Starting phenix.real_space_refine
on Wed Mar 12 08:29:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dc2_27320/03_2025/8dc2_27320.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dc2_27320/03_2025/8dc2_27320.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dc2_27320/03_2025/8dc2_27320.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dc2_27320/03_2025/8dc2_27320.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dc2_27320/03_2025/8dc2_27320.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dc2_27320/03_2025/8dc2_27320.cif"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.179 sd=   1.060
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 132 atoms to isotropic.
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      86      5.49       5
     S      32      5.16       5
     C    4326      2.51       5
     N    1221      2.21       5
     O    1631      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7296
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5483
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 673, 5483
          Classifications: {'peptide': 673}
          Link IDs: {'PTRANS': 10, 'TRANS': 662}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 1069
          Classifications: {'RNA': 51}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 25}
          Link IDs: {'rna2p': 8, 'rna3p': 42}
    Chain: "C"
      Number of atoms: 542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 542
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "D"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 202
          Classifications: {'DNA': 10}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 9}
  Time building chain proxies: 4.92, per 1000 atoms: 0.67
  Number of scatterers: 7296
  At special positions: 0
  Unit cell: (80.28, 92.545, 110.385, 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      32     16.00
     P      86     15.00
     O    1631      8.00
     N    1221      7.00
     C    4326      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.11
  Conformation dependent library (CDL) restraints added in 634.9 milliseconds
  

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1286

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 3 sheets defined
      57.1% alpha, 10.5% beta
      33 base pairs and 58 stacking pairs defined.
    Time for finding SS restraints: 2.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 52
    Processing helix  chain 'A' and resid 56 through 64
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 71 through 79
      removed outlier: 3.607A  pdb=" N   THR A  76 " --> pdb=" O   GLY A  72 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE A  78 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 96 through 112
    Processing helix  chain 'A' and resid 124 through 131
    Processing helix  chain 'A' and resid 132 through 146
    Processing helix  chain 'A' and resid 162 through 177
      removed outlier: 4.302A  pdb=" N   ASN A 177 " --> pdb=" O   GLU A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 195
    Processing helix  chain 'A' and resid 199 through 215
      removed outlier: 4.049A  pdb=" N   ARG A 205 " --> pdb=" O   ASN A 201 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER A 215 " --> pdb=" O   GLU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 234
      removed outlier: 3.944A  pdb=" N   LYS A 234 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 298
    Processing helix  chain 'A' and resid 359 through 365
    Processing helix  chain 'A' and resid 367 through 372
      removed outlier: 3.707A  pdb=" N   LYS A 372 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 386
    Processing helix  chain 'A' and resid 395 through 408
    Processing helix  chain 'A' and resid 413 through 435
      removed outlier: 3.530A  pdb=" N   LYS A 418 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 472
      removed outlier: 3.882A  pdb=" N   ARG A 440 " --> pdb=" O   ASP A 436 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS A 454 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 482
    Processing helix  chain 'A' and resid 483 through 486
    Processing helix  chain 'A' and resid 487 through 523
      removed outlier: 3.501A  pdb=" N   GLY A 523 " --> pdb=" O   PHE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 611
      removed outlier: 3.639A  pdb=" N   ILE A 611 " --> pdb=" O   MET A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 627
      removed outlier: 4.280A  pdb=" N   ASN A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 669
      removed outlier: 3.786A  pdb=" N   VAL A 668 " --> pdb=" O   LYS A 665 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ARG A 669 " --> pdb=" O   HIS A 666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 665 through 669'
    Processing helix  chain 'A' and resid 680 through 695
      removed outlier: 3.842A  pdb=" N   MET A 693 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 702
    Processing helix  chain 'A' and resid 724 through 735
      removed outlier: 3.567A  pdb=" N   LYS A 733 " --> pdb=" O   VAL A 729 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LYS A 734 " --> pdb=" O   ALA A 730 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   GLU A 735 " --> pdb=" O   LYS A 731 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 250
      removed outlier: 5.878A  pdb=" N   ASN A 317 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   SER A 302 " --> pdb=" O   ASP A 315 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ASP A 315 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   VAL A 304 " --> pdb=" O   TYR A 313 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   TYR A 313 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LYS A 306 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   GLU A 311 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ILE A 312 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 287
    Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 391
      removed outlier: 5.267A  pdb=" N   ILE A 348 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 8.188A  pdb=" N   PHE A 391 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   THR A 346 " --> pdb=" O   PHE A 391 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   GLY A 334 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
      removed outlier: 9.447A  pdb=" N   LEU A 349 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
      removed outlier: 13.098A  pdb=" N   VAL A 332 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL A 333 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
      removed outlier: 8.562A  pdb=" N   GLU A 530 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 9.108A  pdb=" N   ILE A 335 " --> pdb=" O   GLU A 530 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL A 527 " --> pdb=" O   SER A 632 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   VAL A 634 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU A 529 " --> pdb=" O   VAL A 634 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   TYR A 718 " --> pdb=" O   VAL A 631 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 720 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)

    293 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      83 hydrogen bonds
      166 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      58 stacking parallelities
  Total time for adding SS restraints: 3.27

  Time building geometry restraints manager: 2.46 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: 1697
        1.33 -     1.45: 2004
        1.45 -     1.57: 3690
        1.57 -     1.69: 170
        1.69 -     1.81: 56
  Bond restraints: 7617
  Sorted by residual:
  bond pdb=" CB  GLU A 417 "
       pdb=" CG  GLU A 417 "
    ideal  model  delta    sigma   weight residual
    1.520  1.478  0.042 3.00e-02 1.11e+03 1.99e+00
  bond pdb=" C3'  DG D  -8 "
       pdb=" O3'  DG D  -8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.87e+00
  bond pdb=" N   SER A 158 "
       pdb=" CA  SER A 158 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.71e+00
  bond pdb=" CG  GLU A 417 "
       pdb=" CD  GLU A 417 "
    ideal  model  delta    sigma   weight residual
    1.516  1.484  0.032 2.50e-02 1.60e+03 1.66e+00
  bond pdb=" CA  SER A 158 "
       pdb=" CB  SER A 158 "
    ideal  model  delta    sigma   weight residual
    1.530  1.510  0.020 1.69e-02 3.50e+03 1.36e+00
  ... (remaining 7612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 10198
        1.18 -     2.36: 375
        2.36 -     3.54: 63
        3.54 -     4.72: 16
        4.72 -     5.90: 5
  Bond angle restraints: 10657
  Sorted by residual:
  angle pdb=" C3'  DG D  -8 "
        pdb=" O3'  DG D  -8 "
        pdb=" P    DA D  -7 "
      ideal   model   delta    sigma   weight residual
     120.20  123.90   -3.70 1.50e+00 4.44e-01 6.09e+00
  angle pdb=" O3'   U B -12 "
        pdb=" C3'   U B -12 "
        pdb=" C2'   U B -12 "
      ideal   model   delta    sigma   weight residual
     113.70  117.04   -3.34 1.50e+00 4.44e-01 4.96e+00
  angle pdb=" C3'   U B -12 "
        pdb=" O3'   U B -12 "
        pdb=" P     G B -11 "
      ideal   model   delta    sigma   weight residual
     120.20  123.48   -3.28 1.50e+00 4.44e-01 4.77e+00
  angle pdb=" C   SER A 158 "
        pdb=" CA  SER A 158 "
        pdb=" CB  SER A 158 "
      ideal   model   delta    sigma   weight residual
     110.42  114.73   -4.31 1.99e+00 2.53e-01 4.69e+00
  angle pdb=" C   ASN A 338 "
        pdb=" CA  ASN A 338 "
        pdb=" CB  ASN A 338 "
      ideal   model   delta    sigma   weight residual
     109.70  113.52   -3.82 1.81e+00 3.05e-01 4.45e+00
  ... (remaining 10652 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.63: 4223
       34.63 -    69.26: 289
       69.26 -   103.89: 19
      103.89 -   138.52: 1
      138.52 -   173.15: 3
  Dihedral angle restraints: 4535
    sinusoidal: 2538
      harmonic: 1997
  Sorted by residual:
  dihedral pdb=" O4'   U B   1 "
           pdb=" C1'   U B   1 "
           pdb=" N1    U B   1 "
           pdb=" C2    U B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   58.85  173.15     1      1.70e+01 3.46e-03 6.62e+01
  dihedral pdb=" CA  MET A 607 "
           pdb=" C   MET A 607 "
           pdb=" N   ILE A 608 "
           pdb=" CA  ILE A 608 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.51   21.49     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  ILE A 157 "
           pdb=" C   ILE A 157 "
           pdb=" N   SER A 158 "
           pdb=" CA  SER A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.88   21.12     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 4532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 856
       0.034 -    0.069: 268
       0.069 -    0.103: 65
       0.103 -    0.138: 24
       0.138 -    0.172: 1
  Chirality restraints: 1214
  Sorted by residual:
  chirality pdb=" C3'   U B -12 "
            pdb=" C4'   U B -12 "
            pdb=" O3'   U B -12 "
            pdb=" C2'   U B -12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.17 2.00e-01 2.50e+01 7.39e-01
  chirality pdb=" CB  THR A 165 "
            pdb=" CA  THR A 165 "
            pdb=" OG1 THR A 165 "
            pdb=" CG2 THR A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.29e-01
  chirality pdb=" CA  ILE A  64 "
            pdb=" N   ILE A  64 "
            pdb=" C   ILE A  64 "
            pdb=" CB  ILE A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 1211 not shown)

  Planarity restraints: 1042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG C -15 "    0.014 2.00e-02 2.50e+03   9.92e-03 2.95e+00
        pdb=" N9   DG C -15 "   -0.011 2.00e-02 2.50e+03
        pdb=" C8   DG C -15 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG C -15 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DG C -15 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG C -15 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6   DG C -15 "    0.010 2.00e-02 2.50e+03
        pdb=" N1   DG C -15 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DG C -15 "   -0.024 2.00e-02 2.50e+03
        pdb=" N2   DG C -15 "    0.013 2.00e-02 2.50e+03
        pdb=" N3   DG C -15 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DG C -15 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 126 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   THR A 126 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   THR A 126 "    0.010 2.00e-02 2.50e+03
        pdb=" N   TYR A 127 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  -3 "   -0.019 2.00e-02 2.50e+03   1.07e-02 2.57e+00
        pdb=" N1    C B  -3 "    0.025 2.00e-02 2.50e+03
        pdb=" C2    C B  -3 "    0.003 2.00e-02 2.50e+03
        pdb=" O2    C B  -3 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    C B  -3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    C B  -3 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C B  -3 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    C B  -3 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    C B  -3 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1039 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 979
        2.75 -     3.29: 7349
        3.29 -     3.83: 13416
        3.83 -     4.36: 15837
        4.36 -     4.90: 24413
  Nonbonded interactions: 61994
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  42 "
            pdb=" OD1 ASN A 140 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" NZ  LYS A 155 "
            pdb=" O   SER A 158 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" NE2 HIS A 612 "
            pdb=" OP1  DT C  -8 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" O   LEU A 121 "
            pdb=" ND2 ASN A 274 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O2'   U B -19 "
            pdb=" OP1   U B -16 "
     model   vdw
     2.301 3.040
  ... (remaining 61989 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.670
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:16.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
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      :  0.003   0.042   7617  Z= 0.181
  Angle     :  0.544   5.898  10657  Z= 0.305
  Chirality :  0.037   0.172   1214
  Planarity :  0.003   0.029   1042
  Dihedral  : 19.786 173.155   3249
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.16 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.33), residues: 667
  helix:  1.96 (0.30), residues: 327
  sheet:  0.43 (0.60), residues: 71
  loop : -0.60 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A   4 
 PHE   0.017   0.001   PHE A 400 
 TYR   0.017   0.001   TYR A 133 
 ARG   0.003   0.000   ARG A 440 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A  174 MET cc_start: 0.6426 (mmp) cc_final: 0.6130 (mmt)
REVERT: A  230 ASP cc_start: 0.7729 (t0) cc_final: 0.7519 (t0)
REVERT: A  288 ASP cc_start: 0.7563 (t70) cc_final: 0.7332 (t70)
REVERT: A  488 ASP cc_start: 0.8276 (p0) cc_final: 0.7965 (p0)
REVERT: A  695 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7545 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.9598
  time to fit residues: 137.5659
Evaluate side-chains
  104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  695 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN
A 140 ASN
A 176 HIS
A 265 ASN
A 413 ASN
A 605 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.087991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.074998 restraints weight = 15624.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.87
r_work: 0.2994 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7617  Z= 0.389
  Angle     :  0.654   6.759  10657  Z= 0.359
  Chirality :  0.043   0.238   1214
  Planarity :  0.004   0.033   1042
  Dihedral  : 21.951 171.263   1889
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.24 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.33), residues: 667
  helix:  1.60 (0.28), residues: 336
  sheet:  0.21 (0.60), residues: 69
  loop : -0.55 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A 185 
 HIS   0.006   0.002   HIS A 176 
 PHE   0.015   0.002   PHE A 651 
 TYR   0.022   0.002   TYR A 133 
 ARG   0.004   0.001   ARG A 240 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8657 (tp30) cc_final: 0.8354 (tp30)
REVERT: A  230 ASP cc_start: 0.8507 (t0) cc_final: 0.8077 (t0)
REVERT: A  233 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8107 (pp)
REVERT: A  288 ASP cc_start: 0.8611 (t70) cc_final: 0.8385 (t70)
REVERT: A  363 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7905 (mt-10)
REVERT: A  488 ASP cc_start: 0.8567 (p0) cc_final: 0.7957 (p0)
REVERT: A  704 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.5458 (ttmt)
  outliers start: 13
  outliers final: 4
  residues processed: 111
  average time/residue: 0.9939
  time to fit residues: 117.9139
Evaluate side-chains
  105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  704 LYS
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    0.0670
   chunk 27 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.7122

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

Flipped N/Q/H residues before XYZ refinement:
A 265 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.091978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.078850 restraints weight = 15728.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.90
r_work: 0.3066 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7617  Z= 0.176
  Angle     :  0.541   5.716  10657  Z= 0.302
  Chirality :  0.037   0.187   1214
  Planarity :  0.003   0.029   1042
  Dihedral  : 21.720 172.925   1887
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.20 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.33), residues: 667
  helix:  1.64 (0.28), residues: 347
  sheet:  0.19 (0.57), residues: 69
  loop : -0.40 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 185 
 HIS   0.002   0.001   HIS A 216 
 PHE   0.013   0.001   PHE A 613 
 TYR   0.017   0.001   TYR A 172 
 ARG   0.002   0.000   ARG A 440 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8536 (tp30) cc_final: 0.8128 (tp30)
REVERT: A  148 MET cc_start: 0.7913 (tpt) cc_final: 0.7472 (tpp)
REVERT: A  206 MET cc_start: 0.8113 (mmm) cc_final: 0.7554 (mmt)
REVERT: A  230 ASP cc_start: 0.8493 (t0) cc_final: 0.8071 (t0)
REVERT: A  233 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.7963 (pp)
REVERT: A  288 ASP cc_start: 0.8563 (t70) cc_final: 0.8308 (t70)
REVERT: A  363 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7940 (mm-30)
REVERT: A  488 ASP cc_start: 0.8511 (p0) cc_final: 0.7973 (p0)
REVERT: A  642 MET cc_start: 0.8342 (ttp) cc_final: 0.8002 (tpp)
REVERT: A  695 ASN cc_start: 0.8006 (t0) cc_final: 0.7338 (t0)
  outliers start: 16
  outliers final: 4
  residues processed: 121
  average time/residue: 0.9005
  time to fit residues: 117.1295
Evaluate side-chains
  107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0670
   chunk 60 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 452 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.091732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.078611 restraints weight = 15689.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.89
r_work: 0.3063 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7617  Z= 0.193
  Angle     :  0.535   5.745  10657  Z= 0.299
  Chirality :  0.038   0.191   1214
  Planarity :  0.003   0.027   1042
  Dihedral  : 21.710 173.531   1887
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.46 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.33), residues: 667
  helix:  1.80 (0.28), residues: 342
  sheet:  0.16 (0.58), residues: 69
  loop : -0.43 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 185 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.018   0.002   PHE A 396 
 TYR   0.024   0.002   TYR A 172 
 ARG   0.002   0.000   ARG A 699 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8563 (tp30) cc_final: 0.8126 (tp30)
REVERT: A  175 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: A  206 MET cc_start: 0.8133 (mmm) cc_final: 0.7570 (mmt)
REVERT: A  230 ASP cc_start: 0.8464 (t0) cc_final: 0.8065 (t0)
REVERT: A  233 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.7982 (pp)
REVERT: A  288 ASP cc_start: 0.8568 (t70) cc_final: 0.8304 (t70)
REVERT: A  488 ASP cc_start: 0.8503 (p0) cc_final: 0.7979 (p0)
REVERT: A  642 MET cc_start: 0.8413 (ttp) cc_final: 0.8011 (tpp)
REVERT: A  695 ASN cc_start: 0.8135 (t0) cc_final: 0.7459 (t0)
  outliers start: 17
  outliers final: 4
  residues processed: 120
  average time/residue: 0.9897
  time to fit residues: 126.8969
Evaluate side-chains
  109 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 65 optimal weight:    0.0570
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.3704

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.090079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.077078 restraints weight = 15760.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.89
r_work: 0.3036 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7617  Z= 0.248
  Angle     :  0.562   5.289  10657  Z= 0.313
  Chirality :  0.039   0.204   1214
  Planarity :  0.003   0.028   1042
  Dihedral  : 21.752 172.539   1887
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.59 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.33), residues: 667
  helix:  1.65 (0.29), residues: 350
  sheet:  0.02 (0.58), residues: 69
  loop : -0.39 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 185 
 HIS   0.004   0.001   HIS A 341 
 PHE   0.018   0.002   PHE A 400 
 TYR   0.021   0.002   TYR A 133 
 ARG   0.002   0.000   ARG A 240 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8621 (tp30) cc_final: 0.8143 (tp30)
REVERT: A  175 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8208 (tm-30)
REVERT: A  206 MET cc_start: 0.8149 (mmm) cc_final: 0.7864 (mmt)
REVERT: A  230 ASP cc_start: 0.8470 (t0) cc_final: 0.8070 (t0)
REVERT: A  233 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8073 (pp)
REVERT: A  288 ASP cc_start: 0.8619 (t70) cc_final: 0.8352 (t70)
REVERT: A  488 ASP cc_start: 0.8496 (p0) cc_final: 0.7953 (p0)
REVERT: A  695 ASN cc_start: 0.8175 (t0) cc_final: 0.7501 (t0)
  outliers start: 16
  outliers final: 6
  residues processed: 110
  average time/residue: 1.0211
  time to fit residues: 120.1453
Evaluate side-chains
  106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 169 GLN
A 347 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.089643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.076470 restraints weight = 15741.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.90
r_work: 0.3023 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7617  Z= 0.279
  Angle     :  0.590   6.924  10657  Z= 0.325
  Chirality :  0.040   0.209   1214
  Planarity :  0.003   0.029   1042
  Dihedral  : 21.786 171.683   1887
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.71 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.33), residues: 667
  helix:  1.46 (0.28), residues: 351
  sheet: -0.01 (0.61), residues: 69
  loop : -0.43 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.004   TRP A 185 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.019   0.002   PHE A 604 
 TYR   0.021   0.002   TYR A 133 
 ARG   0.002   0.000   ARG A 699 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8628 (tp30) cc_final: 0.8151 (tp30)
REVERT: A  206 MET cc_start: 0.8107 (mmm) cc_final: 0.7775 (mmt)
REVERT: A  230 ASP cc_start: 0.8509 (t0) cc_final: 0.8103 (t0)
REVERT: A  233 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8053 (pp)
REVERT: A  288 ASP cc_start: 0.8633 (t70) cc_final: 0.8370 (t70)
REVERT: A  488 ASP cc_start: 0.8490 (p0) cc_final: 0.7934 (p0)
REVERT: A  642 MET cc_start: 0.8463 (ttp) cc_final: 0.8077 (tpp)
REVERT: A  695 ASN cc_start: 0.8018 (t0) cc_final: 0.7347 (t0)
  outliers start: 17
  outliers final: 8
  residues processed: 115
  average time/residue: 0.9596
  time to fit residues: 118.1850
Evaluate side-chains
  104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.087953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.074968 restraints weight = 15843.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.89
r_work: 0.2994 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   7617  Z= 0.356
  Angle     :  0.653   8.584  10657  Z= 0.357
  Chirality :  0.043   0.235   1214
  Planarity :  0.004   0.030   1042
  Dihedral  : 21.926 169.440   1887
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.68 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.33), residues: 667
  helix:  1.32 (0.28), residues: 350
  sheet: -0.18 (0.60), residues: 67
  loop : -0.55 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 185 
 HIS   0.005   0.001   HIS A 341 
 PHE   0.019   0.002   PHE A 400 
 TYR   0.022   0.002   TYR A 133 
 ARG   0.004   0.001   ARG A 240 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8658 (tp30) cc_final: 0.8142 (tp30)
REVERT: A  175 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8157 (tm-30)
REVERT: A  206 MET cc_start: 0.8129 (mmm) cc_final: 0.7736 (mmt)
REVERT: A  230 ASP cc_start: 0.8535 (t0) cc_final: 0.8213 (t0)
REVERT: A  288 ASP cc_start: 0.8681 (t70) cc_final: 0.8402 (t70)
REVERT: A  488 ASP cc_start: 0.8517 (p0) cc_final: 0.7994 (p0)
REVERT: A  695 ASN cc_start: 0.8082 (t0) cc_final: 0.7409 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 104
  average time/residue: 0.9977
  time to fit residues: 111.2383
Evaluate side-chains
  104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  416 MET
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.088486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.075420 restraints weight = 15904.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.90
r_work: 0.3001 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7617  Z= 0.321
  Angle     :  0.652  10.975  10657  Z= 0.352
  Chirality :  0.042   0.226   1214
  Planarity :  0.004   0.030   1042
  Dihedral  : 21.906 169.644   1887
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.65 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.33), residues: 667
  helix:  1.31 (0.28), residues: 349
  sheet: -0.11 (0.61), residues: 69
  loop : -0.53 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 185 
 HIS   0.003   0.001   HIS A   4 
 PHE   0.020   0.002   PHE A 604 
 TYR   0.022   0.002   TYR A 133 
 ARG   0.003   0.000   ARG A 240 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8664 (tp30) cc_final: 0.8143 (tp30)
REVERT: A  175 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7978 (tm-30)
REVERT: A  206 MET cc_start: 0.8146 (mmm) cc_final: 0.7750 (mmt)
REVERT: A  223 LYS cc_start: 0.8257 (ttmm) cc_final: 0.8032 (ttpt)
REVERT: A  230 ASP cc_start: 0.8501 (t0) cc_final: 0.8190 (t0)
REVERT: A  288 ASP cc_start: 0.8675 (t70) cc_final: 0.8393 (t70)
REVERT: A  444 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8145 (mp0)
REVERT: A  465 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8540 (ttpp)
REVERT: A  488 ASP cc_start: 0.8519 (p0) cc_final: 0.8003 (p0)
REVERT: A  695 ASN cc_start: 0.8051 (t0) cc_final: 0.7389 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 105
  average time/residue: 1.0314
  time to fit residues: 116.0422
Evaluate side-chains
  107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ILE
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  416 MET
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 65 optimal weight:    0.3980
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.092473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.079399 restraints weight = 15931.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.91
r_work: 0.3080 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   7617  Z= 0.180
  Angle     :  0.602  14.269  10657  Z= 0.323
  Chirality :  0.039   0.185   1214
  Planarity :  0.003   0.028   1042
  Dihedral  : 21.719 172.824   1887
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.61 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.34), residues: 667
  helix:  1.49 (0.29), residues: 349
  sheet: -0.16 (0.58), residues: 69
  loop : -0.44 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 185 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.011   0.001   PHE A 400 
 TYR   0.015   0.001   TYR A 172 
 ARG   0.002   0.000   ARG A 130 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8563 (tp30) cc_final: 0.8060 (tp30)
REVERT: A  175 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: A  206 MET cc_start: 0.8180 (mmm) cc_final: 0.7614 (mmt)
REVERT: A  230 ASP cc_start: 0.8439 (t0) cc_final: 0.7981 (t0)
REVERT: A  234 LYS cc_start: 0.8668 (mppt) cc_final: 0.8453 (mppt)
REVERT: A  288 ASP cc_start: 0.8633 (t70) cc_final: 0.8361 (t70)
REVERT: A  465 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8534 (mtpp)
REVERT: A  488 ASP cc_start: 0.8430 (p0) cc_final: 0.7885 (p0)
REVERT: A  499 ASN cc_start: 0.8494 (t0) cc_final: 0.8099 (t0)
REVERT: A  693 MET cc_start: 0.8878 (mmm) cc_final: 0.8623 (mmm)
REVERT: A  695 ASN cc_start: 0.7979 (t0) cc_final: 0.7347 (t0)
  outliers start: 16
  outliers final: 7
  residues processed: 117
  average time/residue: 0.9485
  time to fit residues: 119.0970
Evaluate side-chains
  111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 32 optimal weight:    0.2980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.092793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.079651 restraints weight = 16005.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.92
r_work: 0.3084 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   7617  Z= 0.189
  Angle     :  0.617  14.353  10657  Z= 0.328
  Chirality :  0.039   0.241   1214
  Planarity :  0.003   0.027   1042
  Dihedral  : 21.702 173.792   1887
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.58 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.33), residues: 667
  helix:  1.51 (0.29), residues: 344
  sheet: -0.06 (0.59), residues: 67
  loop : -0.42 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 185 
 HIS   0.002   0.001   HIS A 612 
 PHE   0.014   0.001   PHE A 400 
 TYR   0.017   0.001   TYR A 133 
 ARG   0.001   0.000   ARG A 450 

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8550 (tp30) cc_final: 0.8062 (tp30)
REVERT: A  175 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: A  206 MET cc_start: 0.8185 (mmm) cc_final: 0.7590 (mmt)
REVERT: A  250 MET cc_start: 0.8791 (tmm) cc_final: 0.8539 (tpp)
REVERT: A  288 ASP cc_start: 0.8605 (t70) cc_final: 0.8336 (t70)
REVERT: A  465 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8558 (mtpp)
REVERT: A  488 ASP cc_start: 0.8407 (p0) cc_final: 0.7860 (p0)
REVERT: A  499 ASN cc_start: 0.8516 (t0) cc_final: 0.8121 (t0)
REVERT: A  530 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8252 (mt-10)
REVERT: A  695 ASN cc_start: 0.7902 (t0) cc_final: 0.7328 (t0)
REVERT: A  734 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8559 (mtpt)
  outliers start: 10
  outliers final: 8
  residues processed: 116
  average time/residue: 0.9996
  time to fit residues: 124.2091
Evaluate side-chains
  118 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  468 SER
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.091721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.078517 restraints weight = 15772.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.90
r_work: 0.3062 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7617  Z= 0.231
  Angle     :  0.633  13.964  10657  Z= 0.340
  Chirality :  0.040   0.194   1214
  Planarity :  0.003   0.027   1042
  Dihedral  : 21.730 173.237   1887
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.03 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.33), residues: 667
  helix:  1.51 (0.29), residues: 341
  sheet: -0.10 (0.59), residues: 69
  loop : -0.48 (0.41), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 185 
 HIS   0.004   0.001   HIS A 216 
 PHE   0.017   0.002   PHE A 604 
 TYR   0.019   0.002   TYR A 133 
 ARG   0.001   0.000   ARG A 440 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4607.94 seconds
wall clock time: 79 minutes 45.35 seconds (4785.35 seconds total)