final: 0.8881 (m-30) REVERT: E 143 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6740 (t80) outliers start: 30 outliers final: 21 residues processed: 149 average time/residue: 0.1933 time to fit residues: 41.0172 Evaluate side-chains 150 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 95 optimal weight: 0.0270 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9226 Z= 0.180 Angle : 0.598 7.995 12452 Z= 0.298 Chirality : 0.038 0.149 1482 Planarity : 0.004 0.046 1559 Dihedral : 5.265 55.202 1222 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.97 % Allowed : 21.11 % Favored : 75.92 % 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: 0.50 (0.26), residues: 1186 helix: 1.92 (0.21), residues: 716 sheet: -1.79 (0.71), residues: 52 loop : -2.37 (0.26), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.007 0.001 HIS C 41 PHE 0.021 0.001 PHE E 155 TYR 0.012 0.001 TYR E 114 ARG 0.000 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.8299 (ptp) cc_final: 0.7496 (ptm) REVERT: B 209 THR cc_start: 0.8107 (m) cc_final: 0.7752 (t) REVERT: C 103 LYS cc_start: 0.7816 (tppt) cc_final: 0.7414 (pttt) REVERT: C 114 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8526 (mp0) REVERT: C 258 MET cc_start: 0.7332 (ttm) cc_final: 0.7052 (ttm) REVERT: D 116 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8628 (pttm) REVERT: D 169 ASP cc_start: 0.8087 (t0) cc_final: 0.7686 (t0) REVERT: E 97 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8863 (m-30) REVERT: E 143 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6691 (t80) REVERT: E 150 GLU cc_start: 0.7877 (tp30) cc_final: 0.7577 (tp30) outliers start: 29 outliers final: 21 residues processed: 155 average time/residue: 0.1879 time to fit residues: 41.4890 Evaluate side-chains 150 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9226 Z= 0.237 Angle : 0.633 9.206 12452 Z= 0.313 Chirality : 0.039 0.143 1482 Planarity : 0.004 0.046 1559 Dihedral : 5.016 49.750 1218 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.00 % Allowed : 22.95 % Favored : 73.05 % 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: 0.47 (0.26), residues: 1186 helix: 1.89 (0.21), residues: 715 sheet: -1.86 (0.69), residues: 52 loop : -2.32 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.013 0.001 HIS C 230 PHE 0.015 0.001 PHE E 155 TYR 0.010 0.001 TYR A 37 ARG 0.000 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.8295 (ptp) cc_final: 0.7625 (ptm) REVERT: B 209 THR cc_start: 0.8121 (m) cc_final: 0.7765 (t) REVERT: C 114 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: C 258 MET cc_start: 0.7356 (ttm) cc_final: 0.7072 (ttm) REVERT: D 116 LYS cc_start: 0.8912 (ptpp) cc_final: 0.8632 (pttm) REVERT: D 169 ASP cc_start: 0.8166 (t0) cc_final: 0.7773 (t0) REVERT: D 207 MET cc_start: 0.7415 (ppp) cc_final: 0.7203 (tmm) REVERT: E 97 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8683 (m-30) REVERT: E 143 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6747 (t80) REVERT: E 150 GLU cc_start: 0.7897 (tp30) cc_final: 0.7583 (tp30) outliers start: 39 outliers final: 25 residues processed: 156 average time/residue: 0.1814 time to fit residues: 40.5664 Evaluate side-chains 157 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 0.0770 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 225 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9226 Z= 0.191 Angle : 0.618 10.362 12452 Z= 0.306 Chirality : 0.039 0.163 1482 Planarity : 0.004 0.047 1559 Dihedral : 4.894 47.290 1218 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.00 % Allowed : 24.49 % Favored : 71.52 % 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 (0.26), residues: 1186 helix: 1.91 (0.21), residues: 719 sheet: -1.73 (0.70), residues: 52 loop : -2.33 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.006 0.001 HIS C 41 PHE 0.018 0.001 PHE E 155 TYR 0.009 0.001 TYR E 114 ARG 0.000 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.8261 (ptp) cc_final: 0.7506 (ptm) REVERT: B 209 THR cc_start: 0.8146 (m) cc_final: 0.7764 (t) REVERT: C 114 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: C 258 MET cc_start: 0.7272 (ttm) cc_final: 0.7003 (ttm) REVERT: D 116 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8616 (pttm) REVERT: D 169 ASP cc_start: 0.8123 (t0) cc_final: 0.7698 (t0) REVERT: E 97 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8672 (m-30) REVERT: E 143 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6787 (t80) REVERT: E 150 GLU cc_start: 0.7966 (tp30) cc_final: 0.7668 (tp30) outliers start: 39 outliers final: 25 residues processed: 159 average time/residue: 0.1869 time to fit residues: 42.5392 Evaluate side-chains 158 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 143 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9226 Z= 0.207 Angle : 0.637 11.908 12452 Z= 0.312 Chirality : 0.039 0.192 1482 Planarity : 0.004 0.046 1559 Dihedral : 4.644 44.227 1214 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.38 % Allowed : 25.00 % 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: 0.53 (0.26), residues: 1186 helix: 1.92 (0.21), residues: 720 sheet: -1.70 (0.70), residues: 52 loop : -2.34 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 90 HIS 0.005 0.001 HIS C 41 PHE 0.021 0.001 PHE E 155 TYR 0.009 0.001 TYR E 114 ARG 0.000 0.000 ARG E 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8063 (pp30) REVERT: B 207 MET cc_start: 0.8249 (ptp) cc_final: 0.7631 (ptm) REVERT: B 209 THR cc_start: 0.8129 (m) cc_final: 0.7737 (t) REVERT: C 114 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: C 258 MET cc_start: 0.7276 (ttm) cc_final: 0.6990 (ttm) REVERT: D 116 LYS cc_start: 0.8891 (ptpp) cc_final: 0.8582 (pttm) REVERT: D 169 ASP cc_start: 0.8161 (t0) cc_final: 0.7750 (t0) REVERT: D 207 MET cc_start: 0.7238 (ppp) cc_final: 0.6938 (tmm) REVERT: E 97 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8672 (m-30) REVERT: E 143 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6862 (t80) REVERT: E 150 GLU cc_start: 0.7987 (tp30) cc_final: 0.7699 (tp30) outliers start: 33 outliers final: 27 residues processed: 149 average time/residue: 0.1925 time to fit residues: 40.4710 Evaluate side-chains 157 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 143 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 90 optimal weight: 0.1980 chunk 104 optimal weight: 50.0000 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9226 Z= 0.203 Angle : 0.651 12.386 12452 Z= 0.320 Chirality : 0.040 0.202 1482 Planarity : 0.004 0.047 1559 Dihedral : 4.607 42.264 1214 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.00 % Allowed : 25.41 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1186 helix: 1.93 (0.21), residues: 720 sheet: -1.65 (0.71), residues: 52 loop : -2.34 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 90 HIS 0.005 0.001 HIS C 41 PHE 0.024 0.001 PHE E 155 TYR 0.008 0.001 TYR E 114 ARG 0.000 0.000 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: B 207 MET cc_start: 0.8238 (ptp) cc_final: 0.7446 (ptm) REVERT: B 209 THR cc_start: 0.8090 (m) cc_final: 0.7690 (t) REVERT: C 114 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: C 167 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7616 (p0) REVERT: C 258 MET cc_start: 0.7197 (ttm) cc_final: 0.6929 (ttm) REVERT: D 169 ASP cc_start: 0.8158 (t0) cc_final: 0.7751 (t0) REVERT: D 207 MET cc_start: 0.7235 (ppp) cc_final: 0.6941 (tmm) REVERT: E 97 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8678 (m-30) REVERT: E 143 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6847 (t80) REVERT: E 150 GLU cc_start: 0.7976 (tp30) cc_final: 0.7694 (tp30) outliers start: 39 outliers final: 28 residues processed: 156 average time/residue: 0.1899 time to fit residues: 42.5053 Evaluate side-chains 159 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9990 chunk 109 optimal weight: 0.0570 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS D 126 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9226 Z= 0.190 Angle : 0.653 10.904 12452 Z= 0.320 Chirality : 0.040 0.192 1482 Planarity : 0.004 0.047 1559 Dihedral : 4.590 39.195 1214 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.79 % Allowed : 25.82 % Favored : 70.39 % 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: 0.58 (0.26), residues: 1186 helix: 1.95 (0.21), residues: 719 sheet: -1.62 (0.71), residues: 52 loop : -2.32 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 90 HIS 0.005 0.001 HIS C 41 PHE 0.026 0.001 PHE E 155 TYR 0.009 0.001 TYR B 11 ARG 0.000 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: B 207 MET cc_start: 0.8260 (ptp) cc_final: 0.7612 (ptm) REVERT: B 209 THR cc_start: 0.8117 (m) cc_final: 0.7726 (t) REVERT: C 114 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: C 167 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7616 (p0) REVERT: C 258 MET cc_start: 0.7174 (ttm) cc_final: 0.6905 (ttm) REVERT: D 169 ASP cc_start: 0.8146 (t0) cc_final: 0.7745 (t0) REVERT: D 207 MET cc_start: 0.7201 (ppp) cc_final: 0.6905 (tmm) REVERT: E 97 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8688 (m-30) REVERT: E 143 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6819 (t80) REVERT: E 150 GLU cc_start: 0.7964 (tp30) cc_final: 0.7682 (tp30) outliers start: 37 outliers final: 27 residues processed: 153 average time/residue: 0.1845 time to fit residues: 40.3490 Evaluate side-chains 157 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 143 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 109 optimal weight: 0.0670 chunk 94 optimal weight: 0.0040 chunk 9 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS D 126 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9226 Z= 0.179 Angle : 0.662 10.926 12452 Z= 0.322 Chirality : 0.040 0.216 1482 Planarity : 0.004 0.047 1559 Dihedral : 4.534 37.521 1214 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.87 % Allowed : 26.43 % Favored : 70.70 % 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: 0.65 (0.26), residues: 1186 helix: 2.01 (0.21), residues: 718 sheet: -1.50 (0.72), residues: 52 loop : -2.29 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 90 HIS 0.009 0.001 HIS C 230 PHE 0.028 0.001 PHE E 155 TYR 0.017 0.001 TYR E 140 ARG 0.000 0.000 ARG E 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LEU cc_start: 0.7840 (mp) cc_final: 0.7601 (mp) REVERT: B 144 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8044 (pp30) REVERT: B 207 MET cc_start: 0.8170 (ptp) cc_final: 0.7403 (ptm) REVERT: B 209 THR cc_start: 0.8128 (m) cc_final: 0.7710 (t) REVERT: C 114 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: C 167 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7621 (p0) REVERT: C 258 MET cc_start: 0.7077 (ttm) cc_final: 0.6840 (ttm) REVERT: D 169 ASP cc_start: 0.8116 (t0) cc_final: 0.7713 (t0) REVERT: D 207 MET cc_start: 0.7199 (ppp) cc_final: 0.6909 (tmm) REVERT: E 97 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8676 (m-30) REVERT: E 143 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6842 (t80) REVERT: E 150 GLU cc_start: 0.7947 (tp30) cc_final: 0.7673 (tp30) outliers start: 28 outliers final: 21 residues processed: 151 average time/residue: 0.1948 time to fit residues: 41.7746 Evaluate side-chains 152 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 143 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.0270 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.138190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.102739 restraints weight = 20636.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.103800 restraints weight = 10413.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103788 restraints weight = 7728.158| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.390 9226 Z= 0.421 Angle : 0.984 59.193 12452 Z= 0.562 Chirality : 0.042 0.356 1482 Planarity : 0.005 0.117 1559 Dihedral : 4.575 37.506 1214 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 2.77 % Allowed : 26.23 % Favored : 71.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1186 helix: 1.99 (0.21), residues: 718 sheet: -1.49 (0.72), residues: 52 loop : -2.29 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 90 HIS 0.130 0.004 HIS C 230 PHE 0.021 0.001 PHE E 155 TYR 0.013 0.001 TYR E 140 ARG 0.000 0.000 ARG B 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.83 seconds wall clock time: 36 minutes 52.59 seconds (2212.59 seconds total)