Starting phenix.real_space_refine on Thu Feb 13 04:33:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wz7_32905/02_2025/7wz7_32905_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wz7_32905/02_2025/7wz7_32905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wz7_32905/02_2025/7wz7_32905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wz7_32905/02_2025/7wz7_32905.map" model { file = "/net/cci-nas-00/data/ceres_data/7wz7_32905/02_2025/7wz7_32905_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wz7_32905/02_2025/7wz7_32905_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5553 2.51 5 N 1487 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8676 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1734 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "E" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2130 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 2 Time building chain proxies: 5.23, per 1000 atoms: 0.60 Number of scatterers: 8676 At special positions: 0 Unit cell: (93.96, 117.72, 131.76, 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 57 16.00 O 1579 8.00 N 1487 7.00 C 5553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 38.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 49 through 66 removed outlier: 3.673A pdb=" N ASN A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.863A pdb=" N ASN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.767A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 375 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 53 through 56 removed outlier: 4.168A pdb=" N GLY C 56 " --> pdb=" O SER C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.923A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 removed outlier: 3.624A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 removed outlier: 3.574A pdb=" N ASP E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'R' and resid 568 through 573 Processing helix chain 'R' and resid 578 through 580 No H-bonds generated for 'chain 'R' and resid 578 through 580' Processing helix chain 'R' and resid 581 through 611 removed outlier: 4.495A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA R 608 " --> pdb=" O LEU R 604 " (cutoff:3.500A) Processing helix chain 'R' and resid 617 through 646 removed outlier: 3.740A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 688 Processing helix chain 'R' and resid 694 through 707 Processing helix chain 'R' and resid 707 through 722 Processing helix chain 'R' and resid 744 through 768 Proline residue: R 750 - end of helix Processing helix chain 'R' and resid 785 through 801 Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 813 Processing helix chain 'R' and resid 814 through 817 removed outlier: 3.962A pdb=" N LEU R 817 " --> pdb=" O SER R 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 814 through 817' Processing helix chain 'R' and resid 818 through 828 Processing helix chain 'R' and resid 829 through 837 Processing helix chain 'R' and resid 842 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.632A pdb=" N LYS A 42 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU A 245 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 44 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 46 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS A 345 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 289 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.522A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.652A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.039A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.594A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.630A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.614A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.620A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.181A pdb=" N GLY C 10 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'C' and resid 134 through 136 removed outlier: 3.652A pdb=" N GLU C 234 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 166 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU C 175 " --> pdb=" O LEU C 166 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1239 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: 2.64 Time building geometry restraints manager: 2.67 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: 2793 1.34 - 1.46: 2168 1.46 - 1.59: 3808 1.59 - 1.71: 0 1.71 - 1.83: 86 Bond restraints: 8855 Sorted by residual: bond pdb=" N TYR C 223 " pdb=" CA TYR C 223 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.31e-02 5.83e+03 8.72e+00 bond pdb=" N LYS R 728 " pdb=" CA LYS R 728 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.15e-02 7.56e+03 7.32e+00 bond pdb=" N SER C 52 " pdb=" CA SER C 52 " ideal model delta sigma weight residual 1.454 1.424 0.030 1.16e-02 7.43e+03 6.72e+00 bond pdb=" CA LYS R 728 " pdb=" C LYS R 728 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.31e-02 5.83e+03 6.35e+00 ... (remaining 8850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 11516 2.11 - 4.22: 387 4.22 - 6.33: 61 6.33 - 8.43: 18 8.43 - 10.54: 7 Bond angle restraints: 11989 Sorted by residual: angle pdb=" N SER A 13 " pdb=" CA SER A 13 " pdb=" C SER A 13 " ideal model delta sigma weight residual 107.28 117.82 -10.54 1.75e+00 3.27e-01 3.63e+01 angle pdb=" C SER A 339 " pdb=" CA SER A 339 " pdb=" CB SER A 339 " ideal model delta sigma weight residual 109.83 115.12 -5.29 9.90e-01 1.02e+00 2.86e+01 angle pdb=" N GLY B 202 " pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 111.04 102.18 8.86 1.77e+00 3.19e-01 2.51e+01 angle pdb=" C TYR C 223 " pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " ideal model delta sigma weight residual 109.56 117.59 -8.03 1.64e+00 3.72e-01 2.40e+01 angle pdb=" C SER A 13 " pdb=" CA SER A 13 " pdb=" CB SER A 13 " ideal model delta sigma weight residual 111.51 105.11 6.40 1.38e+00 5.25e-01 2.15e+01 ... (remaining 11984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 4866 15.49 - 30.98: 290 30.98 - 46.48: 66 46.48 - 61.97: 21 61.97 - 77.46: 2 Dihedral angle restraints: 5245 sinusoidal: 2049 harmonic: 3196 Sorted by residual: dihedral pdb=" CB CYS R 657 " pdb=" SG CYS R 657 " pdb=" SG CYS R 733 " pdb=" CB CYS R 733 " ideal model delta sinusoidal sigma weight residual -86.00 -126.67 40.67 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA SER A 13 " pdb=" C SER A 13 " pdb=" N ALA A 14 " pdb=" CA ALA A 14 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1072 0.064 - 0.129: 273 0.129 - 0.193: 28 0.193 - 0.257: 6 0.257 - 0.321: 3 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LEU B 308 " pdb=" N LEU B 308 " pdb=" C LEU B 308 " pdb=" CB LEU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU B 55 " pdb=" CB LEU B 55 " pdb=" CD1 LEU B 55 " pdb=" CD2 LEU B 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1379 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 817 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C LEU R 817 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU R 817 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA R 818 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 196 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C SER C 196 " 0.045 2.00e-02 2.50e+03 pdb=" O SER C 196 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 197 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 62 " 0.019 2.00e-02 2.50e+03 1.87e-02 5.25e+00 pdb=" CG HIS B 62 " -0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS B 62 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 62 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 62 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 62 " 0.008 2.00e-02 2.50e+03 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1700 2.76 - 3.30: 8447 3.30 - 3.83: 14526 3.83 - 4.37: 17482 4.37 - 4.90: 30504 Nonbonded interactions: 72659 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.230 3.040 nonbonded pdb=" O LEU A 291 " pdb=" OG1 THR A 347 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.266 3.040 nonbonded pdb=" O ARG A 314 " pdb=" OH TYR A 326 " model vdw 2.270 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.287 3.040 ... (remaining 72654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 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 : 0.010 0.076 8855 Z= 0.664 Angle : 0.954 10.542 11989 Z= 0.541 Chirality : 0.057 0.321 1382 Planarity : 0.005 0.046 1502 Dihedral : 11.502 77.459 3169 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.69 (0.25), residues: 1086 helix: 0.60 (0.28), residues: 361 sheet: -0.86 (0.27), residues: 302 loop : -0.93 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 99 HIS 0.018 0.002 HIS B 62 PHE 0.034 0.004 PHE B 151 TYR 0.032 0.004 TYR B 105 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7002 (mt) cc_final: 0.6552 (tt) REVERT: A 235 PHE cc_start: 0.8013 (m-80) cc_final: 0.7514 (m-80) REVERT: A 285 VAL cc_start: 0.7074 (t) cc_final: 0.6797 (m) REVERT: C 180 MET cc_start: 0.6158 (ttm) cc_final: 0.5955 (tpp) REVERT: R 833 PHE cc_start: 0.7256 (m-10) cc_final: 0.7027 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.9574 time to fit residues: 220.0065 Evaluate side-chains 192 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN E 44 HIS R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.179871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.151674 restraints weight = 12407.537| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.39 r_work: 0.3842 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8855 Z= 0.252 Angle : 0.649 9.190 11989 Z= 0.334 Chirality : 0.045 0.190 1382 Planarity : 0.004 0.043 1502 Dihedral : 5.198 23.262 1185 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.20 % Allowed : 10.90 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1086 helix: 1.44 (0.28), residues: 356 sheet: -0.70 (0.28), residues: 291 loop : -0.85 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 PHE 0.021 0.002 PHE A 357 TYR 0.016 0.002 TYR C 178 ARG 0.007 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.910 Fit side-chains REVERT: A 233 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7370 (mmtt) REVERT: A 235 PHE cc_start: 0.7958 (m-80) cc_final: 0.7374 (m-80) REVERT: A 343 PHE cc_start: 0.7131 (m-10) cc_final: 0.6900 (m-80) REVERT: B 130 GLU cc_start: 0.7862 (mp0) cc_final: 0.7568 (mp0) REVERT: B 230 ASN cc_start: 0.8039 (m-40) cc_final: 0.7819 (m110) REVERT: B 325 MET cc_start: 0.7587 (mmt) cc_final: 0.7194 (mtt) REVERT: C 90 ASP cc_start: 0.7236 (m-30) cc_final: 0.6920 (m-30) REVERT: C 180 MET cc_start: 0.6256 (ttm) cc_final: 0.6026 (tpp) REVERT: R 582 PHE cc_start: 0.7608 (m-80) cc_final: 0.7272 (m-80) REVERT: R 827 ASN cc_start: 0.7128 (m-40) cc_final: 0.6609 (m-40) REVERT: R 833 PHE cc_start: 0.7261 (m-10) cc_final: 0.7002 (m-80) outliers start: 21 outliers final: 8 residues processed: 201 average time/residue: 0.9842 time to fit residues: 213.9177 Evaluate side-chains 185 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 88 ASN B 176 GLN E 18 GLN R 820 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.178272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.150286 restraints weight = 12583.088| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.37 r_work: 0.3827 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8855 Z= 0.297 Angle : 0.634 8.328 11989 Z= 0.325 Chirality : 0.045 0.165 1382 Planarity : 0.004 0.042 1502 Dihedral : 5.072 25.486 1185 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.94 % Allowed : 13.42 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.05 (0.26), residues: 1086 helix: 1.65 (0.28), residues: 356 sheet: -0.82 (0.28), residues: 290 loop : -0.79 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.007 0.001 HIS A 345 PHE 0.029 0.002 PHE A 357 TYR 0.017 0.002 TYR C 178 ARG 0.010 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.851 Fit side-chains REVERT: A 233 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7420 (mmtt) REVERT: A 235 PHE cc_start: 0.7896 (m-10) cc_final: 0.7331 (m-80) REVERT: A 285 VAL cc_start: 0.7255 (t) cc_final: 0.7047 (m) REVERT: A 294 MET cc_start: 0.6850 (ptt) cc_final: 0.6611 (ptt) REVERT: A 343 PHE cc_start: 0.7139 (m-10) cc_final: 0.6916 (m-80) REVERT: B 38 ASP cc_start: 0.8153 (m-30) cc_final: 0.7898 (m-30) REVERT: B 129 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.7934 (mmm-85) REVERT: B 130 GLU cc_start: 0.7901 (mp0) cc_final: 0.7607 (mp0) REVERT: B 325 MET cc_start: 0.7562 (mmt) cc_final: 0.7216 (mtt) REVERT: C 65 LYS cc_start: 0.7964 (tppt) cc_final: 0.7755 (tttm) REVERT: C 90 ASP cc_start: 0.7272 (m-30) cc_final: 0.7014 (m-30) REVERT: E 50 LEU cc_start: 0.7852 (mt) cc_final: 0.7540 (mt) REVERT: R 582 PHE cc_start: 0.7637 (m-80) cc_final: 0.7321 (m-80) REVERT: R 693 MET cc_start: 0.6536 (ptt) cc_final: 0.6276 (ptt) outliers start: 28 outliers final: 15 residues processed: 195 average time/residue: 1.0080 time to fit residues: 212.2055 Evaluate side-chains 197 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain R residue 763 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 230 ASN R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.179091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150990 restraints weight = 12389.351| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.34 r_work: 0.3843 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8855 Z= 0.267 Angle : 0.609 8.187 11989 Z= 0.313 Chirality : 0.044 0.159 1382 Planarity : 0.004 0.059 1502 Dihedral : 4.928 25.728 1185 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.25 % Allowed : 14.36 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.05 (0.26), residues: 1086 helix: 1.69 (0.27), residues: 360 sheet: -0.89 (0.28), residues: 294 loop : -0.60 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.008 0.001 HIS A 345 PHE 0.025 0.002 PHE A 357 TYR 0.016 0.002 TYR C 178 ARG 0.009 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.960 Fit side-chains REVERT: A 212 PHE cc_start: 0.6245 (p90) cc_final: 0.6027 (p90) REVERT: A 233 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7361 (mmtt) REVERT: A 235 PHE cc_start: 0.7843 (m-10) cc_final: 0.7354 (m-80) REVERT: A 266 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7358 (pp) REVERT: A 285 VAL cc_start: 0.7220 (t) cc_final: 0.7018 (m) REVERT: A 294 MET cc_start: 0.6883 (ptt) cc_final: 0.6584 (ptt) REVERT: B 38 ASP cc_start: 0.8116 (m-30) cc_final: 0.7870 (m-30) REVERT: B 129 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.7919 (mmm-85) REVERT: B 130 GLU cc_start: 0.7831 (mp0) cc_final: 0.7547 (mp0) REVERT: B 325 MET cc_start: 0.7517 (mmt) cc_final: 0.7189 (mtt) REVERT: C 90 ASP cc_start: 0.7198 (m-30) cc_final: 0.6912 (m-30) REVERT: E 50 LEU cc_start: 0.7864 (mt) cc_final: 0.7553 (mt) REVERT: R 582 PHE cc_start: 0.7720 (m-80) cc_final: 0.7364 (m-80) REVERT: R 693 MET cc_start: 0.6611 (ptt) cc_final: 0.6291 (ptt) REVERT: R 827 ASN cc_start: 0.7197 (m-40) cc_final: 0.6762 (m-40) REVERT: R 833 PHE cc_start: 0.7133 (m-80) cc_final: 0.6538 (m-80) outliers start: 31 outliers final: 19 residues processed: 199 average time/residue: 1.0209 time to fit residues: 219.0841 Evaluate side-chains 208 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 230 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.178558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150432 restraints weight = 12432.674| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.35 r_work: 0.3838 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8855 Z= 0.306 Angle : 0.624 9.643 11989 Z= 0.319 Chirality : 0.044 0.155 1382 Planarity : 0.004 0.061 1502 Dihedral : 4.904 25.723 1185 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.25 % Allowed : 15.20 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.06 (0.26), residues: 1086 helix: 1.77 (0.27), residues: 360 sheet: -0.89 (0.28), residues: 283 loop : -0.68 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS A 345 PHE 0.016 0.002 PHE B 241 TYR 0.016 0.002 TYR C 178 ARG 0.009 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.987 Fit side-chains REVERT: A 233 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7373 (mmtt) REVERT: A 235 PHE cc_start: 0.7924 (m-10) cc_final: 0.7371 (m-80) REVERT: A 266 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7435 (pp) REVERT: A 270 MET cc_start: 0.7016 (ttt) cc_final: 0.6421 (tpp) REVERT: A 285 VAL cc_start: 0.7262 (t) cc_final: 0.7051 (m) REVERT: A 294 MET cc_start: 0.6925 (ptt) cc_final: 0.6576 (ptt) REVERT: B 38 ASP cc_start: 0.8118 (m-30) cc_final: 0.7873 (m-30) REVERT: B 50 THR cc_start: 0.8101 (m) cc_final: 0.7897 (t) REVERT: B 130 GLU cc_start: 0.7835 (mp0) cc_final: 0.7538 (mp0) REVERT: B 325 MET cc_start: 0.7528 (mmt) cc_final: 0.7214 (mtt) REVERT: C 90 ASP cc_start: 0.7237 (m-30) cc_final: 0.6983 (m-30) REVERT: C 174 GLN cc_start: 0.7988 (tt0) cc_final: 0.7725 (pt0) REVERT: C 180 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5630 (ttp) REVERT: C 218 MET cc_start: 0.6808 (ttp) cc_final: 0.6555 (ttm) REVERT: C 221 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7587 (tm) REVERT: R 582 PHE cc_start: 0.7761 (m-80) cc_final: 0.7359 (m-80) REVERT: R 693 MET cc_start: 0.6539 (ptt) cc_final: 0.6225 (ptt) REVERT: R 799 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8200 (tp) REVERT: R 833 PHE cc_start: 0.7130 (m-80) cc_final: 0.6609 (m-80) outliers start: 31 outliers final: 17 residues processed: 198 average time/residue: 1.0411 time to fit residues: 223.3693 Evaluate side-chains 201 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 0.0030 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 266 HIS R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.179049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150774 restraints weight = 12419.053| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.36 r_work: 0.3838 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8855 Z= 0.289 Angle : 0.616 9.178 11989 Z= 0.314 Chirality : 0.044 0.152 1382 Planarity : 0.004 0.058 1502 Dihedral : 4.845 24.936 1185 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.46 % Allowed : 15.93 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.11 (0.26), residues: 1086 helix: 1.79 (0.27), residues: 360 sheet: -0.77 (0.29), residues: 275 loop : -0.72 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS A 345 PHE 0.023 0.002 PHE A 343 TYR 0.016 0.002 TYR C 178 ARG 0.010 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.962 Fit side-chains REVERT: A 233 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7385 (mmtt) REVERT: A 235 PHE cc_start: 0.7934 (m-10) cc_final: 0.7322 (m-80) REVERT: A 266 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7209 (pp) REVERT: A 270 MET cc_start: 0.7006 (ttt) cc_final: 0.6501 (tpp) REVERT: A 285 VAL cc_start: 0.7240 (t) cc_final: 0.7033 (m) REVERT: A 294 MET cc_start: 0.6972 (ptt) cc_final: 0.6624 (ptt) REVERT: B 38 ASP cc_start: 0.8088 (m-30) cc_final: 0.7840 (m-30) REVERT: B 50 THR cc_start: 0.8105 (m) cc_final: 0.7881 (t) REVERT: B 130 GLU cc_start: 0.7774 (mp0) cc_final: 0.7497 (mp0) REVERT: B 325 MET cc_start: 0.7497 (mmt) cc_final: 0.7214 (mtt) REVERT: C 90 ASP cc_start: 0.7234 (m-30) cc_final: 0.7007 (m-30) REVERT: C 174 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: C 180 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5662 (ttp) REVERT: R 582 PHE cc_start: 0.7757 (m-80) cc_final: 0.7312 (m-80) REVERT: R 693 MET cc_start: 0.6517 (ptt) cc_final: 0.6256 (ptt) REVERT: R 799 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8215 (tp) REVERT: R 833 PHE cc_start: 0.7211 (m-80) cc_final: 0.6595 (m-80) outliers start: 33 outliers final: 18 residues processed: 194 average time/residue: 1.0367 time to fit residues: 216.9828 Evaluate side-chains 202 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain R residue 698 MET Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN R 820 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.180472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.152805 restraints weight = 12387.434| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.32 r_work: 0.3863 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8855 Z= 0.222 Angle : 0.585 9.941 11989 Z= 0.300 Chirality : 0.043 0.152 1382 Planarity : 0.004 0.048 1502 Dihedral : 4.688 23.322 1185 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.56 % Allowed : 16.35 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.24 (0.26), residues: 1086 helix: 1.97 (0.27), residues: 359 sheet: -0.80 (0.29), residues: 286 loop : -0.62 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 211 HIS 0.004 0.001 HIS A 344 PHE 0.025 0.002 PHE A 343 TYR 0.014 0.001 TYR C 178 ARG 0.009 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7715 (mmtt) cc_final: 0.7368 (mmtt) REVERT: A 235 PHE cc_start: 0.7906 (m-10) cc_final: 0.7442 (m-80) REVERT: A 270 MET cc_start: 0.6974 (ttt) cc_final: 0.6512 (tpp) REVERT: A 343 PHE cc_start: 0.7150 (m-10) cc_final: 0.6911 (m-80) REVERT: B 38 ASP cc_start: 0.8029 (m-30) cc_final: 0.7784 (m-30) REVERT: B 130 GLU cc_start: 0.7714 (mp0) cc_final: 0.7463 (mp0) REVERT: B 325 MET cc_start: 0.7541 (mmt) cc_final: 0.7262 (mtt) REVERT: C 4 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7849 (mp) REVERT: C 45 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.6076 (pt) REVERT: C 90 ASP cc_start: 0.7106 (m-30) cc_final: 0.6839 (m-30) REVERT: C 174 GLN cc_start: 0.7981 (tt0) cc_final: 0.7745 (pt0) REVERT: C 180 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5588 (ttp) REVERT: E 50 LEU cc_start: 0.7920 (mt) cc_final: 0.7666 (mt) REVERT: R 582 PHE cc_start: 0.7723 (m-80) cc_final: 0.7254 (m-80) REVERT: R 693 MET cc_start: 0.6519 (ptt) cc_final: 0.6285 (ptt) REVERT: R 793 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7600 (tp) REVERT: R 799 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8235 (tp) outliers start: 34 outliers final: 19 residues processed: 201 average time/residue: 1.0031 time to fit residues: 217.9905 Evaluate side-chains 200 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 0.0050 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN R 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.180382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152042 restraints weight = 12584.377| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.37 r_work: 0.3846 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8855 Z= 0.252 Angle : 0.616 11.370 11989 Z= 0.313 Chirality : 0.043 0.153 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.701 24.622 1185 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.56 % Allowed : 17.30 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.30 (0.26), residues: 1086 helix: 2.04 (0.27), residues: 357 sheet: -0.70 (0.29), residues: 286 loop : -0.63 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 211 HIS 0.004 0.001 HIS A 345 PHE 0.016 0.002 PHE B 241 TYR 0.015 0.002 TYR C 178 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7374 (mmtt) REVERT: A 235 PHE cc_start: 0.7896 (m-10) cc_final: 0.7431 (m-80) REVERT: A 270 MET cc_start: 0.7032 (ttt) cc_final: 0.6561 (tpp) REVERT: A 343 PHE cc_start: 0.7229 (m-10) cc_final: 0.6959 (m-80) REVERT: B 38 ASP cc_start: 0.8056 (m-30) cc_final: 0.7817 (m-30) REVERT: B 61 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7809 (pp-130) REVERT: B 129 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.7972 (mmm-85) REVERT: B 130 GLU cc_start: 0.7724 (mp0) cc_final: 0.7463 (mp0) REVERT: B 325 MET cc_start: 0.7502 (mmt) cc_final: 0.7257 (mtt) REVERT: C 45 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6123 (pt) REVERT: C 90 ASP cc_start: 0.7159 (m-30) cc_final: 0.6883 (m-30) REVERT: C 160 THR cc_start: 0.7635 (m) cc_final: 0.7399 (t) REVERT: C 174 GLN cc_start: 0.7937 (tt0) cc_final: 0.7712 (pt0) REVERT: C 180 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5576 (ttp) REVERT: R 582 PHE cc_start: 0.7764 (m-80) cc_final: 0.7344 (m-80) REVERT: R 693 MET cc_start: 0.6519 (ptt) cc_final: 0.6308 (ptt) REVERT: R 799 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8238 (tp) outliers start: 34 outliers final: 22 residues processed: 195 average time/residue: 1.0188 time to fit residues: 214.2206 Evaluate side-chains 202 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain R residue 671 LEU Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 56 optimal weight: 0.1980 chunk 11 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.180982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.152733 restraints weight = 12454.637| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.34 r_work: 0.3859 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8855 Z= 0.238 Angle : 0.616 11.834 11989 Z= 0.313 Chirality : 0.043 0.155 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.677 26.118 1185 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.04 % Allowed : 17.92 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.34 (0.26), residues: 1086 helix: 2.10 (0.27), residues: 359 sheet: -0.62 (0.30), residues: 274 loop : -0.70 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 211 HIS 0.004 0.001 HIS C 220 PHE 0.022 0.002 PHE C 200 TYR 0.014 0.002 TYR C 178 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7371 (mmtt) REVERT: A 235 PHE cc_start: 0.7893 (m-10) cc_final: 0.7305 (m-80) REVERT: A 270 MET cc_start: 0.6992 (ttt) cc_final: 0.6518 (tpp) REVERT: A 343 PHE cc_start: 0.7214 (m-10) cc_final: 0.6947 (m-80) REVERT: B 38 ASP cc_start: 0.7994 (m-30) cc_final: 0.7763 (m-30) REVERT: B 129 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7954 (mmm-85) REVERT: B 130 GLU cc_start: 0.7666 (mp0) cc_final: 0.7437 (mp0) REVERT: B 289 TYR cc_start: 0.8192 (m-80) cc_final: 0.7545 (m-80) REVERT: B 325 MET cc_start: 0.7521 (mmt) cc_final: 0.7278 (mtt) REVERT: C 38 ARG cc_start: 0.8294 (mtm180) cc_final: 0.8047 (mtp85) REVERT: C 45 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6096 (pt) REVERT: C 174 GLN cc_start: 0.7918 (tt0) cc_final: 0.7704 (pt0) REVERT: C 180 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5453 (ttp) REVERT: R 573 MET cc_start: 0.7711 (mtp) cc_final: 0.7446 (mtm) REVERT: R 582 PHE cc_start: 0.7742 (m-80) cc_final: 0.7330 (m-80) REVERT: R 693 MET cc_start: 0.6580 (ptt) cc_final: 0.6355 (ptt) REVERT: R 799 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8245 (tp) outliers start: 29 outliers final: 21 residues processed: 200 average time/residue: 0.9923 time to fit residues: 214.5262 Evaluate side-chains 200 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 176 GLN B 266 HIS B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.181022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.152981 restraints weight = 12447.706| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.36 r_work: 0.3857 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8855 Z= 0.241 Angle : 0.626 12.297 11989 Z= 0.317 Chirality : 0.044 0.181 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.688 23.626 1185 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.94 % Allowed : 18.34 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.41 (0.26), residues: 1086 helix: 2.15 (0.27), residues: 359 sheet: -0.55 (0.29), residues: 285 loop : -0.67 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 211 HIS 0.006 0.001 HIS B 266 PHE 0.026 0.002 PHE C 200 TYR 0.014 0.002 TYR C 178 ARG 0.009 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.5508 (mmm) cc_final: 0.5195 (mtm) REVERT: A 233 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7352 (mmtt) REVERT: A 270 MET cc_start: 0.7032 (ttt) cc_final: 0.6662 (tpp) REVERT: A 343 PHE cc_start: 0.7212 (m-10) cc_final: 0.6951 (m-80) REVERT: B 38 ASP cc_start: 0.7965 (m-30) cc_final: 0.7735 (m-30) REVERT: B 129 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.7957 (mmm-85) REVERT: B 130 GLU cc_start: 0.7674 (mp0) cc_final: 0.7449 (mp0) REVERT: B 186 ASP cc_start: 0.7978 (p0) cc_final: 0.7248 (p0) REVERT: B 289 TYR cc_start: 0.8189 (m-80) cc_final: 0.7525 (m-80) REVERT: B 325 MET cc_start: 0.7522 (mmt) cc_final: 0.7291 (mtt) REVERT: C 38 ARG cc_start: 0.8279 (mtm180) cc_final: 0.8041 (mtp85) REVERT: C 45 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.6073 (pt) REVERT: C 174 GLN cc_start: 0.7915 (tt0) cc_final: 0.7696 (pt0) REVERT: R 582 PHE cc_start: 0.7726 (m-80) cc_final: 0.7306 (m-80) REVERT: R 693 MET cc_start: 0.6535 (ptt) cc_final: 0.6321 (ptt) REVERT: R 799 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8253 (tp) outliers start: 28 outliers final: 23 residues processed: 200 average time/residue: 1.0138 time to fit residues: 218.5989 Evaluate side-chains 205 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain R residue 671 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.179043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.150604 restraints weight = 12456.191| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.36 r_work: 0.3832 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8855 Z= 0.354 Angle : 0.668 12.511 11989 Z= 0.341 Chirality : 0.046 0.227 1382 Planarity : 0.004 0.042 1502 Dihedral : 4.894 25.088 1185 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.73 % Allowed : 19.29 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1086 helix: 2.03 (0.27), residues: 359 sheet: -0.57 (0.30), residues: 275 loop : -0.77 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 211 HIS 0.005 0.001 HIS C 220 PHE 0.032 0.002 PHE A 282 TYR 0.018 0.002 TYR B 85 ARG 0.009 0.001 ARG R 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6361.86 seconds wall clock time: 113 minutes 8.56 seconds (6788.56 seconds total)