Starting phenix.real_space_refine
on Fri Aug 22 22:33:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fti_29433/08_2025/8fti_29433.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fti_29433/08_2025/8fti_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2025/8fti_29433.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2025/8fti_29433.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2025/8fti_29433.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2025/8fti_29433.map"
  }
  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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.58, per 1000 atoms: 0.19
  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: 0.57
  Conformation dependent library (CDL) restraints added in 140.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 1.06
  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: 1.46

  Time building geometry restraints manager: 0.73 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: 4895
       34.54 -    69.07: 289
       69.07 -   103.61: 24
      103.61 -   138.15: 0
      138.15 -   172.68: 1
  Dihedral angle restraints: 5209
    sinusoidal: 3059
      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 5206 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:                  0.000
  Normalize map: mean=0, sd=1:             2.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
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  : 18.080 172.685   3829
  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 aren 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
  covalent geometry    : bond        0.00245 ( 8492)
  covalent geometry    : angle       0.55921 (11885)
  hydrogen bonds       : bond        0.18413 (  371)
  hydrogen bonds       : angle       5.79611 ( 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  : 0.264 
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: 0.0965
  time to fit residues: 13.9508
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  : 0.162 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.160824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.124171 restraints weight = 15553.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.127107 restraints weight = 9146.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.127860 restraints weight = 5859.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.128133 restraints weight = 5454.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.128361 restraints weight = 5148.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1412

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= 0.122
  Angle     :  0.534   5.900  11885  Z= 0.285
  Chirality :  0.034   0.154   1354
  Planarity :  0.003   0.044   1162
  Dihedral  : 19.275 163.218   2353
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 14.73 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.31), residues: 729
  helix:  1.48 (0.25), residues: 431
  sheet: -0.17 (1.18), residues: 27
  loop : -1.33 (0.33), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 459 
 TYR   0.012   0.001   TYR A 321 
 PHE   0.020   0.001   PHE A 638 
 TRP   0.009   0.001   TRP A 402 
 HIS   0.003   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8492)
  covalent geometry    : angle       0.53395 (11885)
  hydrogen bonds       : bond        0.05174 (  371)
  hydrogen bonds       : angle       4.03683 ( 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
  95 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 PHE cc_start: 0.7843 (t80) cc_final: 0.7533 (t80)
REVERT: A  191 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.4944 (mtt-85)
REVERT: A  334 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7965 (tt)
REVERT: A  608 ARG cc_start: 0.5613 (tpt-90) cc_final: 0.5364 (ttt-90)
REVERT: A  657 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7636 (tpp80)
REVERT: A  663 MET cc_start: 0.6962 (tpt) cc_final: 0.6665 (tpt)
REVERT: A  770 TRP cc_start: 0.5538 (OUTLIER) cc_final: 0.3569 (m-90)
  outliers start: 24
  outliers final: 17
  residues processed: 92
  average time/residue: 0.0845
  time to fit residues: 10.5183
Evaluate side-chains
  81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.2980
   chunk 4 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A  52 HIS
A 353 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.159679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.122948 restraints weight = 15487.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.125949 restraints weight = 9279.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.126878 restraints weight = 5923.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.126931 restraints weight = 5486.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.127116 restraints weight = 5160.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8492  Z= 0.127
  Angle     :  0.528   6.332  11885  Z= 0.280
  Chirality :  0.035   0.168   1354
  Planarity :  0.003   0.044   1162
  Dihedral  : 19.175 162.945   2347
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 15.99 %
    Favored  : 79.78 %
  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 aren not related in a simple way.
  whole:  0.65 (0.31), residues: 729
  helix:  1.68 (0.25), residues: 422
  sheet: -0.36 (1.11), residues: 29
  loop : -1.50 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 351 
 TYR   0.013   0.001   TYR A 321 
 PHE   0.021   0.001   PHE A 638 
 TRP   0.009   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8492)
  covalent geometry    : angle       0.52838 (11885)
  hydrogen bonds       : bond        0.04819 (  371)
  hydrogen bonds       : angle       3.83866 ( 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
  86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 59
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.4579 (mtt-85)
REVERT: A  334 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7946 (tt)
REVERT: A  518 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6900 (mmmt)
REVERT: A  657 ARG cc_start: 0.7871 (tpp80) cc_final: 0.7363 (tpp80)
REVERT: A  663 MET cc_start: 0.7279 (tpt) cc_final: 0.6961 (tpt)
REVERT: A  698 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7585 (mm-30)
REVERT: A  745 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.6075 (t-90)
REVERT: A  770 TRP cc_start: 0.5533 (OUTLIER) cc_final: 0.3549 (m-90)
  outliers start: 27
  outliers final: 15
  residues processed: 84
  average time/residue: 0.1094
  time to fit residues: 12.1748
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  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
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  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  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  648 VAL
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=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:    0.0670
   chunk 72 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.9722

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.160437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.120302 restraints weight = 15677.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.124213 restraints weight = 8728.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.126661 restraints weight = 6171.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.128107 restraints weight = 5026.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.128818 restraints weight = 4448.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8492  Z= 0.111
  Angle     :  0.497   6.360  11885  Z= 0.265
  Chirality :  0.034   0.168   1354
  Planarity :  0.003   0.041   1162
  Dihedral  : 18.951 162.409   2339
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 16.77 %
    Favored  : 78.06 %
  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 aren not related in a simple way.
  whole:  0.74 (0.31), residues: 729
  helix:  1.75 (0.25), residues: 424
  sheet: -0.33 (1.10), residues: 29
  loop : -1.48 (0.33), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 681 
 TYR   0.016   0.001   TYR A  61 
 PHE   0.020   0.001   PHE A 638 
 TRP   0.012   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 8492)
  covalent geometry    : angle       0.49723 (11885)
  hydrogen bonds       : bond        0.04335 (  371)
  hydrogen bonds       : angle       3.64084 ( 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
  96 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 63
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.6836 (ttm170)
REVERT: A  110 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7955 (tm-30)
REVERT: A  191 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.4611 (mtt-85)
REVERT: A  247 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7663 (mt)
REVERT: A  334 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7953 (tt)
REVERT: A  608 ARG cc_start: 0.5151 (tpt-90) cc_final: 0.4923 (tpt-90)
REVERT: A  657 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7394 (tpp80)
REVERT: A  663 MET cc_start: 0.7302 (tpt) cc_final: 0.6991 (tpt)
REVERT: A  745 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.6056 (t-90)
  outliers start: 33
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1165
  time to fit residues: 14.2709
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  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 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  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  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  640 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  771 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0060
   chunk 6 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    2.2002

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.156042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.115138 restraints weight = 15656.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.118790 restraints weight = 8914.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.121099 restraints weight = 6406.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.122390 restraints weight = 5260.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.123199 restraints weight = 4709.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8492  Z= 0.189
  Angle     :  0.595   7.211  11885  Z= 0.313
  Chirality :  0.038   0.288   1354
  Planarity :  0.004   0.045   1162
  Dihedral  : 19.083 163.617   2336
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 17.71 %
    Favored  : 76.96 %
  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 aren not related in a simple way.
  whole:  0.45 (0.31), residues: 729
  helix:  1.55 (0.25), residues: 422
  sheet: -0.47 (1.11), residues: 29
  loop : -1.65 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 191 
 TYR   0.021   0.002   TYR A 175 
 PHE   0.023   0.002   PHE A 638 
 TRP   0.009   0.002   TRP A  60 
 HIS   0.005   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8492)
  covalent geometry    : angle       0.59522 (11885)
  hydrogen bonds       : bond        0.05678 (  371)
  hydrogen bonds       : angle       3.98188 ( 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
  97 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 63
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: A  191 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5513 (mtt-85)
REVERT: A  247 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7787 (mt)
REVERT: A  334 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8061 (tt)
REVERT: A  518 LYS cc_start: 0.7438 (mmmt) cc_final: 0.7063 (tptp)
REVERT: A  608 ARG cc_start: 0.5509 (tpt-90) cc_final: 0.5176 (tpt-90)
REVERT: A  657 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7453 (tpp80)
REVERT: A  663 MET cc_start: 0.7389 (tpt) cc_final: 0.7168 (tpt)
REVERT: A  745 HIS cc_start: 0.6654 (OUTLIER) cc_final: 0.6037 (t-90)
REVERT: A  770 TRP cc_start: 0.5724 (OUTLIER) cc_final: 0.3616 (m-90)
  outliers start: 34
  outliers final: 25
  residues processed: 93
  average time/residue: 0.1134
  time to fit residues: 13.7626
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  : 0.287 
-------------------------------------------------------------------------------
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   73 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  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  412 MET
Chi-restraints excluded: chain A residue  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  573 ILE
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  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:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 25 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0010
   chunk 34 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.7592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.157114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.116223 restraints weight = 15494.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.119946 restraints weight = 8831.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.122277 restraints weight = 6341.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.123638 restraints weight = 5202.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.124220 restraints weight = 4634.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8492  Z= 0.158
  Angle     :  0.561   6.738  11885  Z= 0.298
  Chirality :  0.036   0.221   1354
  Planarity :  0.004   0.051   1162
  Dihedral  : 18.973 163.334   2336
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 18.81 %
    Favored  : 76.18 %
  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 aren not related in a simple way.
  whole:  0.40 (0.30), residues: 729
  helix:  1.54 (0.25), residues: 419
  sheet: -0.47 (1.05), residues: 31
  loop : -1.69 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  51 
 TYR   0.016   0.001   TYR A 321 
 PHE   0.023   0.002   PHE A 638 
 TRP   0.011   0.001   TRP A 402 
 HIS   0.004   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8492)
  covalent geometry    : angle       0.56124 (11885)
  hydrogen bonds       : bond        0.05183 (  371)
  hydrogen bonds       : angle       3.86811 ( 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
  91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 59
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7984 (tm-30)
REVERT: A  191 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.4978 (mtt-85)
REVERT: A  247 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7783 (mt)
REVERT: A  334 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8041 (tt)
REVERT: A  518 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7030 (tptp)
REVERT: A  657 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7421 (tpp80)
REVERT: A  745 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.6063 (t-90)
REVERT: A  770 TRP cc_start: 0.5723 (OUTLIER) cc_final: 0.3584 (m-90)
  outliers start: 32
  outliers final: 24
  residues processed: 88
  average time/residue: 0.1021
  time to fit residues: 11.9709
Evaluate side-chains
  86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
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   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  284 THR
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  573 ILE
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  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:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 35 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.157110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.116182 restraints weight = 15668.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.119914 restraints weight = 8917.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.122241 restraints weight = 6381.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.123498 restraints weight = 5235.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.124500 restraints weight = 4686.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8492  Z= 0.154
  Angle     :  0.559   6.635  11885  Z= 0.296
  Chirality :  0.036   0.197   1354
  Planarity :  0.004   0.047   1162
  Dihedral  : 18.954 163.216   2336
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 18.34 %
    Favored  : 76.18 %
  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 aren not related in a simple way.
  whole:  0.39 (0.31), residues: 729
  helix:  1.55 (0.25), residues: 419
  sheet: -0.48 (1.05), residues: 31
  loop : -1.72 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  51 
 TYR   0.023   0.001   TYR A 175 
 PHE   0.023   0.002   PHE A 638 
 TRP   0.010   0.001   TRP A 402 
 HIS   0.004   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8492)
  covalent geometry    : angle       0.55930 (11885)
  hydrogen bonds       : bond        0.05134 (  371)
  hydrogen bonds       : angle       3.84326 ( 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
  96 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 61
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7979 (tm-30)
REVERT: A  191 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.4862 (mtt-85)
REVERT: A  247 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7795 (mt)
REVERT: A  334 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7996 (tt)
REVERT: A  518 LYS cc_start: 0.7503 (mmmt) cc_final: 0.7089 (tptp)
REVERT: A  657 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7416 (tpp80)
REVERT: A  740 ARG cc_start: 0.7908 (ptt90) cc_final: 0.7432 (mmp-170)
REVERT: A  745 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6017 (t-90)
REVERT: A  770 TRP cc_start: 0.5719 (OUTLIER) cc_final: 0.3585 (m-90)
  outliers start: 35
  outliers final: 25
  residues processed: 93
  average time/residue: 0.0983
  time to fit residues: 12.3407
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   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  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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 30 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    1.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.157250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.116755 restraints weight = 15533.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.120467 restraints weight = 8871.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.122774 restraints weight = 6366.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.124246 restraints weight = 5218.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.124904 restraints weight = 4627.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8492  Z= 0.153
  Angle     :  0.557   6.672  11885  Z= 0.296
  Chirality :  0.036   0.205   1354
  Planarity :  0.004   0.048   1162
  Dihedral  : 18.951 163.179   2336
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 18.81 %
    Favored  : 76.02 %
  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 aren not related in a simple way.
  whole:  0.41 (0.31), residues: 729
  helix:  1.56 (0.25), residues: 419
  sheet: -0.50 (1.04), residues: 31
  loop : -1.70 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 681 
 TYR   0.015   0.001   TYR A 321 
 PHE   0.023   0.002   PHE A 638 
 TRP   0.010   0.001   TRP A 402 
 HIS   0.004   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 8492)
  covalent geometry    : angle       0.55725 (11885)
  hydrogen bonds       : bond        0.05104 (  371)
  hydrogen bonds       : angle       3.85261 ( 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
  91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 58
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7975 (tm-30)
REVERT: A  191 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.4824 (mtt-85)
REVERT: A  247 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7792 (mt)
REVERT: A  334 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7993 (tt)
REVERT: A  392 ASP cc_start: 0.7524 (p0) cc_final: 0.7271 (p0)
REVERT: A  608 ARG cc_start: 0.5085 (tpt-90) cc_final: 0.4760 (tpt-90)
REVERT: A  657 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7427 (tpp80)
REVERT: A  663 MET cc_start: 0.7254 (tpt) cc_final: 0.6987 (tpp)
REVERT: A  745 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.6046 (t-90)
REVERT: A  770 TRP cc_start: 0.5726 (OUTLIER) cc_final: 0.3592 (m-90)
  outliers start: 33
  outliers final: 25
  residues processed: 88
  average time/residue: 0.1023
  time to fit residues: 12.1043
Evaluate side-chains
  88 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 58
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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   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  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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.160738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.120466 restraints weight = 15635.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.124373 restraints weight = 8810.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.126830 restraints weight = 6269.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.128293 restraints weight = 5103.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.129054 restraints weight = 4522.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8492  Z= 0.105
  Angle     :  0.509   7.537  11885  Z= 0.269
  Chirality :  0.034   0.181   1354
  Planarity :  0.003   0.043   1162
  Dihedral  : 18.775 161.980   2336
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.59 %
    Favored  : 76.02 %
  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 aren not related in a simple way.
  whole:  0.69 (0.31), residues: 729
  helix:  1.80 (0.25), residues: 422
  sheet: -0.26 (1.09), residues: 29
  loop : -1.67 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 740 
 TYR   0.024   0.001   TYR A 175 
 PHE   0.018   0.001   PHE A 638 
 TRP   0.010   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 8492)
  covalent geometry    : angle       0.50900 (11885)
  hydrogen bonds       : bond        0.03899 (  371)
  hydrogen bonds       : angle       3.56497 ( 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
  93 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: A  191 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.4802 (mtt-85)
REVERT: A  247 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7592 (mt)
REVERT: A  334 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7943 (tt)
REVERT: A  608 ARG cc_start: 0.4944 (tpt-90) cc_final: 0.4673 (tpt-90)
REVERT: A  657 ARG cc_start: 0.7894 (tpp80) cc_final: 0.7457 (tpp80)
REVERT: A  740 ARG cc_start: 0.7841 (ptt90) cc_final: 0.7426 (mmp-170)
REVERT: A  743 PHE cc_start: 0.8658 (m-10) cc_final: 0.8257 (m-80)
REVERT: A  745 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.5977 (t-90)
  outliers start: 28
  outliers final: 19
  residues processed: 92
  average time/residue: 0.0960
  time to fit residues: 12.0432
Evaluate side-chains
  80 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
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   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  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
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  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:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.159789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.118906 restraints weight = 15869.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.122767 restraints weight = 8946.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.125219 restraints weight = 6360.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.126639 restraints weight = 5186.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.127553 restraints weight = 4604.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8492  Z= 0.118
  Angle     :  0.531   7.699  11885  Z= 0.281
  Chirality :  0.034   0.188   1354
  Planarity :  0.003   0.042   1162
  Dihedral  : 18.791 161.839   2336
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.22 %
    Favored  : 76.18 %
  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 aren not related in a simple way.
  whole:  0.67 (0.31), residues: 729
  helix:  1.80 (0.26), residues: 422
  sheet: -0.27 (1.09), residues: 29
  loop : -1.70 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 681 
 TYR   0.012   0.001   TYR A 321 
 PHE   0.021   0.001   PHE A 638 
 TRP   0.010   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8492)
  covalent geometry    : angle       0.53065 (11885)
  hydrogen bonds       : bond        0.04272 (  371)
  hydrogen bonds       : angle       3.57955 ( 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
  83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 60
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7938 (tm-30)
REVERT: A  191 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.4745 (mtt-85)
REVERT: A  247 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7701 (mt)
REVERT: A  334 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7961 (tt)
REVERT: A  608 ARG cc_start: 0.5013 (tpt-90) cc_final: 0.4694 (tpt-90)
REVERT: A  657 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7441 (tpp80)
REVERT: A  740 ARG cc_start: 0.7799 (ptt90) cc_final: 0.7436 (mmp-170)
  outliers start: 23
  outliers final: 18
  residues processed: 83
  average time/residue: 0.0998
  time to fit residues: 11.1567
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  : 0.270 
-------------------------------------------------------------------------------
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   73 THR
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  433 PHE
Chi-restraints excluded: chain A residue  445 LEU
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  659 CYS
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:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0070
   chunk 48 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0020
   chunk 24 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.8012

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

Flipped N/Q/H residues before XYZ refinement:
A  92 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.157149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.116395 restraints weight = 15964.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.119889 restraints weight = 9503.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.122094 restraints weight = 6975.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.123378 restraints weight = 5804.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.124162 restraints weight = 5213.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8492  Z= 0.163
  Angle     :  0.580   7.141  11885  Z= 0.306
  Chirality :  0.036   0.222   1354
  Planarity :  0.004   0.044   1162
  Dihedral  : 18.916 162.721   2334
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.38 %
    Favored  : 76.02 %
  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 aren not related in a simple way.
  whole:  0.44 (0.31), residues: 729
  helix:  1.61 (0.25), residues: 422
  sheet: -0.39 (1.11), residues: 29
  loop : -1.78 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 681 
 TYR   0.027   0.001   TYR A 175 
 PHE   0.024   0.002   PHE A 638 
 TRP   0.011   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8492)
  covalent geometry    : angle       0.57990 (11885)
  hydrogen bonds       : bond        0.05210 (  371)
  hydrogen bonds       : angle       3.81556 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1574.87 seconds
wall clock time: 27 minutes 50.52 seconds (1670.52 seconds total)