Starting phenix.real_space_refine on Fri Mar 14 04:44:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x17_21991/03_2025/6x17_21991.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x17_21991/03_2025/6x17_21991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x17_21991/03_2025/6x17_21991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x17_21991/03_2025/6x17_21991.map" model { file = "/net/cci-nas-00/data/ceres_data/6x17_21991/03_2025/6x17_21991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x17_21991/03_2025/6x17_21991.cif" } resolution = 3.66 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 51 5.16 5 C 6195 2.51 5 N 1500 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9390 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3086 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: C, B Time building chain proxies: 6.01, per 1000 atoms: 0.64 Number of scatterers: 9390 At special positions: 0 Unit cell: (109.472, 106.252, 82.6403, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 3 15.00 O 1641 8.00 N 1500 7.00 C 6195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.533A pdb=" N LYS A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.537A pdb=" N VAL A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.639A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 175 through 220 removed outlier: 3.573A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 227 through 254 removed outlier: 3.978A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 5.806A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.558A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.558A pdb=" N ILE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.009A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 389 through 416 removed outlier: 3.624A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 11 through 33 removed outlier: 3.532A pdb=" N LYS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.536A pdb=" N VAL B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.639A pdb=" N ILE B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 175 through 220 removed outlier: 3.573A pdb=" N ASP B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Proline residue: B 206 - end of helix Processing helix chain 'B' and resid 227 through 254 removed outlier: 3.978A pdb=" N VAL B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 5.807A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.559A pdb=" N TYR B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 301 " --> pdb=" O GLY B 297 " (cutoff:3.500A) Proline residue: B 304 - end of helix Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 337 through 352 removed outlier: 3.557A pdb=" N ILE B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.008A pdb=" N ILE B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 387 Processing helix chain 'B' and resid 389 through 416 removed outlier: 3.624A pdb=" N LEU B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 11 through 33 removed outlier: 3.532A pdb=" N LYS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.537A pdb=" N VAL C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY C 47 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.640A pdb=" N ILE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 169 Processing helix chain 'C' and resid 175 through 220 removed outlier: 3.572A pdb=" N ASP C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 227 through 254 removed outlier: 3.978A pdb=" N VAL C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 276 removed outlier: 5.807A pdb=" N ASP C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 276 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.558A pdb=" N TYR C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 337 through 352 removed outlier: 3.558A pdb=" N ILE C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 removed outlier: 4.009A pdb=" N ILE C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 387 Processing helix chain 'C' and resid 389 through 416 removed outlier: 3.624A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 2118 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: 2.42 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1440 1.31 - 1.43: 2305 1.43 - 1.56: 5672 1.56 - 1.68: 51 1.68 - 1.80: 99 Bond restraints: 9567 Sorted by residual: bond pdb=" C16 6OU C 501 " pdb=" O18 6OU C 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C16 6OU B 501 " pdb=" O18 6OU B 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C31 6OU C 501 " pdb=" O30 6OU C 501 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 9562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 12738 3.13 - 6.26: 222 6.26 - 9.39: 45 9.39 - 12.51: 6 12.51 - 15.64: 3 Bond angle restraints: 13014 Sorted by residual: angle pdb=" O22 6OU C 501 " pdb=" P23 6OU C 501 " pdb=" O26 6OU C 501 " ideal model delta sigma weight residual 93.95 109.59 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.57 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " pdb=" O26 6OU B 501 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" N ALA B 205 " pdb=" CA ALA B 205 " pdb=" C ALA B 205 " ideal model delta sigma weight residual 109.81 119.47 -9.66 2.21e+00 2.05e-01 1.91e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 119.45 -9.64 2.21e+00 2.05e-01 1.90e+01 ... (remaining 13009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 5297 25.60 - 51.21: 331 51.21 - 76.81: 30 76.81 - 102.42: 0 102.42 - 128.02: 6 Dihedral angle restraints: 5664 sinusoidal: 2130 harmonic: 3534 Sorted by residual: dihedral pdb=" CA LEU C 333 " pdb=" C LEU C 333 " pdb=" N THR C 334 " pdb=" CA THR C 334 " ideal model delta harmonic sigma weight residual 180.00 141.62 38.38 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA LEU B 333 " pdb=" C LEU B 333 " pdb=" N THR B 334 " pdb=" CA THR B 334 " ideal model delta harmonic sigma weight residual 180.00 141.63 38.37 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA LEU A 333 " pdb=" C LEU A 333 " pdb=" N THR A 334 " pdb=" CA THR A 334 " ideal model delta harmonic sigma weight residual 180.00 141.67 38.33 0 5.00e+00 4.00e-02 5.88e+01 ... (remaining 5661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1028 0.040 - 0.080: 412 0.080 - 0.119: 111 0.119 - 0.159: 39 0.159 - 0.199: 24 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CA SER C 74 " pdb=" N SER C 74 " pdb=" C SER C 74 " pdb=" CB SER C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA SER A 74 " pdb=" N SER A 74 " pdb=" C SER A 74 " pdb=" CB SER A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA SER B 74 " pdb=" N SER B 74 " pdb=" C SER B 74 " pdb=" CB SER B 74 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1611 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 405 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" CG ASP A 405 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP A 405 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 405 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 405 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" CG ASP C 405 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP C 405 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP C 405 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 405 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" CG ASP B 405 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP B 405 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 405 " 0.018 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2620 2.81 - 3.33: 8925 3.33 - 3.85: 15445 3.85 - 4.38: 16959 4.38 - 4.90: 30388 Nonbonded interactions: 74337 Sorted by model distance: nonbonded pdb=" O SER C 65 " pdb=" OG SER C 300 " model vdw 2.284 3.040 nonbonded pdb=" O SER A 65 " pdb=" OG SER A 300 " model vdw 2.284 3.040 nonbonded pdb=" O SER B 65 " pdb=" OG SER B 300 " model vdw 2.284 3.040 nonbonded pdb=" O GLN A 337 " pdb=" OG1 THR A 340 " model vdw 2.295 3.040 nonbonded pdb=" O GLN C 337 " pdb=" OG1 THR C 340 " model vdw 2.295 3.040 ... (remaining 74332 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.450 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.007 0.089 9567 Z= 0.482 Angle : 1.053 15.642 13014 Z= 0.533 Chirality : 0.051 0.199 1614 Planarity : 0.008 0.063 1593 Dihedral : 16.083 128.021 3426 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.18), residues: 1239 helix: -2.09 (0.12), residues: 984 sheet: None (None), residues: 0 loop : -3.16 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 264 PHE 0.009 0.001 PHE A 301 TYR 0.018 0.002 TYR A 299 ARG 0.002 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.981 Fit side-chains REVERT: A 105 ARG cc_start: 0.8383 (mtp-110) cc_final: 0.8178 (mtm180) REVERT: A 115 LEU cc_start: 0.7992 (pp) cc_final: 0.7682 (pp) REVERT: A 203 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8159 (tp-100) REVERT: A 362 MET cc_start: 0.8084 (mtp) cc_final: 0.7740 (mtp) REVERT: B 105 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7915 (mtm180) REVERT: B 120 GLN cc_start: 0.6800 (pp30) cc_final: 0.6566 (pp30) REVERT: B 401 ASN cc_start: 0.8127 (m-40) cc_final: 0.7725 (m-40) REVERT: C 312 ASP cc_start: 0.8933 (m-30) cc_final: 0.8468 (m-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1870 time to fit residues: 71.6889 Evaluate side-chains 204 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 318 GLN A 327 ASN B 14 GLN B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS C 318 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.117005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.099173 restraints weight = 12612.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.101637 restraints weight = 7421.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.103420 restraints weight = 5174.177| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9567 Z= 0.169 Angle : 0.593 8.825 13014 Z= 0.293 Chirality : 0.038 0.136 1614 Planarity : 0.005 0.049 1593 Dihedral : 10.311 93.053 1440 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.16 % Allowed : 16.05 % Favored : 81.79 % 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: -0.78 (0.22), residues: 1239 helix: 0.13 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -2.81 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 32 PHE 0.011 0.001 PHE B 323 TYR 0.013 0.001 TYR C 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.940 Fit side-chains REVERT: A 33 TYR cc_start: 0.7776 (m-10) cc_final: 0.7547 (m-10) REVERT: A 269 MET cc_start: 0.8416 (mtp) cc_final: 0.8075 (mtm) REVERT: A 286 MET cc_start: 0.9051 (mtp) cc_final: 0.8824 (mtm) REVERT: A 362 MET cc_start: 0.8113 (mtp) cc_final: 0.7848 (mtp) REVERT: B 18 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8547 (mp) REVERT: B 128 PRO cc_start: 0.8339 (Cg_endo) cc_final: 0.8136 (Cg_exo) REVERT: B 362 MET cc_start: 0.7919 (mtp) cc_final: 0.7590 (ttm) REVERT: C 103 MET cc_start: 0.8779 (tpp) cc_final: 0.8554 (mmt) outliers start: 21 outliers final: 14 residues processed: 241 average time/residue: 0.1826 time to fit residues: 63.3847 Evaluate side-chains 232 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 223 HIS B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS C 14 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.115617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.097851 restraints weight = 12857.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.100222 restraints weight = 7639.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.102066 restraints weight = 5374.221| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9567 Z= 0.191 Angle : 0.590 9.298 13014 Z= 0.289 Chirality : 0.039 0.132 1614 Planarity : 0.004 0.045 1593 Dihedral : 9.732 79.206 1440 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.37 % Allowed : 19.44 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1239 helix: 1.02 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 32 PHE 0.008 0.001 PHE C 323 TYR 0.016 0.001 TYR C 299 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.894 Fit side-chains REVERT: A 269 MET cc_start: 0.8428 (mtp) cc_final: 0.8148 (mtm) REVERT: A 362 MET cc_start: 0.8074 (mtp) cc_final: 0.7862 (mtp) REVERT: B 340 THR cc_start: 0.9017 (p) cc_final: 0.8813 (p) REVERT: C 103 MET cc_start: 0.8822 (tpp) cc_final: 0.8553 (mmt) REVERT: C 134 LEU cc_start: 0.7890 (tt) cc_final: 0.7465 (mp) REVERT: C 136 ASP cc_start: 0.7529 (t0) cc_final: 0.6992 (t0) REVERT: C 286 MET cc_start: 0.8792 (mtm) cc_final: 0.8409 (mtp) outliers start: 23 outliers final: 17 residues processed: 233 average time/residue: 0.1839 time to fit residues: 61.4733 Evaluate side-chains 224 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.115723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.097802 restraints weight = 12748.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.100322 restraints weight = 7550.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.102082 restraints weight = 5260.461| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9567 Z= 0.187 Angle : 0.586 12.738 13014 Z= 0.286 Chirality : 0.039 0.154 1614 Planarity : 0.004 0.043 1593 Dihedral : 9.221 66.829 1440 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.57 % Allowed : 21.30 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1239 helix: 1.42 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.44 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 32 PHE 0.010 0.001 PHE B 323 TYR 0.015 0.001 TYR B 299 ARG 0.005 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 1.020 Fit side-chains REVERT: A 115 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7865 (pp) REVERT: A 194 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8711 (mmt) REVERT: A 269 MET cc_start: 0.8446 (mtp) cc_final: 0.8172 (mtm) REVERT: B 340 THR cc_start: 0.8993 (p) cc_final: 0.8726 (p) REVERT: B 362 MET cc_start: 0.8118 (mtp) cc_final: 0.7694 (ttm) REVERT: C 103 MET cc_start: 0.8787 (tpp) cc_final: 0.8549 (mmt) REVERT: C 134 LEU cc_start: 0.7844 (tt) cc_final: 0.7420 (mp) REVERT: C 136 ASP cc_start: 0.7430 (t0) cc_final: 0.6993 (t0) REVERT: C 286 MET cc_start: 0.8717 (mtm) cc_final: 0.8325 (mtp) outliers start: 25 outliers final: 17 residues processed: 227 average time/residue: 0.1918 time to fit residues: 62.1559 Evaluate side-chains 226 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 105 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 0.0040 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.116388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.098442 restraints weight = 12746.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.100968 restraints weight = 7564.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.102707 restraints weight = 5287.698| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9567 Z= 0.181 Angle : 0.574 9.821 13014 Z= 0.280 Chirality : 0.039 0.136 1614 Planarity : 0.004 0.043 1593 Dihedral : 8.940 65.887 1440 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.29 % Allowed : 21.40 % Favored : 75.31 % 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: 1.30 (0.24), residues: 1239 helix: 1.64 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.40 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.011 0.001 PHE B 323 TYR 0.013 0.001 TYR C 299 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.878 Fit side-chains REVERT: A 194 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8867 (mmt) REVERT: A 269 MET cc_start: 0.8452 (mtp) cc_final: 0.8211 (mtm) REVERT: A 362 MET cc_start: 0.7896 (mtp) cc_final: 0.7405 (mtp) REVERT: B 136 ASP cc_start: 0.7470 (t0) cc_final: 0.7042 (t0) REVERT: B 169 MET cc_start: 0.8604 (mmm) cc_final: 0.7894 (mtp) REVERT: B 340 THR cc_start: 0.8975 (p) cc_final: 0.8670 (p) REVERT: C 136 ASP cc_start: 0.7362 (t0) cc_final: 0.6970 (t0) REVERT: C 286 MET cc_start: 0.8724 (mtm) cc_final: 0.8319 (mtp) outliers start: 32 outliers final: 23 residues processed: 238 average time/residue: 0.1884 time to fit residues: 64.5040 Evaluate side-chains 237 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 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 223 HIS B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.118236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.100136 restraints weight = 12703.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.102530 restraints weight = 7598.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.104368 restraints weight = 5386.993| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9567 Z= 0.161 Angle : 0.588 15.017 13014 Z= 0.283 Chirality : 0.039 0.145 1614 Planarity : 0.004 0.042 1593 Dihedral : 8.702 67.785 1440 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.91 % Allowed : 21.50 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1239 helix: 1.81 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.27 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.009 0.001 PHE B 323 TYR 0.019 0.001 TYR A 88 ARG 0.007 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 0.967 Fit side-chains REVERT: A 269 MET cc_start: 0.8433 (mtp) cc_final: 0.8180 (mtm) REVERT: A 362 MET cc_start: 0.7763 (mtp) cc_final: 0.7328 (mtp) REVERT: B 136 ASP cc_start: 0.7366 (t0) cc_final: 0.6926 (t0) REVERT: B 169 MET cc_start: 0.8543 (mmm) cc_final: 0.7950 (mtp) REVERT: B 362 MET cc_start: 0.7978 (mtp) cc_final: 0.7738 (ttm) REVERT: C 123 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7199 (tm-30) REVERT: C 136 ASP cc_start: 0.7245 (t0) cc_final: 0.6875 (t0) REVERT: C 286 MET cc_start: 0.8689 (mtm) cc_final: 0.8360 (mtp) outliers start: 38 outliers final: 27 residues processed: 252 average time/residue: 0.1779 time to fit residues: 64.9594 Evaluate side-chains 244 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 0.0170 chunk 110 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.116080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.098309 restraints weight = 12848.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.100736 restraints weight = 7679.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.102542 restraints weight = 5404.842| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9567 Z= 0.186 Angle : 0.594 15.708 13014 Z= 0.288 Chirality : 0.039 0.147 1614 Planarity : 0.004 0.042 1593 Dihedral : 8.342 72.152 1440 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.60 % Allowed : 22.84 % Favored : 73.56 % 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: 1.71 (0.24), residues: 1239 helix: 1.92 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.20 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.000 HIS B 32 PHE 0.009 0.001 PHE A 323 TYR 0.021 0.001 TYR A 88 ARG 0.006 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.926 Fit side-chains REVERT: A 269 MET cc_start: 0.8441 (mtp) cc_final: 0.8215 (mtm) REVERT: A 362 MET cc_start: 0.7852 (mtp) cc_final: 0.7382 (mtp) REVERT: B 136 ASP cc_start: 0.7426 (t0) cc_final: 0.7060 (t0) REVERT: B 169 MET cc_start: 0.8564 (mmm) cc_final: 0.7877 (mtm) REVERT: B 242 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.6757 (tp40) REVERT: B 362 MET cc_start: 0.8114 (mtp) cc_final: 0.7644 (ttm) REVERT: C 123 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7208 (tm-30) REVERT: C 136 ASP cc_start: 0.7280 (t0) cc_final: 0.6932 (t0) REVERT: C 286 MET cc_start: 0.8692 (mtm) cc_final: 0.8358 (mtp) outliers start: 35 outliers final: 30 residues processed: 236 average time/residue: 0.2000 time to fit residues: 68.3205 Evaluate side-chains 244 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 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 223 HIS B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.114847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.097180 restraints weight = 13004.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.099690 restraints weight = 7705.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.101445 restraints weight = 5376.181| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9567 Z= 0.205 Angle : 0.611 15.431 13014 Z= 0.294 Chirality : 0.039 0.131 1614 Planarity : 0.004 0.042 1593 Dihedral : 8.199 75.145 1440 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.70 % Allowed : 22.74 % Favored : 73.56 % 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: 1.77 (0.24), residues: 1239 helix: 1.93 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.07 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.009 0.001 PHE A 323 TYR 0.021 0.001 TYR A 88 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.995 Fit side-chains REVERT: A 269 MET cc_start: 0.8379 (mtp) cc_final: 0.8148 (mtm) REVERT: A 362 MET cc_start: 0.7909 (mtp) cc_final: 0.7407 (mtp) REVERT: B 136 ASP cc_start: 0.7451 (t0) cc_final: 0.7094 (t0) REVERT: B 169 MET cc_start: 0.8555 (mmm) cc_final: 0.8203 (mtm) REVERT: B 242 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.6951 (tp40) REVERT: B 362 MET cc_start: 0.8176 (mtp) cc_final: 0.7703 (ttm) REVERT: C 123 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7252 (tm-30) REVERT: C 136 ASP cc_start: 0.7321 (t0) cc_final: 0.6994 (t0) REVERT: C 286 MET cc_start: 0.8692 (mtm) cc_final: 0.8349 (mtp) outliers start: 36 outliers final: 29 residues processed: 240 average time/residue: 0.1842 time to fit residues: 63.8209 Evaluate side-chains 242 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 6 optimal weight: 0.0570 chunk 45 optimal weight: 0.0270 chunk 4 optimal weight: 0.6980 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 40 HIS B 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.119008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.101171 restraints weight = 12720.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.103669 restraints weight = 7625.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.105414 restraints weight = 5372.462| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9567 Z= 0.157 Angle : 0.599 14.691 13014 Z= 0.287 Chirality : 0.039 0.138 1614 Planarity : 0.004 0.041 1593 Dihedral : 8.008 76.435 1440 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.88 % Allowed : 23.35 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1239 helix: 2.07 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -1.99 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.000 HIS B 32 PHE 0.006 0.001 PHE A 323 TYR 0.018 0.001 TYR A 88 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.967 Fit side-chains REVERT: A 13 LEU cc_start: 0.8385 (mt) cc_final: 0.8111 (mt) REVERT: A 18 ILE cc_start: 0.8731 (mt) cc_final: 0.8525 (mp) REVERT: A 30 LEU cc_start: 0.8977 (mt) cc_final: 0.8768 (mt) REVERT: A 194 MET cc_start: 0.8859 (mmt) cc_final: 0.8564 (mmp) REVERT: A 269 MET cc_start: 0.8425 (mtp) cc_final: 0.8199 (mtm) REVERT: A 362 MET cc_start: 0.7729 (mtp) cc_final: 0.7412 (mtp) REVERT: B 136 ASP cc_start: 0.7557 (t0) cc_final: 0.7178 (t0) REVERT: B 169 MET cc_start: 0.8472 (mmm) cc_final: 0.7860 (mtm) REVERT: B 242 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.6543 (tp40) REVERT: B 362 MET cc_start: 0.8035 (mtp) cc_final: 0.7685 (ttm) REVERT: C 13 LEU cc_start: 0.8274 (mt) cc_final: 0.8030 (mt) REVERT: C 53 LEU cc_start: 0.9017 (mt) cc_final: 0.8799 (mt) REVERT: C 136 ASP cc_start: 0.7274 (t0) cc_final: 0.6950 (t0) REVERT: C 286 MET cc_start: 0.8619 (mtm) cc_final: 0.8348 (mtp) outliers start: 28 outliers final: 23 residues processed: 241 average time/residue: 0.1797 time to fit residues: 62.8757 Evaluate side-chains 237 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.117430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.099688 restraints weight = 12905.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102137 restraints weight = 7697.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.103973 restraints weight = 5425.344| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9567 Z= 0.179 Angle : 0.615 14.344 13014 Z= 0.294 Chirality : 0.039 0.129 1614 Planarity : 0.004 0.041 1593 Dihedral : 7.962 75.482 1440 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.88 % Allowed : 23.77 % Favored : 73.35 % 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: 2.05 (0.24), residues: 1239 helix: 2.12 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -1.94 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.007 0.001 PHE A 323 TYR 0.017 0.001 TYR C 299 ARG 0.005 0.000 ARG A 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 1.311 Fit side-chains REVERT: A 18 ILE cc_start: 0.8734 (mt) cc_final: 0.8532 (mp) REVERT: A 269 MET cc_start: 0.8386 (mtp) cc_final: 0.8173 (mtm) REVERT: A 362 MET cc_start: 0.7901 (mtp) cc_final: 0.7450 (mtp) REVERT: B 136 ASP cc_start: 0.7542 (t0) cc_final: 0.7171 (t0) REVERT: B 169 MET cc_start: 0.8496 (mmm) cc_final: 0.7924 (mtm) REVERT: B 242 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.6501 (tp40) REVERT: B 261 PHE cc_start: 0.8966 (t80) cc_final: 0.8700 (t80) REVERT: B 362 MET cc_start: 0.8091 (mtp) cc_final: 0.7619 (ttm) REVERT: B 385 MET cc_start: 0.8412 (tmm) cc_final: 0.8212 (ttt) REVERT: C 13 LEU cc_start: 0.8295 (mt) cc_final: 0.8047 (mt) REVERT: C 53 LEU cc_start: 0.9050 (mt) cc_final: 0.8840 (mt) REVERT: C 123 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7038 (tm-30) REVERT: C 136 ASP cc_start: 0.7228 (t0) cc_final: 0.6930 (t0) outliers start: 28 outliers final: 24 residues processed: 234 average time/residue: 0.2258 time to fit residues: 76.8687 Evaluate side-chains 238 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 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 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.114845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.097207 restraints weight = 12953.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.099720 restraints weight = 7696.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.101397 restraints weight = 5385.883| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.003 0.056 9567 Z= 0.209 Angle : 0.620 14.326 13014 Z= 0.300 Chirality : 0.040 0.128 1614 Planarity : 0.004 0.042 1593 Dihedral : 8.017 75.030 1440 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.19 % Allowed : 23.77 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.24), residues: 1239 helix: 2.06 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -1.84 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.008 0.001 PHE A 323 TYR 0.017 0.001 TYR A 88 ARG 0.004 0.000 ARG A 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2817.60 seconds wall clock time: 50 minutes 30.49 seconds (3030.49 seconds total)