Starting phenix.real_space_refine
on Thu Jul  2 10:31:50 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8fti_29433/07_2026/8fti_29433.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fti_29433/07_2026/8fti_29433.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fti_29433/07_2026/8fti_29433.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fti_29433/07_2026/8fti_29433.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8fti_29433/07_2026/8fti_29433.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8fti_29433/07_2026/8fti_29433.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fti_29433/07_2026/8fti_29433.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fti_29433/07_2026/8fti_29433.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
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=   0.020
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      97      5.49       5
     S      24      5.16       5
     C    4792      2.51       5
     N    1443      2.21       5
     O    1770      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8126
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 737, 6062
          Classifications: {'peptide': 737}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 725}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 2064
          Classifications: {'RNA': 97}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 45, 'rna3p_pyr': 38}
          Link IDs: {'rna2p': 13, 'rna3p': 83}
          Chain breaks: 1
  Time building chain proxies: 1.86, per 1000 atoms: 0.23
  Number of scatterers: 8126
  At special positions: 0
  Unit cell: (77.43, 81.78, 137.46, 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      24     16.00
     P      97     15.00
     O    1770      8.00
     N    1443      7.00
     C    4792      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: 0.82
  Conformation dependent library (CDL) restraints added in 231.6 milliseconds
  

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1380

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      61.9% alpha, 3.7% beta
      33 base pairs and 55 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 24
      removed outlier: 3.639A  pdb=" N   ARG A  23 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 41
      removed outlier: 3.980A  pdb=" N   ILE A  29 " --> pdb=" O   TRP A  25 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA A  30 " --> pdb=" O   CYS A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 50
    Processing helix  chain 'A' and resid 62 through 72
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 3.641A  pdb=" N   LYS A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 123
      removed outlier: 3.509A  pdb=" N   THR A 107 " --> pdb=" O   ASP A 103 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ARG A 123 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 151
      removed outlier: 4.133A  pdb=" N   PHE A 151 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 162
    Processing helix  chain 'A' and resid 166 through 170
      removed outlier: 3.676A  pdb=" N   LYS A 170 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 184
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 3.616A  pdb=" N   ASP A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 221
      removed outlier: 3.751A  pdb=" N   TYR A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 258
      removed outlier: 3.707A  pdb=" N   PHE A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 338
      removed outlier: 3.624A  pdb=" N   TYR A 330 " --> pdb=" O   ASN A 326 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A 336 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLN A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY A 338 " --> pdb=" O   LEU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 360
      removed outlier: 3.652A  pdb=" N   ALA A 343 " --> pdb=" O   LYS A 339 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ARG A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   GLN A 352 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASP A 359 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 373 through 380
      removed outlier: 3.741A  pdb=" N   LEU A 377 " --> pdb=" O   PRO A 373 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   HIS A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 408
    Processing helix  chain 'A' and resid 413 through 429
      removed outlier: 3.777A  pdb=" N   TYR A 424 " --> pdb=" O   ASP A 420 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 425 " --> pdb=" O   ILE A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 447
      removed outlier: 3.992A  pdb=" N   ASN A 439 " --> pdb=" O   PRO A 435 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ARG A 440 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 463
      removed outlier: 3.624A  pdb=" N   PHE A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA A 463 " --> pdb=" O   ARG A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 476
      removed outlier: 3.844A  pdb=" N   TYR A 471 " --> pdb=" O   ASP A 467 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   GLN A 476 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 497
    Processing helix  chain 'A' and resid 500 through 508
    Processing helix  chain 'A' and resid 516 through 527
      removed outlier: 3.691A  pdb=" N   LYS A 520 " --> pdb=" O   ASP A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 540
      removed outlier: 3.723A  pdb=" N   LYS A 537 " --> pdb=" O   GLY A 533 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS A 538 " --> pdb=" O   PHE A 534 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE A 539 " --> pdb=" O   LEU A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 558
      removed outlier: 3.592A  pdb=" N   HIS A 554 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 606
      removed outlier: 3.758A  pdb=" N   LEU A 586 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU A 588 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ALA A 591 " --> pdb=" O   TYR A 587 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   LEU A 595 " --> pdb=" O   ALA A 591 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 604 " --> pdb=" O   ALA A 600 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 606 " --> pdb=" O   TYR A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 644
    Processing helix  chain 'A' and resid 652 through 662
      removed outlier: 3.628A  pdb=" N   GLY A 656 " --> pdb=" O   ALA A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 706
      removed outlier: 3.970A  pdb=" N   PHE A 680 " --> pdb=" O   TYR A 676 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   ARG A 681 " --> pdb=" O   GLU A 677 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA A 682 " --> pdb=" O   LYS A 678 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LYS A 689 " --> pdb=" O   ASP A 685 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LYS A 706 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 725
    Processing helix  chain 'A' and resid 728 through 744
    Processing helix  chain 'A' and resid 750 through 764
      removed outlier: 4.374A  pdb=" N   PHE A 754 " --> pdb=" O   VAL A 750 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   GLY A 755 " --> pdb=" O   ILE A 751 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TYR A 764 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 291
      removed outlier: 3.831A  pdb=" N   VAL A 289 " --> pdb=" O   HIS A 267 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   HIS A 267 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   SER A 300 " --> pdb=" O   ARG A 266 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 314
      removed outlier: 4.226A  pdb=" N   LYS A 314 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY A 317 " --> pdb=" O   LYS A 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 618

    290 hydrogen bonds defined for protein.
    852 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      81 hydrogen bonds
      162 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      55 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 1.06 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.33: 1843
        1.33 -     1.45: 2318
        1.45 -     1.57: 4105
        1.57 -     1.69: 192
        1.69 -     1.81: 34
  Bond restraints: 8492
  Sorted by residual:
  bond pdb=" C   TRP A 770 "
       pdb=" N   LYS A 771 "
    ideal  model  delta    sigma   weight residual
    1.328  1.339 -0.011 1.30e-02 5.92e+03 6.93e-01
  bond pdb=" CA  GLN A  74 "
       pdb=" CB  GLN A  74 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 6.55e-01
  bond pdb=" N   LYS A 771 "
       pdb=" CA  LYS A 771 "
    ideal  model  delta    sigma   weight residual
    1.460  1.471 -0.011 1.42e-02 4.96e+03 6.01e-01
  bond pdb=" C   LEU A 649 "
       pdb=" N   ASP A 650 "
    ideal  model  delta    sigma   weight residual
    1.327  1.334 -0.007 9.40e-03 1.13e+04 5.85e-01
  bond pdb=" N   ASN A 238 "
       pdb=" CA  ASN A 238 "
    ideal  model  delta    sigma   weight residual
    1.463  1.456  0.008 1.08e-02 8.57e+03 5.11e-01
  ... (remaining 8487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 11509
        1.37 -     2.75: 308
        2.75 -     4.12: 56
        4.12 -     5.50: 11
        5.50 -     6.87: 1
  Bond angle restraints: 11885
  Sorted by residual:
  angle pdb=" C   THR A  73 "
        pdb=" N   GLN A  74 "
        pdb=" CA  GLN A  74 "
      ideal   model   delta    sigma   weight residual
     121.54  128.41   -6.87 1.91e+00 2.74e-01 1.29e+01
  angle pdb=" C   ALA A 463 "
        pdb=" N   GLU A 464 "
        pdb=" CA  GLU A 464 "
      ideal   model   delta    sigma   weight residual
     122.74  126.45   -3.71 1.44e+00 4.82e-01 6.65e+00
  angle pdb=" N   ASN A 583 "
        pdb=" CA  ASN A 583 "
        pdb=" C   ASN A 583 "
      ideal   model   delta    sigma   weight residual
     109.81  114.81   -5.00 2.21e+00 2.05e-01 5.11e+00
  angle pdb=" CA  ASN A 583 "
        pdb=" C   ASN A 583 "
        pdb=" N   PRO A 584 "
      ideal   model   delta    sigma   weight residual
     118.44  121.89   -3.45 1.59e+00 3.96e-01 4.72e+00
  angle pdb=" C   PRO A 773 "
        pdb=" N   VAL A 774 "
        pdb=" CA  VAL A 774 "
      ideal   model   delta    sigma   weight residual
     121.97  125.86   -3.89 1.80e+00 3.09e-01 4.66e+00
  ... (remaining 11880 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.54: 4738
       34.54 -    69.07: 133
       69.07 -   103.61: 5
      103.61 -   138.15: 0
      138.15 -   172.68: 1
  Dihedral angle restraints: 4877
    sinusoidal: 2727
      harmonic: 2150
  Sorted by residual:
  dihedral pdb=" CA  GLY A 644 "
           pdb=" C   GLY A 644 "
           pdb=" N   LYS A 645 "
           pdb=" CA  LYS A 645 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.23  -19.77     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" C4'   C B  -1 "
           pdb=" C3'   C B  -1 "
           pdb=" O3'   C B  -1 "
           pdb=" P     G B   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   32.68 -172.68     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  ARG A 349 "
           pdb=" C   ARG A 349 "
           pdb=" N   TYR A 350 "
           pdb=" CA  TYR A 350 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.97  -18.03     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 4874 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 979
       0.028 -    0.056: 264
       0.056 -    0.083: 66
       0.083 -    0.111: 34
       0.111 -    0.139: 11
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" C1'   A B -24 "
            pdb=" O4'   A B -24 "
            pdb=" C2'   A B -24 "
            pdb=" N9    A B -24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.32    0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  ILE A 213 "
            pdb=" N   ILE A 213 "
            pdb=" C   ILE A 213 "
            pdb=" CB  ILE A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  ILE A 636 "
            pdb=" N   ILE A 636 "
            pdb=" C   ILE A 636 "
            pdb=" CB  ILE A 636 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.93e-01
  ... (remaining 1351 not shown)

  Planarity restraints: 1162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 583 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO A 584 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 584 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 584 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   4 "    0.018 2.00e-02 2.50e+03   9.03e-03 2.44e+00
        pdb=" N9    G B   4 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8    G B   4 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    G B   4 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G B   4 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B   4 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G B   4 "    0.002 2.00e-02 2.50e+03
        pdb=" N1    G B   4 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G B   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G B   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G B   4 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B -24 "   -0.019 2.00e-02 2.50e+03   8.87e-03 2.16e+00
        pdb=" N9    A B -24 "    0.022 2.00e-02 2.50e+03
        pdb=" C8    A B -24 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A B -24 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A B -24 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A B -24 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A B -24 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A B -24 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A B -24 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A B -24 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    A B -24 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1159 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1653
        2.77 -     3.30: 7856
        3.30 -     3.83: 13459
        3.83 -     4.37: 15275
        4.37 -     4.90: 23661
  Nonbonded interactions: 61904
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 253 "
            pdb=" OG  SER A 335 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OE1 GLN A 257 "
            pdb=" OH  TYR A 602 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   GLU A 104 "
            pdb=" OG1 THR A 107 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   PHE A 147 "
            pdb=" OG  SER A 150 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OE1 GLU A 552 "
            pdb=" NE  ARG A 594 "
     model   vdw
     2.303 3.120
  ... (remaining 61899 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 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:                  0.010
  Normalize map: mean=0, sd=1:             1.830
  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:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.430
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
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      :  0.002   0.026   8492  Z= 0.129
  Angle     :  0.559   6.869  11885  Z= 0.323
  Chirality :  0.032   0.139   1354
  Planarity :  0.003   0.047   1162
  Dihedral  : 13.710 172.685   3497
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 10.34 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.31), residues: 729
  helix:  1.10 (0.25), residues: 419
  sheet: -0.24 (1.17), residues: 27
  loop : -1.24 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  51 
 TYR   0.013   0.001   TYR A 321 
 PHE   0.017   0.001   PHE A 638 
 TRP   0.010   0.001   TRP A 402 
 HIS   0.003   0.001   HIS A 554 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.13 ( 8492)
  covalent geometry    : angle       0.55921 /  0.32 (11885)
  hydrogen bonds       : bond        0.18413 / 11.87 (  371)
  hydrogen bonds       : angle       5.79611 /  4.24 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5421 (mtt-85)
REVERT: A  518 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7689 (mmmt)
REVERT: A  761 MET cc_start: 0.7806 (tpt) cc_final: 0.7345 (tpp)
REVERT: A  770 TRP cc_start: 0.5377 (OUTLIER) cc_final: 0.3557 (m-90)
  outliers start: 29
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1248
  time to fit residues: 17.9095
Evaluate side-chains
  73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 TYR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  266 ARG
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  770 TRP
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 397 HIS
A 476 GLN
A 561 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.160926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.124292 restraints weight = 15608.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.127422 restraints weight = 9171.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.128128 restraints weight = 5799.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.128376 restraints weight = 5444.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.128523 restraints weight = 5122.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8492  Z= 0.121
  Angle     :  0.529   5.957  11885  Z= 0.283
  Chirality :  0.034   0.158   1354
  Planarity :  0.003   0.043   1162
  Dihedral  : 12.523 163.057   2021
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 14.58 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.31), residues: 729
  helix:  1.54 (0.25), residues: 429
  sheet: -0.17 (1.18), residues: 27
  loop : -1.33 (0.33), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 459 
 TYR   0.013   0.001   TYR A 321 
 PHE   0.020   0.001   PHE A 638 
 TRP   0.010   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.12 ( 8492)
  covalent geometry    : angle       0.52883 /  0.28 (11885)
  hydrogen bonds       : bond        0.05094 /  3.39 (  371)
  hydrogen bonds       : angle       3.99560 /  2.90 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 PHE cc_start: 0.7877 (t80) cc_final: 0.7574 (t80)
REVERT: A  191 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.4942 (mtt-85)
REVERT: A  334 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7978 (tt)
REVERT: A  608 ARG cc_start: 0.5597 (tpt-90) cc_final: 0.5346 (ttt-90)
REVERT: A  657 ARG cc_start: 0.7943 (tpp80) cc_final: 0.7579 (tpp80)
REVERT: A  663 MET cc_start: 0.7013 (tpt) cc_final: 0.6717 (tpt)
REVERT: A  770 TRP cc_start: 0.5531 (OUTLIER) cc_final: 0.3557 (m-90)
  outliers start: 26
  outliers final: 18
  residues processed: 92
  average time/residue: 0.1040
  time to fit residues: 12.9213
Evaluate side-chains
  80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   61 TYR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  266 ARG
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  770 TRP
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   overall best weight:    2.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  52 HIS
** A 353 HIS ** 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 = 0.4236 r_free = 0.4236 target = 0.156016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.115172 restraints weight = 15257.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.118778 restraints weight = 8656.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.121035 restraints weight = 6216.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.122407 restraints weight = 5120.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.122977 restraints weight = 4567.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8492  Z= 0.209
  Angle     :  0.625   7.741  11885  Z= 0.329
  Chirality :  0.038   0.196   1354
  Planarity :  0.004   0.052   1162
  Dihedral  : 12.856 164.457   2015
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 15.67 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.30), residues: 729
  helix:  1.36 (0.25), residues: 419
  sheet: -0.50 (1.05), residues: 31
  loop : -1.65 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 351 
 TYR   0.019   0.002   TYR A 321 
 PHE   0.023   0.002   PHE A 638 
 TRP   0.012   0.002   TRP A  60 
 HIS   0.006   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.21 ( 8492)
  covalent geometry    : angle       0.62452 /  0.33 (11885)
  hydrogen bonds       : bond        0.06357 /  4.26 (  371)
  hydrogen bonds       : angle       4.27304 /  3.08 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 59
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.4651 (mtt-85)
REVERT: A  247 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7783 (mt)
REVERT: A  334 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8134 (tt)
REVERT: A  518 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6927 (mmmt)
REVERT: A  657 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7491 (tpp80)
REVERT: A  770 TRP cc_start: 0.5505 (OUTLIER) cc_final: 0.3389 (m-90)
  outliers start: 33
  outliers final: 22
  residues processed: 89
  average time/residue: 0.1039
  time to fit residues: 12.3539
Evaluate side-chains
  82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 55
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  266 ARG
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  770 TRP
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0980
   chunk 36 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    1.9986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 353 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.155998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.115313 restraints weight = 15752.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.118985 restraints weight = 8997.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.121280 restraints weight = 6472.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.122497 restraints weight = 5316.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.123449 restraints weight = 4770.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8492  Z= 0.172
  Angle     :  0.575   7.158  11885  Z= 0.306
  Chirality :  0.037   0.189   1354
  Planarity :  0.004   0.053   1162
  Dihedral  : 12.651 163.884   2011
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 18.03 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.30), residues: 729
  helix:  1.35 (0.25), residues: 419
  sheet: -0.56 (1.03), residues: 31
  loop : -1.76 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 681 
 TYR   0.017   0.002   TYR A 321 
 PHE   0.023   0.002   PHE A 638 
 TRP   0.013   0.002   TRP A  60 
 HIS   0.004   0.001   HIS A 554 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.17 ( 8492)
  covalent geometry    : angle       0.57484 /  0.31 (11885)
  hydrogen bonds       : bond        0.05612 /  3.75 (  371)
  hydrogen bonds       : angle       4.06075 /  2.92 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 58
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7067 (ttm170)
REVERT: A  191 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.4673 (mtt-85)
REVERT: A  247 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7786 (mt)
REVERT: A  334 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8034 (tt)
REVERT: A  518 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6978 (mmmt)
REVERT: A  698 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7683 (mm-30)
REVERT: A  745 HIS cc_start: 0.6650 (OUTLIER) cc_final: 0.6081 (t-90)
REVERT: A  770 TRP cc_start: 0.5622 (OUTLIER) cc_final: 0.3484 (m-90)
  outliers start: 36
  outliers final: 23
  residues processed: 92
  average time/residue: 0.0988
  time to fit residues: 12.3983
Evaluate side-chains
  85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 55
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  770 TRP
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    3.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 724 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.151914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.110334 restraints weight = 16213.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.113927 restraints weight = 9329.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.116151 restraints weight = 6752.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.117427 restraints weight = 5593.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.118376 restraints weight = 5015.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   8492  Z= 0.269
  Angle     :  0.692   8.069  11885  Z= 0.363
  Chirality :  0.041   0.215   1354
  Planarity :  0.005   0.054   1162
  Dihedral  : 13.061 166.062   2007
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  7.05 %
    Allowed  : 18.18 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.30), residues: 729
  helix:  0.95 (0.25), residues: 419
  sheet: -0.62 (1.04), residues: 31
  loop : -1.95 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 374 
 TYR   0.022   0.002   TYR A 321 
 PHE   0.025   0.002   PHE A 638 
 TRP   0.012   0.002   TRP A  60 
 HIS   0.007   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00582 /  0.27 ( 8492)
  covalent geometry    : angle       0.69182 /  0.36 (11885)
  hydrogen bonds       : bond        0.07022 /  4.70 (  371)
  hydrogen bonds       : angle       4.46357 /  3.20 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 53
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8000 (ttt-90)
REVERT: A  191 ARG cc_start: 0.6022 (OUTLIER) cc_final: 0.5209 (mtt-85)
REVERT: A  247 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7831 (mt)
REVERT: A  334 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8182 (tt)
REVERT: A  518 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6929 (mmmt)
REVERT: A  573 ILE cc_start: 0.6235 (OUTLIER) cc_final: 0.5964 (tt)
REVERT: A  745 HIS cc_start: 0.6684 (OUTLIER) cc_final: 0.6150 (t-90)
REVERT: A  770 TRP cc_start: 0.5600 (OUTLIER) cc_final: 0.3316 (m-90)
  outliers start: 45
  outliers final: 30
  residues processed: 94
  average time/residue: 0.1092
  time to fit residues: 13.6675
Evaluate side-chains
  91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 53
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   25 TRP
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  496 CYS
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  603 PHE
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  770 TRP
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 37 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 73 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.156563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.115990 restraints weight = 15437.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.119705 restraints weight = 8778.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.122017 restraints weight = 6282.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.123424 restraints weight = 5160.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.124180 restraints weight = 4589.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8492  Z= 0.143
  Angle     :  0.562   6.831  11885  Z= 0.299
  Chirality :  0.036   0.178   1354
  Planarity :  0.004   0.054   1162
  Dihedral  : 12.580 163.326   2006
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 19.44 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.30), residues: 729
  helix:  1.33 (0.25), residues: 419
  sheet: -0.53 (1.03), residues: 31
  loop : -1.84 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 681 
 TYR   0.014   0.001   TYR A 321 
 PHE   0.022   0.001   PHE A 638 
 TRP   0.013   0.001   TRP A 402 
 HIS   0.003   0.001   HIS A 353 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 ( 8492)
  covalent geometry    : angle       0.56193 /  0.30 (11885)
  hydrogen bonds       : bond        0.05158 /  3.43 (  371)
  hydrogen bonds       : angle       3.96961 /  2.85 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 56
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.6939 (ttm170)
REVERT: A  191 ARG cc_start: 0.6076 (OUTLIER) cc_final: 0.4839 (mtt-85)
REVERT: A  334 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7998 (tt)
REVERT: A  518 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6907 (mmmt)
REVERT: A  745 HIS cc_start: 0.6697 (OUTLIER) cc_final: 0.6067 (t-90)
REVERT: A  770 TRP cc_start: 0.5630 (OUTLIER) cc_final: 0.3425 (m-90)
  outliers start: 36
  outliers final: 24
  residues processed: 89
  average time/residue: 0.1021
  time to fit residues: 12.1948
Evaluate side-chains
  85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 55
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  603 PHE
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  770 TRP
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.157956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.117310 restraints weight = 15625.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.121067 restraints weight = 8837.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.123457 restraints weight = 6313.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.124908 restraints weight = 5161.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.125676 restraints weight = 4576.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8492  Z= 0.126
  Angle     :  0.540   7.399  11885  Z= 0.288
  Chirality :  0.035   0.184   1354
  Planarity :  0.003   0.052   1162
  Dihedral  : 12.345 162.312   2006
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 20.53 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.31), residues: 729
  helix:  1.53 (0.25), residues: 419
  sheet: -0.43 (1.04), residues: 31
  loop : -1.82 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 681 
 TYR   0.023   0.001   TYR A 175 
 PHE   0.021   0.001   PHE A 638 
 TRP   0.011   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.13 ( 8492)
  covalent geometry    : angle       0.54013 /  0.29 (11885)
  hydrogen bonds       : bond        0.04672 /  3.11 (  371)
  hydrogen bonds       : angle       3.77674 /  2.72 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.6857 (ttm170)
REVERT: A  110 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: A  191 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.5593 (mtt-85)
REVERT: A  247 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7691 (mt)
REVERT: A  334 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7991 (tt)
REVERT: A  518 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6942 (mmmt)
REVERT: A  740 ARG cc_start: 0.7858 (ptt90) cc_final: 0.7373 (mmp-170)
REVERT: A  745 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.6039 (t-90)
  outliers start: 33
  outliers final: 24
  residues processed: 91
  average time/residue: 0.1004
  time to fit residues: 12.4091
Evaluate side-chains
  89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  603 PHE
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  648 VAL
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  695 LEU
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.160166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.119635 restraints weight = 15765.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.123617 restraints weight = 8734.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.126020 restraints weight = 6153.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.127451 restraints weight = 4994.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.128188 restraints weight = 4422.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8492  Z= 0.110
  Angle     :  0.518   7.885  11885  Z= 0.276
  Chirality :  0.034   0.182   1354
  Planarity :  0.003   0.049   1162
  Dihedral  : 12.071 161.395   2004
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.32 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.31), residues: 729
  helix:  1.74 (0.25), residues: 422
  sheet: -0.35 (1.09), residues: 29
  loop : -1.75 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 681 
 TYR   0.011   0.001   TYR A 321 
 PHE   0.018   0.001   PHE A 638 
 TRP   0.011   0.001   TRP A  60 
 HIS   0.002   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00231 /  0.11 ( 8492)
  covalent geometry    : angle       0.51835 /  0.28 (11885)
  hydrogen bonds       : bond        0.04039 /  2.68 (  371)
  hydrogen bonds       : angle       3.60630 /  2.60 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 67
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.6797 (ttm170)
REVERT: A  110 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: A  191 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.4928 (mtt-85)
REVERT: A  247 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7591 (mt)
REVERT: A  334 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7918 (tt)
REVERT: A  740 ARG cc_start: 0.7836 (ptt90) cc_final: 0.7406 (mmp-170)
REVERT: A  743 PHE cc_start: 0.8686 (m-10) cc_final: 0.8149 (m-80)
REVERT: A  745 HIS cc_start: 0.6640 (OUTLIER) cc_final: 0.6052 (t-90)
  outliers start: 28
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1048
  time to fit residues: 13.0596
Evaluate side-chains
  82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  412 MET
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  603 PHE
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0470
   chunk 74 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.1682

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.159254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.118835 restraints weight = 15633.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.122492 restraints weight = 9003.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.124765 restraints weight = 6534.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.126127 restraints weight = 5395.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.126847 restraints weight = 4816.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8492  Z= 0.127
  Angle     :  0.550   9.782  11885  Z= 0.290
  Chirality :  0.035   0.208   1354
  Planarity :  0.003   0.048   1162
  Dihedral  : 12.003 161.586   2003
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 21.79 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.31), residues: 729
  helix:  1.75 (0.26), residues: 422
  sheet: -0.36 (1.10), residues: 29
  loop : -1.76 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 681 
 TYR   0.025   0.001   TYR A 175 
 PHE   0.027   0.001   PHE A 118 
 TRP   0.011   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 554 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 ( 8492)
  covalent geometry    : angle       0.55001 /  0.29 (11885)
  hydrogen bonds       : bond        0.04490 /  3.00 (  371)
  hydrogen bonds       : angle       3.65102 /  2.63 ( 1014)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7766 (ttt-90)
REVERT: A  110 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7937 (tm-30)
REVERT: A  191 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.5013 (mtt-85)
REVERT: A  247 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7710 (mt)
REVERT: A  334 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7956 (tt)
REVERT: A  458 LYS cc_start: 0.8720 (tppt) cc_final: 0.8507 (pttm)
REVERT: A  657 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7443 (tpp80)
REVERT: A  740 ARG cc_start: 0.7789 (ptt90) cc_final: 0.7437 (mmp-170)
REVERT: A  745 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.6042 (t-90)
  outliers start: 24
  outliers final: 17
  residues processed: 83
  average time/residue: 0.1082
  time to fit residues: 12.0307
Evaluate side-chains
  81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  412 MET
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  603 PHE
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 42 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 7 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0980
   chunk 60 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.162366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.122066 restraints weight = 15804.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.126032 restraints weight = 8722.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.128534 restraints weight = 6144.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.130051 restraints weight = 4970.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.130931 restraints weight = 4385.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8492  Z= 0.102
  Angle     :  0.522   9.392  11885  Z= 0.275
  Chirality :  0.033   0.188   1354
  Planarity :  0.003   0.043   1162
  Dihedral  : 11.785 160.806   2001
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.41 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.31), residues: 729
  helix:  1.85 (0.26), residues: 423
  sheet: -0.30 (1.06), residues: 29
  loop : -1.72 (0.33), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 681 
 TYR   0.016   0.001   TYR A 471 
 PHE   0.016   0.001   PHE A 638 
 TRP   0.012   0.001   TRP A  60 
 HIS   0.002   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.10 ( 8492)
  covalent geometry    : angle       0.52180 /  0.27 (11885)
  hydrogen bonds       : bond        0.03647 /  2.41 (  371)
  hydrogen bonds       : angle       3.48352 /  2.51 ( 1014)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1458 Ramachandran restraints generated.
    729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.6679 (ttm170)
REVERT: A  110 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: A  191 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.4829 (mtt-85)
REVERT: A  334 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7894 (tt)
REVERT: A  657 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7476 (tpp80)
REVERT: A  740 ARG cc_start: 0.7743 (ptt90) cc_final: 0.7395 (mmp-170)
REVERT: A  743 PHE cc_start: 0.8661 (m-10) cc_final: 0.8091 (m-80)
REVERT: A  745 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.6037 (t-90)
  outliers start: 21
  outliers final: 16
  residues processed: 82
  average time/residue: 0.1002
  time to fit residues: 11.1466
Evaluate side-chains
  79 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  194 LYS
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  603 PHE
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  659 CYS
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  771 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    3.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.154885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.113746 restraints weight = 15695.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.117377 restraints weight = 8984.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.119637 restraints weight = 6487.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.121017 restraints weight = 5341.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.121769 restraints weight = 4758.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8492  Z= 0.251
  Angle     :  0.676   8.412  11885  Z= 0.353
  Chirality :  0.040   0.233   1354
  Planarity :  0.004   0.048   1162
  Dihedral  : 12.336 163.828   2001
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.94 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.30), residues: 729
  helix:  1.32 (0.25), residues: 422
  sheet: -0.48 (1.11), residues: 29
  loop : -1.90 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 594 
 TYR   0.026   0.002   TYR A 175 
 PHE   0.027   0.002   PHE A 118 
 TRP   0.012   0.002   TRP A  60 
 HIS   0.005   0.001   HIS A 415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00547 /  0.25 ( 8492)
  covalent geometry    : angle       0.67631 /  0.35 (11885)
  hydrogen bonds       : bond        0.06309 /  4.23 (  371)
  hydrogen bonds       : angle       4.14077 /  2.97 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1694.81 seconds
wall clock time: 30 minutes 3.42 seconds (1803.42 seconds total)