Starting phenix.real_space_refine (version: dev) on Sun Feb 19 10:26:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/02_2023/6n3q_0336.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/02_2023/6n3q_0336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/02_2023/6n3q_0336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/02_2023/6n3q_0336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/02_2023/6n3q_0336.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/02_2023/6n3q_0336.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.066 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 Process input model Symmetric amino acids flipped Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9931 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2960 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3779 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 28, 'TRANS': 458} Chain breaks: 4 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 17, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 124 Chain: "E" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1095 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 132} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1433 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 5.99, per 1000 atoms: 0.60 Number of scatterers: 9931 At special positions: 0 Unit cell: (105.56, 126.44, 127.6, 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 38 16.00 O 1720 8.00 N 1678 7.00 C 6495 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: 4.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 67.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 removed outlier: 3.806A pdb=" N ILE A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 99 Processing helix chain 'A' and resid 107 through 137 Processing helix chain 'A' and resid 148 through 173 Processing helix chain 'A' and resid 179 through 199 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.545A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 243 through 261 Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.803A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 385 removed outlier: 4.202A pdb=" N GLU A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 408 through 440 Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.883A pdb=" N LYS C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 79 removed outlier: 3.839A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.705A pdb=" N ILE D 18 " --> pdb=" O TRP D 14 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 67 removed outlier: 3.877A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 113 removed outlier: 3.646A pdb=" N ASN D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 249 removed outlier: 4.449A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) Proline residue: D 236 - end of helix removed outlier: 3.541A pdb=" N TYR D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.777A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.750A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.739A pdb=" N LYS D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 343 removed outlier: 4.606A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.672A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.708A pdb=" N ILE D 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 401 through 408 removed outlier: 4.301A pdb=" N GLU D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 424 removed outlier: 3.686A pdb=" N HIS D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 487 through 493 removed outlier: 3.998A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 545 Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.591A pdb=" N TYR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 124 removed outlier: 3.746A pdb=" N LEU E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 127 through 156 removed outlier: 3.543A pdb=" N TRP E 131 " --> pdb=" O GLY E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 182 removed outlier: 4.177A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'F' and resid 21 through 42 removed outlier: 3.526A pdb=" N ASN F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 71 Processing helix chain 'F' and resid 73 through 91 Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix removed outlier: 3.712A pdb=" N ILE F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.646A pdb=" N ALA F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.551A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 removed outlier: 3.592A pdb=" N ALA F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 192 removed outlier: 3.812A pdb=" N ARG F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.832A pdb=" N ASN A 204 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 205 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.627A pdb=" N GLY A 279 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 281 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 267 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 430 through 436 removed outlier: 4.910A pdb=" N LYS D 432 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 454 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 434 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.863A pdb=" N GLY D 584 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL D 610 " --> pdb=" O GLY D 584 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 586 " --> pdb=" O MET D 608 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1866 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: 2.83 Time building geometry restraints manager: 4.34 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: 2909 1.34 - 1.46: 1541 1.46 - 1.57: 5620 1.57 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 10129 Sorted by residual: bond pdb=" C LEU D 235 " pdb=" N PRO D 236 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.26e+01 bond pdb=" C THR A 291 " pdb=" N PRO A 292 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.34e+00 bond pdb=" CB CYS E 167 " pdb=" SG CYS E 167 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.29e+00 bond pdb=" CG1 ILE D 280 " pdb=" CD1 ILE D 280 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.68e+00 bond pdb=" C ALA E 114 " pdb=" N PRO E 115 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.45e+00 ... (remaining 10124 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.17: 251 106.17 - 113.15: 5617 113.15 - 120.13: 3545 120.13 - 127.11: 4216 127.11 - 134.09: 109 Bond angle restraints: 13738 Sorted by residual: angle pdb=" C THR A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta sigma weight residual 122.74 129.32 -6.58 1.44e+00 4.82e-01 2.09e+01 angle pdb=" C ILE A 417 " pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 120.33 123.96 -3.63 8.00e-01 1.56e+00 2.05e+01 angle pdb=" C ILE C 79 " pdb=" N VAL C 80 " pdb=" CA VAL C 80 " ideal model delta sigma weight residual 121.70 128.70 -7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CA GLY A 178 " pdb=" C GLY A 178 " pdb=" O GLY A 178 " ideal model delta sigma weight residual 122.22 119.78 2.44 6.50e-01 2.37e+00 1.41e+01 angle pdb=" N GLN A 99 " pdb=" CA GLN A 99 " pdb=" C GLN A 99 " ideal model delta sigma weight residual 112.58 108.19 4.39 1.22e+00 6.72e-01 1.30e+01 ... (remaining 13733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 5657 15.28 - 30.55: 318 30.55 - 45.83: 93 45.83 - 61.11: 2 61.11 - 76.38: 6 Dihedral angle restraints: 6076 sinusoidal: 2332 harmonic: 3744 Sorted by residual: dihedral pdb=" CA LEU F 137 " pdb=" C LEU F 137 " pdb=" N ILE F 138 " pdb=" CA ILE F 138 " ideal model delta harmonic sigma weight residual -180.00 -143.35 -36.65 0 5.00e+00 4.00e-02 5.37e+01 dihedral pdb=" CA PHE D 501 " pdb=" C PHE D 501 " pdb=" N ALA D 502 " pdb=" CA ALA D 502 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA PRO D 463 " pdb=" C PRO D 463 " pdb=" N LEU D 464 " pdb=" CA LEU D 464 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 6073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1062 0.044 - 0.089: 418 0.089 - 0.133: 126 0.133 - 0.177: 28 0.177 - 0.222: 9 Chirality restraints: 1643 Sorted by residual: chirality pdb=" CB ILE A 49 " pdb=" CA ILE A 49 " pdb=" CG1 ILE A 49 " pdb=" CG2 ILE A 49 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU D 235 " pdb=" N LEU D 235 " pdb=" C LEU D 235 " pdb=" CB LEU D 235 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB THR A 453 " pdb=" CA THR A 453 " pdb=" OG1 THR A 453 " pdb=" CG2 THR A 453 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 1640 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 137 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C LEU F 137 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU F 137 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE F 138 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO F 48 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 141 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO A 142 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.036 5.00e-02 4.00e+02 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2967 2.83 - 3.34: 9609 3.34 - 3.86: 16151 3.86 - 4.38: 16894 4.38 - 4.90: 29885 Nonbonded interactions: 75506 Sorted by model distance: nonbonded pdb=" O SER D 512 " pdb=" OG1 THR D 595 " model vdw 2.308 2.440 nonbonded pdb=" O GLY D 27 " pdb=" OG1 THR D 30 " model vdw 2.309 2.440 nonbonded pdb=" OD1 ASN A 204 " pdb=" OG SER D 205 " model vdw 2.318 2.440 nonbonded pdb=" O LYS E 79 " pdb=" OG SER E 82 " model vdw 2.320 2.440 nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 66 " model vdw 2.334 2.440 ... (remaining 75501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6495 2.51 5 N 1678 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.760 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: 4.270 Check model and map are aligned: 0.150 Process input model: 27.830 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 0.068 10129 Z= 0.359 Angle : 1.032 10.714 13738 Z= 0.547 Chirality : 0.053 0.222 1643 Planarity : 0.008 0.060 1703 Dihedral : 10.912 76.383 3644 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.18), residues: 1264 helix: -1.92 (0.13), residues: 817 sheet: -2.55 (0.56), residues: 64 loop : -2.34 (0.27), residues: 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 342 time to evaluate : 1.204 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 346 average time/residue: 0.2528 time to fit residues: 118.3558 Evaluate side-chains 186 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0921 time to fit residues: 1.8052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 192 GLN A 204 ASN D 345 ASN D 494 GLN D 539 ASN ** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN F 80 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 10129 Z= 0.221 Angle : 0.663 7.734 13738 Z= 0.331 Chirality : 0.041 0.252 1643 Planarity : 0.005 0.046 1703 Dihedral : 4.905 23.838 1363 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 4.03 % 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: -0.87 (0.22), residues: 1264 helix: 0.18 (0.17), residues: 816 sheet: -1.96 (0.58), residues: 69 loop : -1.79 (0.29), residues: 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 1.437 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 246 average time/residue: 0.1912 time to fit residues: 69.0182 Evaluate side-chains 204 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0920 time to fit residues: 5.6822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 0.0470 chunk 115 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 ASN E 88 HIS ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10129 Z= 0.210 Angle : 0.642 9.408 13738 Z= 0.315 Chirality : 0.041 0.187 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.602 20.634 1363 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1264 helix: 0.97 (0.18), residues: 815 sheet: -1.57 (0.61), residues: 69 loop : -1.47 (0.30), residues: 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 1.182 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 231 average time/residue: 0.1991 time to fit residues: 68.1365 Evaluate side-chains 181 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1008 time to fit residues: 3.9085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 ASN E 98 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 10129 Z= 0.198 Angle : 0.635 10.086 13738 Z= 0.305 Chirality : 0.040 0.210 1643 Planarity : 0.004 0.039 1703 Dihedral : 4.350 20.483 1363 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 2.98 % 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: 0.66 (0.24), residues: 1264 helix: 1.43 (0.18), residues: 817 sheet: -1.29 (0.60), residues: 73 loop : -1.40 (0.31), residues: 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 227 average time/residue: 0.2092 time to fit residues: 66.7676 Evaluate side-chains 185 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0910 time to fit residues: 4.1132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 1 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 10129 Z= 0.314 Angle : 0.704 14.697 13738 Z= 0.339 Chirality : 0.042 0.184 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.368 20.537 1363 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 3.36 % 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 (0.24), residues: 1264 helix: 1.50 (0.18), residues: 816 sheet: -1.37 (0.59), residues: 73 loop : -1.40 (0.32), residues: 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.203 Fit side-chains outliers start: 35 outliers final: 18 residues processed: 199 average time/residue: 0.1998 time to fit residues: 57.8962 Evaluate side-chains 181 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1218 time to fit residues: 5.2438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10129 Z= 0.202 Angle : 0.677 14.149 13738 Z= 0.317 Chirality : 0.040 0.201 1643 Planarity : 0.004 0.042 1703 Dihedral : 4.213 19.146 1363 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1264 helix: 1.67 (0.18), residues: 814 sheet: -1.24 (0.61), residues: 73 loop : -1.32 (0.32), residues: 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.082 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 198 average time/residue: 0.1959 time to fit residues: 56.7601 Evaluate side-chains 177 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0935 time to fit residues: 2.8974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10129 Z= 0.201 Angle : 0.675 13.345 13738 Z= 0.317 Chirality : 0.041 0.217 1643 Planarity : 0.004 0.042 1703 Dihedral : 4.167 19.406 1363 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1264 helix: 1.72 (0.18), residues: 818 sheet: -1.14 (0.61), residues: 73 loop : -1.24 (0.33), residues: 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.270 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 184 average time/residue: 0.1985 time to fit residues: 54.3569 Evaluate side-chains 171 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1218 time to fit residues: 3.5529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10129 Z= 0.244 Angle : 0.721 12.981 13738 Z= 0.339 Chirality : 0.041 0.217 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.175 19.264 1363 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.25 % 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: 1.01 (0.24), residues: 1264 helix: 1.69 (0.18), residues: 817 sheet: -1.12 (0.62), residues: 73 loop : -1.24 (0.33), residues: 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 1.228 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 184 average time/residue: 0.2275 time to fit residues: 61.9587 Evaluate side-chains 165 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0957 time to fit residues: 2.6540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10129 Z= 0.257 Angle : 0.721 12.890 13738 Z= 0.340 Chirality : 0.042 0.231 1643 Planarity : 0.004 0.042 1703 Dihedral : 4.211 19.741 1363 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.25 % 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: 0.92 (0.24), residues: 1264 helix: 1.63 (0.18), residues: 818 sheet: -1.30 (0.58), residues: 84 loop : -1.26 (0.34), residues: 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.112 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 165 average time/residue: 0.1912 time to fit residues: 47.1219 Evaluate side-chains 162 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1113 time to fit residues: 2.9043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10129 Z= 0.228 Angle : 0.730 13.416 13738 Z= 0.340 Chirality : 0.041 0.235 1643 Planarity : 0.004 0.042 1703 Dihedral : 4.179 18.870 1363 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.15 % 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: 0.99 (0.25), residues: 1264 helix: 1.68 (0.18), residues: 815 sheet: -1.28 (0.58), residues: 84 loop : -1.19 (0.34), residues: 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.369 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 167 average time/residue: 0.2129 time to fit residues: 52.4843 Evaluate side-chains 164 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1012 time to fit residues: 3.2763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 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 = 0.3538 r_free = 0.3538 target = 0.116402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101259 restraints weight = 18659.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103363 restraints weight = 11350.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.104756 restraints weight = 7969.655| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 10129 Z= 0.287 Angle : 0.754 12.943 13738 Z= 0.357 Chirality : 0.043 0.236 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.254 19.693 1363 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.77 % 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 (0.25), residues: 1264 helix: 1.58 (0.18), residues: 817 sheet: -1.24 (0.59), residues: 84 loop : -1.22 (0.34), residues: 363 =============================================================================== Job complete usr+sys time: 1997.20 seconds wall clock time: 37 minutes 33.44 seconds (2253.44 seconds total)