Starting phenix.real_space_refine
on Fri Aug 22 12:39:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pjp_17718/08_2025/8pjp_17718.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pjp_17718/08_2025/8pjp_17718.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pjp_17718/08_2025/8pjp_17718.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pjp_17718/08_2025/8pjp_17718.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pjp_17718/08_2025/8pjp_17718.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pjp_17718/08_2025/8pjp_17718.map"
  }
  resolution = 2.92
  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=   0.002 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S       9      5.16       5
     C    1342      2.51       5
     N     371      2.21       5
     O     434      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2157
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1197
          Classifications: {'peptide': 161}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 156}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 931
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 4, 'TRANS': 120}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {'G3P': 1, 'WKE': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.12, per 1000 atoms: 0.52
  Number of scatterers: 2157
  At special positions: 0
  Unit cell: (61.06, 71.38, 111.8, 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       9     16.00
     P       1     15.00
     O     434      8.00
     N     371      7.00
     C    1342      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 120 " - pdb=" SG  CYS A 154 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  98 " 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 98.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  516

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 5 sheets defined
      26.2% alpha, 30.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 3.523A  pdb=" N   LEU A   6 " --> pdb=" O   THR A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 42
      removed outlier: 4.376A  pdb=" N   TYR A  27 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU A  35 " --> pdb=" O   ALA A  31 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ALA A  36 " --> pdb=" O   GLN A  32 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY A  42 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 55
      removed outlier: 3.569A  pdb=" N   VAL A  47 " --> pdb=" O   GLN A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 65
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 146 through 150
    Processing helix  chain 'C' and resid 89 through 93
      removed outlier: 3.517A  pdb=" N   THR C  93 " --> pdb=" O   PRO C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 113
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83
      removed outlier: 3.797A  pdb=" N   SER A  79 " --> pdb=" O   GLN A  90 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125
      removed outlier: 3.511A  pdb=" N   ALA A 135 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 9
      removed outlier: 4.091A  pdb=" N   THR C  80 " --> pdb=" O   ASP C  75 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 14
      removed outlier: 6.986A  pdb=" N   ILE C  36 " --> pdb=" O   CYS C  52 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   CYS C  52 " --> pdb=" O   ILE C  36 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   TRP C  38 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14
      removed outlier: 7.034A  pdb=" N   ALA C 100 " --> pdb=" O   ASP C 116 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    249 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: 0.28

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 709
        1.34 -     1.46: 348
        1.46 -     1.57: 1121
        1.57 -     1.69: 1
        1.69 -     1.81: 13
  Bond restraints: 2192
  Sorted by residual:
  bond pdb=" O1P G3P A 201 "
       pdb=" P   G3P A 201 "
    ideal  model  delta    sigma   weight residual
    1.726  1.609  0.117 2.00e-02 2.50e+03 3.44e+01
  bond pdb=" C6  WKE A 202 "
       pdb=" O6  WKE A 202 "
    ideal  model  delta    sigma   weight residual
    1.401  1.433 -0.032 2.00e-02 2.50e+03 2.48e+00
  bond pdb=" C8  WKE A 202 "
       pdb=" C9  WKE A 202 "
    ideal  model  delta    sigma   weight residual
    1.531  1.500  0.031 2.00e-02 2.50e+03 2.43e+00
  bond pdb=" C10 WKE A 202 "
       pdb=" O5  WKE A 202 "
    ideal  model  delta    sigma   weight residual
    1.405  1.432 -0.027 2.00e-02 2.50e+03 1.79e+00
  bond pdb=" C9  WKE A 202 "
       pdb=" O4  WKE A 202 "
    ideal  model  delta    sigma   weight residual
    1.404  1.431 -0.027 2.00e-02 2.50e+03 1.79e+00
  ... (remaining 2187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 2941
        1.82 -     3.64: 25
        3.64 -     5.46: 6
        5.46 -     7.28: 4
        7.28 -     9.10: 1
  Bond angle restraints: 2977
  Sorted by residual:
  angle pdb=" O1P G3P A 201 "
        pdb=" P   G3P A 201 "
        pdb=" O4P G3P A 201 "
      ideal   model   delta    sigma   weight residual
     100.65  109.75   -9.10 3.00e+00 1.11e-01 9.20e+00
  angle pdb=" O2P G3P A 201 "
        pdb=" P   G3P A 201 "
        pdb=" O4P G3P A 201 "
      ideal   model   delta    sigma   weight residual
     115.71  109.69    6.02 3.00e+00 1.11e-01 4.02e+00
  angle pdb=" C   SER A  62 "
        pdb=" N   SER A  63 "
        pdb=" CA  SER A  63 "
      ideal   model   delta    sigma   weight residual
     122.60  119.64    2.96 1.56e+00 4.11e-01 3.59e+00
  angle pdb=" O3P G3P A 201 "
        pdb=" P   G3P A 201 "
        pdb=" O4P G3P A 201 "
      ideal   model   delta    sigma   weight residual
     115.20  109.66    5.54 3.00e+00 1.11e-01 3.42e+00
  angle pdb=" O1P G3P A 201 "
        pdb=" P   G3P A 201 "
        pdb=" O3P G3P A 201 "
      ideal   model   delta    sigma   weight residual
     104.20  109.74   -5.54 3.00e+00 1.11e-01 3.41e+00
  ... (remaining 2972 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 1147
       16.87 -    33.73: 119
       33.73 -    50.60: 43
       50.60 -    67.46: 7
       67.46 -    84.33: 3
  Dihedral angle restraints: 1319
    sinusoidal: 507
      harmonic: 812
  Sorted by residual:
  dihedral pdb=" CB  CYS C  24 "
           pdb=" SG  CYS C  24 "
           pdb=" SG  CYS C  98 "
           pdb=" CB  CYS C  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.87   37.13     1      1.00e+01 1.00e-02 1.95e+01
  dihedral pdb=" CB  GLU A  35 "
           pdb=" CG  GLU A  35 "
           pdb=" CD  GLU A  35 "
           pdb=" OE1 GLU A  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.33   84.33     1      3.00e+01 1.11e-03 9.61e+00
  dihedral pdb=" N   LYS A 101 "
           pdb=" CA  LYS A 101 "
           pdb=" CB  LYS A 101 "
           pdb=" CG  LYS A 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.55   53.55     3      1.50e+01 4.44e-03 9.21e+00
  ... (remaining 1316 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 212
       0.025 -    0.050: 69
       0.050 -    0.074: 35
       0.074 -    0.099: 13
       0.099 -    0.124: 16
  Chirality restraints: 345
  Sorted by residual:
  chirality pdb=" CA  ILE C 105 "
            pdb=" N   ILE C 105 "
            pdb=" C   ILE C 105 "
            pdb=" CB  ILE C 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  chirality pdb=" CA  VAL C  95 "
            pdb=" N   VAL C  95 "
            pdb=" C   VAL C  95 "
            pdb=" CB  VAL C  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.46e-01
  chirality pdb=" CA  VAL A  80 "
            pdb=" N   VAL A  80 "
            pdb=" C   VAL A  80 "
            pdb=" CB  VAL A  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.42e-01
  ... (remaining 342 not shown)

  Planarity restraints: 380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C7  WKE A 202 "    0.053 2.00e-02 2.50e+03   4.32e-02 2.34e+01
        pdb=" C8  WKE A 202 "   -0.015 2.00e-02 2.50e+03
        pdb=" C9  WKE A 202 "    0.040 2.00e-02 2.50e+03
        pdb=" N1  WKE A 202 "   -0.068 2.00e-02 2.50e+03
        pdb=" O3  WKE A 202 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   WKE A 202 "   -0.019 2.00e-02 2.50e+03   1.21e-02 1.83e+00
        pdb=" C3  WKE A 202 "    0.014 2.00e-02 2.50e+03
        pdb=" C4  WKE A 202 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5  WKE A 202 "   -0.004 2.00e-02 2.50e+03
        pdb=" O1  WKE A 202 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  21 "   -0.015 5.00e-02 4.00e+02   2.29e-02 8.42e-01
        pdb=" N   PRO A  22 "    0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A  22 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A  22 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 377 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 794
        2.87 -     3.38: 1665
        3.38 -     3.89: 3277
        3.89 -     4.39: 3602
        4.39 -     4.90: 6594
  Nonbonded interactions: 15932
  Sorted by model distance:
  nonbonded pdb=" O   ASP C  32 "
            pdb=" OG  SER C  55 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" NH2 ARG C  69 "
            pdb=" OD2 ASP C  92 "
     model   vdw
     2.456 3.120
  nonbonded pdb=" N   ASP C 116 "
            pdb=" OD1 ASP C 116 "
     model   vdw
     2.482 3.120
  nonbonded pdb=" C3  G3P A 201 "
            pdb=" O1  G3P A 201 "
     model   vdw
     2.541 2.752
  nonbonded pdb=" OE2 GLU A  49 "
            pdb=" ND2 ASN A  53 "
     model   vdw
     2.542 3.120
  ... (remaining 15927 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:             4.040
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.670
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
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      :  0.004   0.117   2196  Z= 0.227
  Angle     :  0.528   9.098   2981  Z= 0.244
  Chirality :  0.040   0.124    345
  Planarity :  0.003   0.043    380
  Dihedral  : 15.916  84.330    797
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 18.75 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.52), residues: 282
  helix:  1.00 (0.70), residues: 59
  sheet:  0.81 (0.60), residues: 71
  loop :  0.35 (0.55), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 155 
 TYR   0.005   0.000   TYR C  97 
 PHE   0.002   0.000   PHE A   1 
 TRP   0.003   0.000   TRP A 108 
 HIS   0.001   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 2192)
  covalent geometry    : angle       0.52852 ( 2977)
  SS BOND              : bond        0.00111 (    2)
  SS BOND              : angle       0.29764 (    4)
  hydrogen bonds       : bond        0.22387 (   90)
  hydrogen bonds       : angle       7.11717 (  249)
  Misc. bond           : bond        0.04980 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  132 THR cc_start: 0.9216 (p) cc_final: 0.9013 (t)
  outliers start: 3
  outliers final: 1
  residues processed: 77
  average time/residue: 0.4892
  time to fit residues: 38.5273
Evaluate side-chains
  64 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.0050
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 25 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.1998

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.081098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.053583 restraints weight = 4648.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.2606 rms_B_bonded: 2.83
r_work: 0.2491 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2378 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8936
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2196  Z= 0.116
  Angle     :  0.564   7.717   2981  Z= 0.283
  Chirality :  0.041   0.130    345
  Planarity :  0.003   0.021    380
  Dihedral  :  4.220  21.874    340
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 24.11 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.53), residues: 282
  helix:  1.95 (0.74), residues: 53
  sheet:  0.93 (0.62), residues: 72
  loop :  0.42 (0.54), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  21 
 TYR   0.008   0.001   TYR C  97 
 PHE   0.013   0.001   PHE C  29 
 TRP   0.007   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2192)
  covalent geometry    : angle       0.56372 ( 2977)
  SS BOND              : bond        0.00183 (    2)
  SS BOND              : angle       0.50948 (    4)
  hydrogen bonds       : bond        0.03418 (   90)
  hydrogen bonds       : angle       4.60864 (  249)
  Misc. bond           : bond        0.00273 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  132 THR cc_start: 0.9522 (p) cc_final: 0.9164 (t)
REVERT: C   75 ASP cc_start: 0.8614 (t0) cc_final: 0.8173 (t0)
REVERT: C   78 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8149 (ptpp)
REVERT: C   79 ASN cc_start: 0.9097 (m110) cc_final: 0.8807 (m110)
REVERT: C   88 LEU cc_start: 0.9201 (mm) cc_final: 0.8981 (mm)
REVERT: C   92 ASP cc_start: 0.8938 (m-30) cc_final: 0.8503 (m-30)
  outliers start: 13
  outliers final: 4
  residues processed: 78
  average time/residue: 0.4424
  time to fit residues: 35.3251
Evaluate side-chains
  71 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue  122 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0050
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 17 optimal weight:    0.2980
   chunk 8 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.082106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.054530 restraints weight = 4704.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.2628 rms_B_bonded: 2.86
r_work: 0.2513 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2400 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2196  Z= 0.093
  Angle     :  0.549   8.262   2981  Z= 0.269
  Chirality :  0.040   0.123    345
  Planarity :  0.003   0.022    380
  Dihedral  :  3.723  22.678    339
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 26.79 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.52), residues: 282
  helix:  1.92 (0.72), residues: 53
  sheet:  0.95 (0.61), residues: 71
  loop :  0.33 (0.54), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  21 
 TYR   0.004   0.001   TYR C  97 
 PHE   0.011   0.001   PHE C  29 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.001   0.001   HIS C  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 2192)
  covalent geometry    : angle       0.54887 ( 2977)
  SS BOND              : bond        0.00163 (    2)
  SS BOND              : angle       0.36482 (    4)
  hydrogen bonds       : bond        0.02729 (   90)
  hydrogen bonds       : angle       4.31260 (  249)
  Misc. bond           : bond        0.00251 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8881 (tm-30)
REVERT: A  142 ASP cc_start: 0.9118 (p0) cc_final: 0.8684 (p0)
REVERT: C   46 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8362 (tp30)
REVERT: C   75 ASP cc_start: 0.8636 (t0) cc_final: 0.8141 (t0)
REVERT: C   78 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8281 (ptpp)
REVERT: C   88 LEU cc_start: 0.9207 (mm) cc_final: 0.8960 (mm)
REVERT: C   92 ASP cc_start: 0.9007 (m-30) cc_final: 0.8724 (m-30)
  outliers start: 9
  outliers final: 3
  residues processed: 71
  average time/residue: 0.4850
  time to fit residues: 35.2163
Evaluate side-chains
  68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0270
   chunk 26 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.7844

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.079004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.051054 restraints weight = 4740.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.2551 rms_B_bonded: 2.86
r_work: 0.2433 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2319 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2196  Z= 0.138
  Angle     :  0.573   9.156   2981  Z= 0.281
  Chirality :  0.042   0.131    345
  Planarity :  0.003   0.019    380
  Dihedral  :  4.180  30.171    339
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 25.89 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.52), residues: 282
  helix:  1.17 (0.71), residues: 59
  sheet:  0.97 (0.61), residues: 71
  loop :  0.19 (0.54), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  21 
 TYR   0.006   0.001   TYR C  97 
 PHE   0.003   0.001   PHE C  29 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 2192)
  covalent geometry    : angle       0.57315 ( 2977)
  SS BOND              : bond        0.00126 (    2)
  SS BOND              : angle       0.37476 (    4)
  hydrogen bonds       : bond        0.03574 (   90)
  hydrogen bonds       : angle       4.14207 (  249)
  Misc. bond           : bond        0.00304 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 ASP cc_start: 0.9152 (p0) cc_final: 0.8720 (p0)
REVERT: C   15 GLN cc_start: 0.9040 (pm20) cc_final: 0.8586 (pm20)
REVERT: C   75 ASP cc_start: 0.8689 (t0) cc_final: 0.8170 (t0)
REVERT: C   78 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8150 (ptpp)
REVERT: C   88 LEU cc_start: 0.9145 (mm) cc_final: 0.8837 (mm)
REVERT: C   92 ASP cc_start: 0.8915 (m-30) cc_final: 0.8700 (m-30)
  outliers start: 11
  outliers final: 6
  residues processed: 72
  average time/residue: 0.4501
  time to fit residues: 33.1522
Evaluate side-chains
  68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 138 ASN
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.075323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2504 r_free = 0.2504 target = 0.047310 restraints weight = 4795.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.2462 rms_B_bonded: 2.82
r_work: 0.2350 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2238 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   2196  Z= 0.279
  Angle     :  0.682   8.797   2981  Z= 0.342
  Chirality :  0.046   0.155    345
  Planarity :  0.003   0.019    380
  Dihedral  :  5.149  43.090    339
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 26.34 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.51), residues: 282
  helix:  0.82 (0.70), residues: 59
  sheet:  0.99 (0.59), residues: 77
  loop : -0.16 (0.53), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  21 
 TYR   0.010   0.001   TYR C  97 
 PHE   0.013   0.002   PHE C  29 
 TRP   0.008   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 ( 2192)
  covalent geometry    : angle       0.68197 ( 2977)
  SS BOND              : bond        0.00258 (    2)
  SS BOND              : angle       0.49626 (    4)
  hydrogen bonds       : bond        0.05134 (   90)
  hydrogen bonds       : angle       4.43562 (  249)
  Misc. bond           : bond        0.00384 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6831 (tt0)
REVERT: A  142 ASP cc_start: 0.9127 (p0) cc_final: 0.8698 (p0)
REVERT: C   15 GLN cc_start: 0.9155 (pm20) cc_final: 0.8705 (pm20)
REVERT: C   75 ASP cc_start: 0.8637 (t0) cc_final: 0.8076 (t0)
REVERT: C   78 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8128 (ptpp)
REVERT: C   88 LEU cc_start: 0.9189 (mm) cc_final: 0.8962 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.4999
  time to fit residues: 35.2445
Evaluate side-chains
  67 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.078774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.050851 restraints weight = 4635.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.2553 rms_B_bonded: 2.83
r_work: 0.2440 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2329 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8922
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2196  Z= 0.115
  Angle     :  0.602   9.149   2981  Z= 0.295
  Chirality :  0.042   0.128    345
  Planarity :  0.003   0.020    380
  Dihedral  :  4.412  39.050    339
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 28.57 %
    Favored  : 67.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.52), residues: 282
  helix:  0.97 (0.73), residues: 59
  sheet:  0.98 (0.55), residues: 87
  loop : -0.03 (0.58), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  21 
 TYR   0.005   0.001   TYR C  97 
 PHE   0.014   0.001   PHE C  29 
 TRP   0.007   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 2192)
  covalent geometry    : angle       0.60227 ( 2977)
  SS BOND              : bond        0.00127 (    2)
  SS BOND              : angle       0.33116 (    4)
  hydrogen bonds       : bond        0.03045 (   90)
  hydrogen bonds       : angle       4.04668 (  249)
  Misc. bond           : bond        0.00283 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 ASP cc_start: 0.9179 (p0) cc_final: 0.8807 (p0)
REVERT: C   15 GLN cc_start: 0.9107 (pm20) cc_final: 0.8651 (pm20)
REVERT: C   75 ASP cc_start: 0.8785 (t0) cc_final: 0.8238 (t0)
REVERT: C   78 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8157 (ptpp)
REVERT: C   88 LEU cc_start: 0.9181 (mm) cc_final: 0.8921 (mm)
  outliers start: 8
  outliers final: 5
  residues processed: 69
  average time/residue: 0.4697
  time to fit residues: 33.1414
Evaluate side-chains
  65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.077738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.049755 restraints weight = 4728.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.2526 rms_B_bonded: 2.83
r_work: 0.2411 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2299 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8967
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2196  Z= 0.155
  Angle     :  0.645  10.378   2981  Z= 0.315
  Chirality :  0.043   0.132    345
  Planarity :  0.003   0.020    380
  Dihedral  :  4.567  42.386    339
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 30.80 %
    Favored  : 66.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.52), residues: 282
  helix:  0.88 (0.72), residues: 59
  sheet:  0.99 (0.56), residues: 87
  loop : -0.07 (0.57), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  21 
 TYR   0.006   0.001   TYR C  97 
 PHE   0.003   0.001   PHE C  39 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 2192)
  covalent geometry    : angle       0.64503 ( 2977)
  SS BOND              : bond        0.00107 (    2)
  SS BOND              : angle       0.41339 (    4)
  hydrogen bonds       : bond        0.03667 (   90)
  hydrogen bonds       : angle       4.11884 (  249)
  Misc. bond           : bond        0.00303 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 ASP cc_start: 0.9188 (p0) cc_final: 0.8815 (p0)
REVERT: C   15 GLN cc_start: 0.9171 (pm20) cc_final: 0.8715 (pm20)
REVERT: C   75 ASP cc_start: 0.8790 (t0) cc_final: 0.8259 (t0)
REVERT: C   78 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8138 (ptpp)
REVERT: C   88 LEU cc_start: 0.9196 (mm) cc_final: 0.8982 (mm)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 0.3508
  time to fit residues: 24.0629
Evaluate side-chains
  65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 18 optimal weight:   20.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.077930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.050063 restraints weight = 4663.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.2543 rms_B_bonded: 2.82
r_work: 0.2429 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2316 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8955
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2196  Z= 0.146
  Angle     :  0.648   9.992   2981  Z= 0.315
  Chirality :  0.043   0.131    345
  Planarity :  0.003   0.020    380
  Dihedral  :  4.571  44.119    339
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 32.14 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.52), residues: 282
  helix:  0.87 (0.72), residues: 59
  sheet:  1.01 (0.56), residues: 87
  loop : -0.04 (0.58), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  21 
 TYR   0.005   0.001   TYR C  97 
 PHE   0.012   0.001   PHE C  29 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 2192)
  covalent geometry    : angle       0.64864 ( 2977)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       0.39086 (    4)
  hydrogen bonds       : bond        0.03385 (   90)
  hydrogen bonds       : angle       4.04276 (  249)
  Misc. bond           : bond        0.00293 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.052 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8921 (tm-30)
REVERT: A  142 ASP cc_start: 0.9192 (p0) cc_final: 0.8845 (p0)
REVERT: C   15 GLN cc_start: 0.9168 (pm20) cc_final: 0.8714 (pm20)
REVERT: C   75 ASP cc_start: 0.8731 (t0) cc_final: 0.8228 (t0)
REVERT: C   78 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8145 (ptpp)
REVERT: C   88 LEU cc_start: 0.9209 (mm) cc_final: 0.8984 (mm)
  outliers start: 5
  outliers final: 5
  residues processed: 65
  average time/residue: 0.3131
  time to fit residues: 20.7935
Evaluate side-chains
  64 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.078313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.050458 restraints weight = 4650.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.2543 rms_B_bonded: 2.81
r_work: 0.2432 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2322 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8940
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   2196  Z= 0.139
  Angle     :  0.660  10.280   2981  Z= 0.321
  Chirality :  0.043   0.130    345
  Planarity :  0.003   0.021    380
  Dihedral  :  4.572  45.232    339
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 30.80 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.52), residues: 282
  helix:  0.89 (0.72), residues: 59
  sheet:  1.05 (0.56), residues: 87
  loop : -0.04 (0.58), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  21 
 TYR   0.006   0.001   TYR C  97 
 PHE   0.002   0.001   PHE C  29 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 2192)
  covalent geometry    : angle       0.66011 ( 2977)
  SS BOND              : bond        0.00100 (    2)
  SS BOND              : angle       0.42195 (    4)
  hydrogen bonds       : bond        0.03287 (   90)
  hydrogen bonds       : angle       4.05134 (  249)
  Misc. bond           : bond        0.00277 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.052 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8920 (tm-30)
REVERT: A  142 ASP cc_start: 0.9180 (p0) cc_final: 0.8824 (p0)
REVERT: C   15 GLN cc_start: 0.9162 (pm20) cc_final: 0.8723 (pm20)
REVERT: C   75 ASP cc_start: 0.8683 (t0) cc_final: 0.8078 (t0)
REVERT: C   78 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8063 (ptpp)
REVERT: C   88 LEU cc_start: 0.9210 (mm) cc_final: 0.8971 (mm)
  outliers start: 6
  outliers final: 5
  residues processed: 65
  average time/residue: 0.3175
  time to fit residues: 21.1114
Evaluate side-chains
  65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0980
   chunk 23 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0970
   chunk 18 optimal weight:   10.0000
   overall best weight:    1.0180

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.079330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.051527 restraints weight = 4804.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.2571 rms_B_bonded: 2.88
r_work: 0.2457 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2344 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8947
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   2196  Z= 0.120
  Angle     :  0.651  10.170   2981  Z= 0.316
  Chirality :  0.043   0.127    345
  Planarity :  0.003   0.022    380
  Dihedral  :  4.465  44.337    339
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 31.70 %
    Favored  : 66.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.53), residues: 282
  helix:  0.98 (0.73), residues: 59
  sheet:  1.04 (0.56), residues: 87
  loop :  0.03 (0.58), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  21 
 TYR   0.004   0.001   TYR C  97 
 PHE   0.012   0.001   PHE C  29 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2192)
  covalent geometry    : angle       0.65154 ( 2977)
  SS BOND              : bond        0.00121 (    2)
  SS BOND              : angle       0.45574 (    4)
  hydrogen bonds       : bond        0.02789 (   90)
  hydrogen bonds       : angle       3.93064 (  249)
  Misc. bond           : bond        0.00239 (    2)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8956 (tm-30)
REVERT: A  142 ASP cc_start: 0.9190 (p0) cc_final: 0.8855 (p0)
REVERT: C   15 GLN cc_start: 0.9146 (pm20) cc_final: 0.8705 (pm20)
REVERT: C   75 ASP cc_start: 0.8691 (t0) cc_final: 0.8082 (t0)
REVERT: C   78 LYS cc_start: 0.8467 (mtmm) cc_final: 0.8021 (ptpp)
REVERT: C   88 LEU cc_start: 0.9244 (mm) cc_final: 0.9004 (mm)
  outliers start: 5
  outliers final: 5
  residues processed: 65
  average time/residue: 0.3839
  time to fit residues: 25.5356
Evaluate side-chains
  65 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  120 CYS
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain C residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.076129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.048225 restraints weight = 4814.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.2486 rms_B_bonded: 2.83
r_work: 0.2371 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2258 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   2196  Z= 0.233
  Angle     :  0.720  10.087   2981  Z= 0.353
  Chirality :  0.046   0.144    345
  Planarity :  0.003   0.018    380
  Dihedral  :  5.048  50.531    339
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 30.80 %
    Favored  : 66.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.52), residues: 282
  helix:  0.77 (0.72), residues: 59
  sheet:  0.88 (0.56), residues: 87
  loop : -0.13 (0.57), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  21 
 TYR   0.008   0.001   TYR C  97 
 PHE   0.003   0.001   PHE C  29 
 TRP   0.007   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 2192)
  covalent geometry    : angle       0.71989 ( 2977)
  SS BOND              : bond        0.00197 (    2)
  SS BOND              : angle       0.48375 (    4)
  hydrogen bonds       : bond        0.04372 (   90)
  hydrogen bonds       : angle       4.22672 (  249)
  Misc. bond           : bond        0.00356 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1233.39 seconds
wall clock time: 21 minutes 43.69 seconds (1303.69 seconds total)