Starting phenix.real_space_refine
on Tue Feb  3 15:14:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kkj_62389/02_2026/9kkj_62389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kkj_62389/02_2026/9kkj_62389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kkj_62389/02_2026/9kkj_62389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kkj_62389/02_2026/9kkj_62389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kkj_62389/02_2026/9kkj_62389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kkj_62389/02_2026/9kkj_62389.cif"
  }
  resolution = 3.26
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2608      2.51       5
     N     694      2.21       5
     O     812      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4126
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "L"
      Number of atoms: 1688
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 218, 1686
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
      Conformer: "B"
        Number of residues, atoms: 218, 1686
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
          bond proxies already assigned to first conformer: 1721
    Chain: "H"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1603
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 99}
          Chain breaks: 1
  Time building chain proxies: 1.25, per 1000 atoms: 0.30
  Number of scatterers: 4126
  At special positions: 0
  Unit cell: (53.235, 63.882, 109.746, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     812      8.00
     N     694      7.00
     C    2608      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H  96 " distance=2.06
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  52 " - pdb=" SG  CYS A 127 " distance=2.03

  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: 0.32
  Conformation dependent library (CDL) restraints added in 240.2 milliseconds
  

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  998

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 16 sheets defined
      5.7% alpha, 39.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'L' and resid 127 through 134
    Processing helix  chain 'L' and resid 189 through 193
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.517A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 194 through 197
    Processing helix  chain 'H' and resid 208 through 211
    Processing helix  chain 'A' and resid 118 through 122
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.663A  pdb=" N   LEU L  79 " --> pdb=" O   ILE L  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 54
      removed outlier: 6.137A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   THR L 103 " --> pdb=" O   GLN L  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 121 through 124
      removed outlier: 4.001A  pdb=" N   ASN L 144 " --> pdb=" O   TYR L 179 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER L 180 " --> pdb=" O   THR L 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 159 through 161
      removed outlier: 4.758A  pdb=" N   TRP L 154 " --> pdb=" O   GLN L 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 8
      removed outlier: 5.733A  pdb=" N   SER H  84 " --> pdb=" O   LEU H  19 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU H  19 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLU H  17 " --> pdb=" O   VAL H  86 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 8
    Processing sheet with id=AA8, first strand: chain 'H' and resid 12 through 13
      removed outlier: 6.591A  pdb=" N   VAL H  35 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   VAL H  51 " --> pdb=" O   VAL H  35 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   TRP H  37 " --> pdb=" O   ILE H  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 12 through 13
      removed outlier: 3.726A  pdb=" N   TYR H 109 " --> pdb=" O   LYS H  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 142 through 143
    Processing sheet with id=AB2, first strand: chain 'H' and resid 146 through 147
    Processing sheet with id=AB3, first strand: chain 'H' and resid 150 through 152
    Processing sheet with id=AB4, first strand: chain 'H' and resid 158 through 160
      removed outlier: 4.516A  pdb=" N   TYR H 201 " --> pdb=" O   VAL H 218 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 34 through 35
    Processing sheet with id=AB6, first strand: chain 'A' and resid 39 through 40
      removed outlier: 4.572A  pdb=" N   GLU A 124 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLN A  64 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
      removed outlier: 8.590A  pdb=" N   GLY A  63 " --> pdb=" O   HIS A  83 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   HIS A  83 " --> pdb=" O   GLY A  63 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL A  65 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   LEU A  81 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   TRP A  67 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 48 through 50

    154 hydrogen bonds defined for protein.
    363 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.44

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 708
        1.32 -     1.44: 1161
        1.44 -     1.57: 2334
        1.57 -     1.69: 1
        1.69 -     1.82: 14
  Bond restraints: 4218
  Sorted by residual:
  bond pdb=" N   PRO A  92 "
       pdb=" CD  PRO A  92 "
    ideal  model  delta    sigma   weight residual
    1.473  1.405  0.068 1.40e-02 5.10e+03 2.39e+01
  bond pdb=" CE1 HIS H 171 "
       pdb=" NE2 HIS H 171 "
    ideal  model  delta    sigma   weight residual
    1.321  1.363 -0.042 1.00e-02 1.00e+04 1.80e+01
  bond pdb=" C   TYR L  55 "
       pdb=" N   PHE L  56 "
    ideal  model  delta    sigma   weight residual
    1.333  1.277  0.056 1.39e-02 5.18e+03 1.65e+01
  bond pdb=" C   LEU L  53 "
       pdb=" N   ILE L  54 "
    ideal  model  delta    sigma   weight residual
    1.332  1.284  0.048 1.23e-02 6.61e+03 1.51e+01
  bond pdb=" N   PHE L 102 "
       pdb=" CA  PHE L 102 "
    ideal  model  delta    sigma   weight residual
    1.456  1.410  0.045 1.25e-02 6.40e+03 1.32e+01
  ... (remaining 4213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.65: 5501
        3.65 -     7.31: 219
        7.31 -    10.96: 13
       10.96 -    14.62: 2
       14.62 -    18.27: 4
  Bond angle restraints: 5739
  Sorted by residual:
  angle pdb=" C   SER L 120 "
        pdb=" CA  SER L 120 "
        pdb=" CB BSER L 120 "
      ideal   model   delta    sigma   weight residual
     110.22  128.49  -18.27 1.67e+00 3.59e-01 1.20e+02
  angle pdb=" N   SER L 120 "
        pdb=" CA  SER L 120 "
        pdb=" CB ASER L 120 "
      ideal   model   delta    sigma   weight residual
     110.17  127.60  -17.43 1.68e+00 3.54e-01 1.08e+02
  angle pdb=" C   SER L 120 "
        pdb=" CA  SER L 120 "
        pdb=" CB ASER L 120 "
      ideal   model   delta    sigma   weight residual
     110.22  126.78  -16.56 1.67e+00 3.59e-01 9.83e+01
  angle pdb=" N   SER L 120 "
        pdb=" CA  SER L 120 "
        pdb=" CB BSER L 120 "
      ideal   model   delta    sigma   weight residual
     110.17  125.80  -15.63 1.68e+00 3.54e-01 8.65e+01
  angle pdb=" N   ASN L 143 "
        pdb=" CA  ASN L 143 "
        pdb=" C   ASN L 143 "
      ideal   model   delta    sigma   weight residual
     111.36  121.43  -10.07 1.09e+00 8.42e-01 8.53e+01
  ... (remaining 5734 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 2358
       16.01 -    32.01: 140
       32.01 -    48.01: 29
       48.01 -    64.02: 5
       64.02 -    80.02: 3
  Dihedral angle restraints: 2535
    sinusoidal: 976
      harmonic: 1559
  Sorted by residual:
  dihedral pdb=" C   SER L 120 "
           pdb=" N   SER L 120 "
           pdb=" CA  SER L 120 "
           pdb=" CB BSER L 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -162.40   39.80     0      2.50e+00 1.60e-01 2.53e+02
  dihedral pdb=" C   SER L 120 "
           pdb=" N   SER L 120 "
           pdb=" CA  SER L 120 "
           pdb=" CB ASER L 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -162.27   39.67     0      2.50e+00 1.60e-01 2.52e+02
  dihedral pdb=" N   SER L 120 "
           pdb=" C   SER L 120 "
           pdb=" CA  SER L 120 "
           pdb=" CB ASER L 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  162.46  -39.66     0      2.50e+00 1.60e-01 2.52e+02
  ... (remaining 2532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.333: 648
       0.333 -    0.666: 2
       0.666 -    0.999: 0
       0.999 -    1.332: 0
       1.332 -    1.665: 2
  Chirality restraints: 652
  Sorted by residual:
  chirality pdb=" CA  SER L 120 "
            pdb=" N   SER L 120 "
            pdb=" C   SER L 120 "
            pdb=" CB ASER L 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.85    1.66 2.00e-01 2.50e+01 6.93e+01
  chirality pdb=" CA  SER L 120 "
            pdb=" N   SER L 120 "
            pdb=" C   SER L 120 "
            pdb=" CB BSER L 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.86    1.65 2.00e-01 2.50e+01 6.81e+01
  chirality pdb=" CA  ALA L  57 "
            pdb=" N   ALA L  57 "
            pdb=" C   ALA L  57 "
            pdb=" CB  ALA L  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.12    0.36 2.00e-01 2.50e+01 3.28e+00
  ... (remaining 649 not shown)

  Planarity restraints: 736
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  41 "    0.054 2.00e-02 2.50e+03   2.96e-02 2.19e+01
        pdb=" CG  TRP L  41 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  41 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  41 "   -0.028 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  41 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  41 "    0.023 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  41 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  41 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  41 "   -0.038 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  41 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  38 "   -0.051 2.00e-02 2.50e+03   3.13e-02 1.96e+01
        pdb=" CG  TYR L  38 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  38 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  38 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  38 "    0.027 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  38 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  38 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR L  38 "   -0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  48 "    0.003 2.00e-02 2.50e+03   2.54e-02 1.62e+01
        pdb=" CG  TRP H  48 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  48 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  48 "   -0.034 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  48 "    0.031 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  48 "    0.016 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  48 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  48 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  48 "    0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  48 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 733 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 102
        2.63 -     3.20: 3948
        3.20 -     3.77: 6119
        3.77 -     4.33: 9488
        4.33 -     4.90: 14985
  Nonbonded interactions: 34642
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN H 204 "
            pdb=" OD1 ASP H 215 "
     model   vdw
     2.067 3.040
  nonbonded pdb=" NE2 GLN L  44 "
            pdb=" OE1 GLN H  40 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   THR H 123 "
            pdb=" OG1 THR H 123 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   LYS H  65 "
            pdb=" OG  SER H  66 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" O   SER H  16 "
            pdb=" OG  SER H  16 "
     model   vdw
     2.381 3.040
  ... (remaining 34637 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=0.50 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:             2.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.340
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.074   4223  Z= 0.650
  Angle     :  1.654  18.273   5749  Z= 1.070
  Chirality :  0.130   1.665    652
  Planarity :  0.007   0.054    736
  Dihedral  : 10.700  80.022   1522
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 26.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.76 %
    Favored  : 91.81 %
  Cbeta Deviations :  1.20 %
  Peptide Plane:
    Cis-proline     : 18.75 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.26 (0.31), residues: 531
  helix: -1.46 (1.14), residues: 16
  sheet: -1.63 (0.33), residues: 230
  loop : -2.71 (0.28), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 115 
 TYR   0.052   0.005   TYR L  38 
 PHE   0.018   0.003   PHE L  77 
 TRP   0.054   0.012   TRP L  41 
 HIS   0.021   0.003   HIS H 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00953 ( 4218)
  covalent geometry    : angle       1.65226 ( 5739)
  SS BOND              : bond        0.01623 (    5)
  SS BOND              : angle       2.58652 (   10)
  hydrogen bonds       : bond        0.22575 (  141)
  hydrogen bonds       : angle      10.91921 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.092 
Fit side-chains
REVERT: L   11 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7719 (mt)
REVERT: L   33 TYR cc_start: 0.7410 (m-80) cc_final: 0.7079 (m-80)
REVERT: L   48 GLN cc_start: 0.8374 (mm110) cc_final: 0.8049 (mt0)
REVERT: L   87 GLU cc_start: 0.8225 (pt0) cc_final: 0.7899 (pm20)
REVERT: L  113 LYS cc_start: 0.8226 (mttt) cc_final: 0.7981 (mtpp)
REVERT: L  194 LYS cc_start: 0.7600 (mttt) cc_final: 0.7218 (tptt)
REVERT: H  107 MET cc_start: 0.8914 (mtm) cc_final: 0.8660 (mtm)
REVERT: H  124 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8062 (tttm)
REVERT: A   40 VAL cc_start: 0.5907 (t) cc_final: 0.5557 (t)
REVERT: A  138 GLN cc_start: 0.7909 (pt0) cc_final: 0.7611 (pp30)
REVERT: A  142 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7806 (mtm110)
  outliers start: 2
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0781
  time to fit residues: 11.8641
Evaluate side-chains
  79 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   11 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 48 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  22 ASN
L  31 ASN
L  35 GLN
L  44 GLN
L  48 GLN
H   6 GLN
H  99 GLN
H 206 ASN
A  77 GLN
A  89 HIS
A 106 ASN
A 119 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.157750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.125021 restraints weight = 11589.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 4.08
r_work: 0.3273 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4223  Z= 0.153
  Angle     :  0.704   9.733   5749  Z= 0.362
  Chirality :  0.047   0.172    652
  Planarity :  0.005   0.067    736
  Dihedral  :  5.132  20.605    581
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 10.78 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.34), residues: 531
  helix: -0.97 (1.19), residues: 16
  sheet: -0.99 (0.33), residues: 236
  loop : -1.18 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  97 
 TYR   0.012   0.001   TYR H  95 
 PHE   0.010   0.002   PHE L  77 
 TRP   0.011   0.001   TRP H 161 
 HIS   0.004   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4218)
  covalent geometry    : angle       0.70376 ( 5739)
  SS BOND              : bond        0.00333 (    5)
  SS BOND              : angle       0.69246 (   10)
  hydrogen bonds       : bond        0.03904 (  141)
  hydrogen bonds       : angle       6.91193 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.147 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7346 (mp0) cc_final: 0.6847 (mt-10)
REVERT: L   33 TYR cc_start: 0.7071 (m-80) cc_final: 0.6773 (m-80)
REVERT: L   48 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8125 (mt0)
REVERT: L   87 GLU cc_start: 0.8353 (pt0) cc_final: 0.7977 (pm20)
REVERT: L  194 LYS cc_start: 0.7710 (mttt) cc_final: 0.7487 (tptt)
REVERT: H  124 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7591 (tttm)
  outliers start: 12
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0534
  time to fit residues: 5.9237
Evaluate side-chains
  76 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  186 THR
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   90 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.149052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.117359 restraints weight = 5237.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.70
r_work: 0.3178 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4223  Z= 0.205
  Angle     :  0.660   7.031   5749  Z= 0.341
  Chirality :  0.046   0.139    652
  Planarity :  0.006   0.062    736
  Dihedral  :  4.851  20.102    579
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 11.85 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.35), residues: 531
  helix: -0.24 (1.29), residues: 16
  sheet: -0.91 (0.31), residues: 246
  loop : -0.56 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 142 
 TYR   0.017   0.002   TYR L  42 
 PHE   0.009   0.002   PHE H  28 
 TRP   0.008   0.001   TRP H  53 
 HIS   0.008   0.002   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 4218)
  covalent geometry    : angle       0.65956 ( 5739)
  SS BOND              : bond        0.00278 (    5)
  SS BOND              : angle       0.90893 (   10)
  hydrogen bonds       : bond        0.03845 (  141)
  hydrogen bonds       : angle       6.20001 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.161 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7527 (mp0) cc_final: 0.7098 (mt-10)
REVERT: L   33 TYR cc_start: 0.7242 (m-80) cc_final: 0.6875 (m-80)
REVERT: L  153 GLN cc_start: 0.7826 (mt0) cc_final: 0.7306 (mm-40)
REVERT: L  194 LYS cc_start: 0.7842 (mttt) cc_final: 0.7577 (tptt)
REVERT: H  124 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7410 (tttm)
REVERT: A  142 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7232 (mtp85)
  outliers start: 15
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0636
  time to fit residues: 7.5510
Evaluate side-chains
  82 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue  218 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0670
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
L 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.148862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116455 restraints weight = 5276.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.83
r_work: 0.3185 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4223  Z= 0.172
  Angle     :  0.620   7.172   5749  Z= 0.312
  Chirality :  0.044   0.137    652
  Planarity :  0.005   0.061    736
  Dihedral  :  4.644  19.261    579
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.66 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.35), residues: 531
  helix: -0.11 (1.30), residues: 16
  sheet: -0.79 (0.31), residues: 246
  loop : -0.48 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.012   0.002   TYR L  42 
 PHE   0.014   0.002   PHE A 137 
 TRP   0.006   0.001   TRP L 154 
 HIS   0.006   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 4218)
  covalent geometry    : angle       0.61927 ( 5739)
  SS BOND              : bond        0.00256 (    5)
  SS BOND              : angle       0.76829 (   10)
  hydrogen bonds       : bond        0.03207 (  141)
  hydrogen bonds       : angle       6.11052 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.154 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7466 (mp0) cc_final: 0.7109 (mt-10)
REVERT: L   33 TYR cc_start: 0.7373 (m-80) cc_final: 0.6931 (m-80)
REVERT: L  153 GLN cc_start: 0.7944 (mt0) cc_final: 0.7483 (mm-40)
REVERT: H  124 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7626 (tttm)
REVERT: A  121 ASP cc_start: 0.7920 (m-30) cc_final: 0.7548 (t0)
REVERT: A  142 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7428 (mtp85)
  outliers start: 16
  outliers final: 9
  residues processed: 87
  average time/residue: 0.0682
  time to fit residues: 7.6048
Evaluate side-chains
  82 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue  160 SER
Chi-restraints excluded: chain H residue  218 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0970
   chunk 14 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    0.2980
   chunk 48 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
L 166 GLN
A  77 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.146967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.113980 restraints weight = 7206.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 3.28
r_work: 0.3170 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4223  Z= 0.125
  Angle     :  0.565   6.714   5749  Z= 0.283
  Chirality :  0.043   0.139    652
  Planarity :  0.005   0.055    736
  Dihedral  :  4.357  17.836    579
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.95 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.36), residues: 531
  helix:  0.28 (1.42), residues: 16
  sheet: -0.65 (0.32), residues: 248
  loop : -0.44 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  67 
 TYR   0.009   0.001   TYR L  98 
 PHE   0.026   0.002   PHE A 132 
 TRP   0.006   0.001   TRP L 154 
 HIS   0.005   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4218)
  covalent geometry    : angle       0.56487 ( 5739)
  SS BOND              : bond        0.00226 (    5)
  SS BOND              : angle       0.64075 (   10)
  hydrogen bonds       : bond        0.02904 (  141)
  hydrogen bonds       : angle       5.61900 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.155 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7395 (mp0) cc_final: 0.7065 (mt-10)
REVERT: L   33 TYR cc_start: 0.7440 (m-80) cc_final: 0.6988 (m-80)
REVERT: L  149 GLU cc_start: 0.7634 (mp0) cc_final: 0.6505 (pp20)
REVERT: L  153 GLN cc_start: 0.7944 (mt0) cc_final: 0.7533 (mm-40)
REVERT: H  124 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7718 (tttm)
REVERT: H  211 ASN cc_start: 0.7834 (t0) cc_final: 0.7599 (t0)
REVERT: A  142 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7416 (mmm-85)
  outliers start: 10
  outliers final: 8
  residues processed: 76
  average time/residue: 0.0713
  time to fit residues: 6.9229
Evaluate side-chains
  75 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  160 SER
Chi-restraints excluded: chain H residue  202 ILE
Chi-restraints excluded: chain H residue  218 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 29 optimal weight:    0.3980
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
A  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.147227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.116078 restraints weight = 5385.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.81
r_work: 0.3194 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4223  Z= 0.139
  Angle     :  0.573   6.858   5749  Z= 0.286
  Chirality :  0.043   0.132    652
  Planarity :  0.005   0.053    736
  Dihedral  :  4.297  18.383    579
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.30 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.36), residues: 531
  helix:  0.40 (1.41), residues: 16
  sheet: -0.53 (0.31), residues: 250
  loop : -0.41 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.010   0.001   TYR L  42 
 PHE   0.007   0.001   PHE L  77 
 TRP   0.004   0.001   TRP H  48 
 HIS   0.006   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4218)
  covalent geometry    : angle       0.57314 ( 5739)
  SS BOND              : bond        0.00229 (    5)
  SS BOND              : angle       0.70030 (   10)
  hydrogen bonds       : bond        0.02859 (  141)
  hydrogen bonds       : angle       5.39898 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.166 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7392 (mp0) cc_final: 0.6946 (mt-10)
REVERT: L   33 TYR cc_start: 0.7598 (m-80) cc_final: 0.7013 (m-80)
REVERT: L  113 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7596 (mtmm)
REVERT: L  149 GLU cc_start: 0.7636 (mp0) cc_final: 0.6517 (pp20)
REVERT: L  153 GLN cc_start: 0.7984 (mt0) cc_final: 0.7557 (mm-40)
REVERT: H  124 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7698 (tttm)
REVERT: H  195 SER cc_start: 0.8210 (p) cc_final: 0.7792 (t)
REVERT: H  211 ASN cc_start: 0.7862 (t0) cc_final: 0.7661 (t0)
REVERT: A  141 LEU cc_start: 0.7862 (tt) cc_final: 0.7203 (mp)
REVERT: A  142 ARG cc_start: 0.7883 (mtp-110) cc_final: 0.7419 (mmm-85)
  outliers start: 15
  outliers final: 9
  residues processed: 81
  average time/residue: 0.0652
  time to fit residues: 6.8320
Evaluate side-chains
  77 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  160 SER
Chi-restraints excluded: chain H residue  202 ILE
Chi-restraints excluded: chain H residue  218 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.114713 restraints weight = 5368.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.78
r_work: 0.3175 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.5038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4223  Z= 0.145
  Angle     :  0.566   6.797   5749  Z= 0.284
  Chirality :  0.043   0.127    652
  Planarity :  0.005   0.053    736
  Dihedral  :  4.271  18.733    579
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.09 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.36), residues: 531
  helix:  0.47 (1.41), residues: 16
  sheet: -0.48 (0.31), residues: 250
  loop : -0.34 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.012   0.001   TYR H  60 
 PHE   0.008   0.001   PHE H  28 
 TRP   0.005   0.001   TRP L 154 
 HIS   0.006   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4218)
  covalent geometry    : angle       0.56592 ( 5739)
  SS BOND              : bond        0.00215 (    5)
  SS BOND              : angle       0.68872 (   10)
  hydrogen bonds       : bond        0.02832 (  141)
  hydrogen bonds       : angle       5.35402 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.160 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7428 (mp0) cc_final: 0.6929 (mt-10)
REVERT: L  113 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7611 (mtmm)
REVERT: L  149 GLU cc_start: 0.7666 (mp0) cc_final: 0.6554 (pp20)
REVERT: L  153 GLN cc_start: 0.7951 (mt0) cc_final: 0.7471 (mm-40)
REVERT: H  124 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7684 (tttm)
REVERT: H  195 SER cc_start: 0.8375 (p) cc_final: 0.8156 (p)
REVERT: A  121 ASP cc_start: 0.7931 (m-30) cc_final: 0.6996 (t0)
REVERT: A  142 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7487 (mmm-85)
  outliers start: 12
  outliers final: 12
  residues processed: 78
  average time/residue: 0.0660
  time to fit residues: 6.6084
Evaluate side-chains
  81 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  160 SER
Chi-restraints excluded: chain H residue  202 ILE
Chi-restraints excluded: chain H residue  218 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0470
   chunk 46 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0030
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.4088

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

Flipped N/Q/H residues before XYZ refinement:
H 211 ASN
A  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114393 restraints weight = 11548.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 4.35
r_work: 0.3108 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4223  Z= 0.110
  Angle     :  0.546   7.590   5749  Z= 0.269
  Chirality :  0.042   0.125    652
  Planarity :  0.005   0.052    736
  Dihedral  :  4.098  17.320    579
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.09 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.36), residues: 531
  helix:  0.48 (1.37), residues: 16
  sheet: -0.39 (0.31), residues: 250
  loop : -0.32 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  67 
 TYR   0.013   0.001   TYR H  60 
 PHE   0.012   0.001   PHE A 137 
 TRP   0.005   0.001   TRP H  48 
 HIS   0.003   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4218)
  covalent geometry    : angle       0.54584 ( 5739)
  SS BOND              : bond        0.00241 (    5)
  SS BOND              : angle       0.64558 (   10)
  hydrogen bonds       : bond        0.02614 (  141)
  hydrogen bonds       : angle       5.16266 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.158 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7445 (mp0) cc_final: 0.6958 (mt-10)
REVERT: L   35 GLN cc_start: 0.8330 (mp10) cc_final: 0.7944 (mm-40)
REVERT: L  113 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7704 (mtmm)
REVERT: L  149 GLU cc_start: 0.7717 (mp0) cc_final: 0.6575 (pp20)
REVERT: L  153 GLN cc_start: 0.8033 (mt0) cc_final: 0.7566 (mm-40)
REVERT: L  164 ASN cc_start: 0.8710 (p0) cc_final: 0.8485 (p0)
REVERT: H  124 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7760 (tttm)
REVERT: H  195 SER cc_start: 0.8355 (p) cc_final: 0.8132 (p)
REVERT: A  121 ASP cc_start: 0.8082 (m-30) cc_final: 0.7075 (t0)
REVERT: A  142 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7531 (mmm-85)
  outliers start: 11
  outliers final: 9
  residues processed: 79
  average time/residue: 0.0677
  time to fit residues: 6.8825
Evaluate side-chains
  79 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  202 ILE
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0370
   chunk 40 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
H 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.145625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.114465 restraints weight = 5421.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.79
r_work: 0.3171 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.5295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4223  Z= 0.150
  Angle     :  0.567   6.988   5749  Z= 0.283
  Chirality :  0.043   0.130    652
  Planarity :  0.005   0.052    736
  Dihedral  :  4.180  18.275    579
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.87 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.36), residues: 531
  helix:  0.59 (1.39), residues: 16
  sheet: -0.35 (0.31), residues: 250
  loop : -0.26 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.011   0.001   TYR L  42 
 PHE   0.008   0.001   PHE H  28 
 TRP   0.005   0.001   TRP H  48 
 HIS   0.006   0.002   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 4218)
  covalent geometry    : angle       0.56651 ( 5739)
  SS BOND              : bond        0.00239 (    5)
  SS BOND              : angle       0.76815 (   10)
  hydrogen bonds       : bond        0.02945 (  141)
  hydrogen bonds       : angle       5.15964 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.156 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7413 (mp0) cc_final: 0.6944 (mt-10)
REVERT: L  113 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7635 (mtmm)
REVERT: L  149 GLU cc_start: 0.7700 (mp0) cc_final: 0.6588 (pp20)
REVERT: L  153 GLN cc_start: 0.7955 (mt0) cc_final: 0.7463 (mm-40)
REVERT: L  164 ASN cc_start: 0.8671 (p0) cc_final: 0.8416 (p0)
REVERT: H  124 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7745 (tttm)
REVERT: H  195 SER cc_start: 0.8375 (p) cc_final: 0.8168 (p)
REVERT: A  121 ASP cc_start: 0.7976 (m-30) cc_final: 0.7036 (t0)
REVERT: A  142 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7535 (mmm-85)
  outliers start: 12
  outliers final: 11
  residues processed: 77
  average time/residue: 0.0696
  time to fit residues: 6.8422
Evaluate side-chains
  79 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain H residue  160 SER
Chi-restraints excluded: chain H residue  202 ILE
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0570
   chunk 16 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
L 143 ASN
H 211 ASN
A  77 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.145741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.112163 restraints weight = 7615.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 3.38
r_work: 0.3132 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.5391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4223  Z= 0.145
  Angle     :  0.564   7.255   5749  Z= 0.282
  Chirality :  0.042   0.131    652
  Planarity :  0.005   0.053    736
  Dihedral  :  4.156  18.011    579
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.30 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.36), residues: 531
  helix:  0.62 (1.37), residues: 16
  sheet: -0.30 (0.31), residues: 248
  loop : -0.28 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  67 
 TYR   0.009   0.001   TYR L  42 
 PHE   0.008   0.001   PHE H  28 
 TRP   0.005   0.001   TRP H  48 
 HIS   0.006   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4218)
  covalent geometry    : angle       0.56357 ( 5739)
  SS BOND              : bond        0.00244 (    5)
  SS BOND              : angle       0.81294 (   10)
  hydrogen bonds       : bond        0.02846 (  141)
  hydrogen bonds       : angle       5.13088 (  363)

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

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

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1062 Ramachandran restraints generated.
    531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.149 
Fit side-chains
REVERT: L   17 GLU cc_start: 0.7414 (mp0) cc_final: 0.6902 (mt-10)
REVERT: L  113 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7644 (mtmm)
REVERT: L  149 GLU cc_start: 0.7720 (mp0) cc_final: 0.6595 (pp20)
REVERT: L  153 GLN cc_start: 0.8040 (mt0) cc_final: 0.7530 (mm-40)
REVERT: L  164 ASN cc_start: 0.8696 (p0) cc_final: 0.8458 (p0)
REVERT: H  124 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7776 (tttm)
REVERT: A  121 ASP cc_start: 0.7950 (m-30) cc_final: 0.7016 (t0)
REVERT: A  141 LEU cc_start: 0.7930 (tt) cc_final: 0.7293 (mp)
REVERT: A  142 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7580 (mmm-85)
  outliers start: 11
  outliers final: 11
  residues processed: 70
  average time/residue: 0.0797
  time to fit residues: 6.9385
Evaluate side-chains
  75 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  186 THR
Chi-restraints excluded: chain L residue  202 VAL
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  160 SER
Chi-restraints excluded: chain H residue  202 ILE
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  118 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.145299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.113946 restraints weight = 11891.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 4.04
r_work: 0.3132 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4223  Z= 0.149
  Angle     :  0.568   7.065   5749  Z= 0.283
  Chirality :  0.043   0.131    652
  Planarity :  0.005   0.053    736
  Dihedral  :  4.179  18.044    579
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.52 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.35), residues: 531
  helix:  0.65 (1.35), residues: 16
  sheet: -0.29 (0.31), residues: 248
  loop : -0.28 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 144 
 TYR   0.009   0.001   TYR L  42 
 PHE   0.008   0.001   PHE H  28 
 TRP   0.005   0.001   TRP H  48 
 HIS   0.006   0.001   HIS L  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4218)
  covalent geometry    : angle       0.56790 ( 5739)
  SS BOND              : bond        0.00223 (    5)
  SS BOND              : angle       0.80160 (   10)
  hydrogen bonds       : bond        0.02858 (  141)
  hydrogen bonds       : angle       5.13712 (  363)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1148.68 seconds
wall clock time: 20 minutes 26.91 seconds (1226.91 seconds total)