Starting phenix.real_space_refine on Mon Mar 11 10:15:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukf_26579/03_2024/7ukf_26579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukf_26579/03_2024/7ukf_26579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukf_26579/03_2024/7ukf_26579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukf_26579/03_2024/7ukf_26579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukf_26579/03_2024/7ukf_26579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukf_26579/03_2024/7ukf_26579.pdb" } resolution = 3.02 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= 0.005 sd= 0.068 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: 6 Type Number sf(0) Gaussians Hg 1 10.96 5 K 4 8.98 5 S 60 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8005 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2000 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' HG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1842 SG CYS A 406 56.243 52.488 57.734 1.00 69.40 S Time building chain proxies: 4.56, per 1000 atoms: 0.57 Number of scatterers: 8005 At special positions: 0 Unit cell: (113.162, 112.336, 84.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 1 79.96 K 4 19.00 S 60 16.00 O 1356 8.00 N 1332 7.00 C 5252 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: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 181 through 206 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.602A pdb=" N SER A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 347 removed outlier: 5.088A pdb=" N SER A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 206 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 293 removed outlier: 4.021A pdb=" N VAL B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL C 290 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.973A pdb=" N PHE C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.603A pdb=" N SER D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.020A pdb=" N VAL D 290 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.972A pdb=" N PHE D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 302 " --> pdb=" O PHE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 347 removed outlier: 5.087A pdb=" N SER D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 3.818A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 400 through 423 removed outlier: 4.252A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1767 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: 2.32 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2440 1.34 - 1.46: 1907 1.46 - 1.58: 3757 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8196 Sorted by residual: bond pdb=" C VAL B 377 " pdb=" N PRO B 378 " ideal model delta sigma weight residual 1.333 1.320 0.013 1.17e-02 7.31e+03 1.22e+00 bond pdb=" C VAL A 377 " pdb=" N PRO A 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.12e+00 bond pdb=" C VAL C 377 " pdb=" N PRO C 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.11e+00 bond pdb=" C VAL D 377 " pdb=" N PRO D 378 " ideal model delta sigma weight residual 1.333 1.320 0.012 1.17e-02 7.31e+03 1.11e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.38e-01 ... (remaining 8191 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.54: 204 106.54 - 113.40: 4511 113.40 - 120.26: 3131 120.26 - 127.12: 3222 127.12 - 133.98: 68 Bond angle restraints: 11136 Sorted by residual: angle pdb=" N LEU C 400 " pdb=" CA LEU C 400 " pdb=" C LEU C 400 " ideal model delta sigma weight residual 109.81 115.30 -5.49 2.21e+00 2.05e-01 6.17e+00 angle pdb=" N LEU D 400 " pdb=" CA LEU D 400 " pdb=" C LEU D 400 " ideal model delta sigma weight residual 109.81 115.27 -5.46 2.21e+00 2.05e-01 6.11e+00 angle pdb=" N LEU A 400 " pdb=" CA LEU A 400 " pdb=" C LEU A 400 " ideal model delta sigma weight residual 109.81 115.26 -5.45 2.21e+00 2.05e-01 6.07e+00 angle pdb=" N LEU B 400 " pdb=" CA LEU B 400 " pdb=" C LEU B 400 " ideal model delta sigma weight residual 109.81 115.24 -5.43 2.21e+00 2.05e-01 6.03e+00 angle pdb=" CA LEU C 271 " pdb=" C LEU C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 118.44 121.56 -3.12 1.59e+00 3.96e-01 3.85e+00 ... (remaining 11131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.14: 4010 10.14 - 20.28: 530 20.28 - 30.43: 176 30.43 - 40.57: 76 40.57 - 50.71: 12 Dihedral angle restraints: 4804 sinusoidal: 1772 harmonic: 3032 Sorted by residual: dihedral pdb=" CB MET D 333 " pdb=" CG MET D 333 " pdb=" SD MET D 333 " pdb=" CE MET D 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.71 -50.71 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CB MET A 333 " pdb=" CG MET A 333 " pdb=" SD MET A 333 " pdb=" CE MET A 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.68 -50.68 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" CB MET B 333 " pdb=" CG MET B 333 " pdb=" SD MET B 333 " pdb=" CE MET B 333 " ideal model delta sinusoidal sigma weight residual 60.00 110.66 -50.66 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 629 0.026 - 0.051: 416 0.051 - 0.077: 183 0.077 - 0.102: 71 0.102 - 0.128: 17 Chirality restraints: 1316 Sorted by residual: chirality pdb=" CA VAL B 207 " pdb=" N VAL B 207 " pdb=" C VAL B 207 " pdb=" CB VAL B 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA VAL C 207 " pdb=" N VAL C 207 " pdb=" C VAL C 207 " pdb=" CB VAL C 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL A 207 " pdb=" N VAL A 207 " pdb=" C VAL A 207 " pdb=" CB VAL A 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1313 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 357 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO C 358 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 357 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO D 358 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 357 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO B 358 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.025 5.00e-02 4.00e+02 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 2973 2.86 - 3.43: 9594 3.43 - 4.00: 14762 4.00 - 4.57: 21588 4.57 - 5.14: 30209 Nonbonded interactions: 79126 Sorted by model distance: nonbonded pdb=" OG1 THR B 166 " pdb=" OE1 GLN B 169 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR D 166 " pdb=" OE1 GLN D 169 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR A 166 " pdb=" OE1 GLN A 169 " model vdw 2.292 2.440 nonbonded pdb=" OG1 THR C 166 " pdb=" OE1 GLN C 169 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR D 188 " pdb=" O PHE D 303 " model vdw 2.339 2.440 ... (remaining 79121 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' and resid 166 through 424) selection = chain 'B' selection = chain 'C' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 9.340 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.400 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.004 0.031 8196 Z= 0.261 Angle : 0.611 6.115 11136 Z= 0.349 Chirality : 0.041 0.128 1316 Planarity : 0.005 0.045 1364 Dihedral : 11.495 50.711 2852 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.20 (0.27), residues: 1028 helix: 0.91 (0.18), residues: 796 sheet: None (None), residues: 0 loop : 0.83 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.001 0.000 HIS C 414 PHE 0.010 0.001 PHE C 326 TYR 0.017 0.002 TYR C 188 ARG 0.002 0.000 ARG B 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.895 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2291 time to fit residues: 37.4744 Evaluate side-chains 111 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8196 Z= 0.365 Angle : 0.588 6.688 11136 Z= 0.307 Chirality : 0.042 0.126 1316 Planarity : 0.005 0.046 1364 Dihedral : 3.902 13.696 1148 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.83 % Allowed : 6.25 % Favored : 92.92 % 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: 0.68 (0.26), residues: 1028 helix: 0.71 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.30 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 172 HIS 0.003 0.001 HIS A 306 PHE 0.011 0.002 PHE D 326 TYR 0.020 0.002 TYR A 225 ARG 0.002 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.945 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 107 average time/residue: 0.1996 time to fit residues: 29.3181 Evaluate side-chains 106 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.0040 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8196 Z= 0.338 Angle : 0.563 6.474 11136 Z= 0.295 Chirality : 0.041 0.133 1316 Planarity : 0.005 0.046 1364 Dihedral : 3.820 13.490 1148 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.83 % Allowed : 9.08 % Favored : 90.09 % 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: 0.81 (0.26), residues: 1028 helix: 0.81 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.32 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 172 HIS 0.004 0.001 HIS B 306 PHE 0.011 0.002 PHE D 326 TYR 0.016 0.002 TYR A 225 ARG 0.003 0.000 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.377 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 106 average time/residue: 0.2488 time to fit residues: 37.4962 Evaluate side-chains 105 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 239 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8196 Z= 0.299 Angle : 0.542 6.307 11136 Z= 0.284 Chirality : 0.041 0.131 1316 Planarity : 0.005 0.046 1364 Dihedral : 3.755 13.267 1148 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.77 % Allowed : 10.26 % Favored : 87.97 % 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: 1.00 (0.26), residues: 1028 helix: 0.96 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.32 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 172 HIS 0.002 0.001 HIS A 306 PHE 0.011 0.002 PHE D 326 TYR 0.014 0.002 TYR A 225 ARG 0.001 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.894 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 106 average time/residue: 0.1687 time to fit residues: 25.8029 Evaluate side-chains 112 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8196 Z= 0.208 Angle : 0.506 6.078 11136 Z= 0.263 Chirality : 0.039 0.138 1316 Planarity : 0.005 0.045 1364 Dihedral : 3.609 12.528 1148 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.83 % Allowed : 12.26 % Favored : 86.91 % 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: 1.36 (0.26), residues: 1028 helix: 1.22 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.23 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 172 HIS 0.001 0.000 HIS B 306 PHE 0.011 0.001 PHE D 326 TYR 0.015 0.001 TYR A 188 ARG 0.001 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.994 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 110 average time/residue: 0.1754 time to fit residues: 27.4383 Evaluate side-chains 104 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8196 Z= 0.210 Angle : 0.501 5.893 11136 Z= 0.261 Chirality : 0.038 0.127 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.550 12.243 1148 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.30 % Allowed : 12.74 % Favored : 85.97 % 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: 1.55 (0.26), residues: 1028 helix: 1.36 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.24 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 172 HIS 0.001 0.000 HIS B 306 PHE 0.011 0.001 PHE C 257 TYR 0.015 0.001 TYR A 188 ARG 0.001 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.905 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 118 average time/residue: 0.1813 time to fit residues: 30.5049 Evaluate side-chains 114 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8196 Z= 0.255 Angle : 0.519 5.694 11136 Z= 0.271 Chirality : 0.039 0.141 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.576 12.243 1148 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.65 % Allowed : 12.85 % Favored : 85.50 % 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: 1.56 (0.26), residues: 1028 helix: 1.37 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.25 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 172 HIS 0.002 0.001 HIS B 306 PHE 0.012 0.001 PHE D 257 TYR 0.014 0.001 TYR A 188 ARG 0.002 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.915 Fit side-chains REVERT: A 411 ARG cc_start: 0.8453 (tmm-80) cc_final: 0.8251 (tmm-80) outliers start: 14 outliers final: 14 residues processed: 113 average time/residue: 0.1951 time to fit residues: 30.4706 Evaluate side-chains 115 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8196 Z= 0.177 Angle : 0.491 5.556 11136 Z= 0.254 Chirality : 0.038 0.128 1316 Planarity : 0.004 0.045 1364 Dihedral : 3.475 12.069 1148 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.94 % Allowed : 14.50 % Favored : 84.55 % 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: 1.84 (0.26), residues: 1028 helix: 1.56 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.13 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 172 HIS 0.001 0.000 HIS B 306 PHE 0.014 0.001 PHE A 257 TYR 0.015 0.001 TYR A 188 ARG 0.002 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.912 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 121 average time/residue: 0.1724 time to fit residues: 29.9653 Evaluate side-chains 118 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8196 Z= 0.194 Angle : 0.497 5.418 11136 Z= 0.258 Chirality : 0.038 0.129 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.458 12.199 1148 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.18 % Allowed : 14.74 % Favored : 84.08 % 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: 1.89 (0.26), residues: 1028 helix: 1.59 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.08 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 362 HIS 0.001 0.000 HIS B 306 PHE 0.015 0.001 PHE D 257 TYR 0.014 0.001 TYR A 188 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.955 Fit side-chains REVERT: C 300 ILE cc_start: 0.7951 (mm) cc_final: 0.7642 (mt) outliers start: 10 outliers final: 10 residues processed: 119 average time/residue: 0.1614 time to fit residues: 27.9152 Evaluate side-chains 120 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 279 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8196 Z= 0.236 Angle : 0.513 5.459 11136 Z= 0.266 Chirality : 0.039 0.128 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.509 12.225 1148 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.53 % Allowed : 15.21 % Favored : 83.25 % 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: 1.79 (0.26), residues: 1028 helix: 1.52 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.09 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 362 HIS 0.002 0.001 HIS B 306 PHE 0.018 0.001 PHE C 257 TYR 0.014 0.001 TYR A 188 ARG 0.002 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.913 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 120 average time/residue: 0.1626 time to fit residues: 28.4124 Evaluate side-chains 122 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** 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 = 0.4360 r_free = 0.4360 target = 0.215393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167688 restraints weight = 6780.970| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.82 r_work: 0.3460 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8196 Z= 0.168 Angle : 0.488 5.209 11136 Z= 0.252 Chirality : 0.037 0.129 1316 Planarity : 0.004 0.044 1364 Dihedral : 3.419 12.023 1148 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.06 % Allowed : 15.57 % Favored : 83.37 % 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: 2.00 (0.27), residues: 1028 helix: 1.66 (0.18), residues: 840 sheet: None (None), residues: 0 loop : 0.01 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 172 HIS 0.001 0.000 HIS A 306 PHE 0.017 0.001 PHE D 257 TYR 0.015 0.001 TYR A 188 ARG 0.002 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.73 seconds wall clock time: 36 minutes 52.86 seconds (2212.86 seconds total)