Starting phenix.real_space_refine
on Tue Feb  3 12:41:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9liv_63124/02_2026/9liv_63124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9liv_63124/02_2026/9liv_63124.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9liv_63124/02_2026/9liv_63124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9liv_63124/02_2026/9liv_63124.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9liv_63124/02_2026/9liv_63124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9liv_63124/02_2026/9liv_63124.cif"
  }
  resolution = 3.1
  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=   0.002
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       6      5.16       5
     C    1401      2.51       5
     N     390      2.21       5
     O     471      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 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: 2268
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "AA"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 756
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 6, 'TRANS': 95}
  Restraints were copied for chains:
    AB, AC
  Time building chain proxies: 0.60, per 1000 atoms: 0.26
  Number of scatterers: 2268
  At special positions: 0
  Unit cell: (97.11, 77.19, 36.52, 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       6     16.00
     O     471      8.00
     N     390      7.00
     C    1401      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYSAA  22 " - pdb=" SG  CYSAA  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYSAB  22 " - pdb=" SG  CYSAB  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYSAC  22 " - pdb=" SG  CYSAC  89 " 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: 0.18
  Conformation dependent library (CDL) restraints added in 101.6 milliseconds
  

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  540

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'AB' and resid 17 through 22
      removed outlier: 6.287A  pdb=" N   ARGAA  17 " --> pdb=" O   VALAB  18 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   ILEAB  20 " --> pdb=" O   ARGAA  17 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   THRAA  19 " --> pdb=" O   ILEAB  20 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   CYSAB  22 " --> pdb=" O   THRAA  19 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   SERAA  21 " --> pdb=" O   CYSAB  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'AB' and resid 27 through 29
      removed outlier: 6.778A  pdb=" N   ASNAA  28 " --> pdb=" O   ILEAB  29 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ASNAC  28 " --> pdb=" O   SERAA  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'AB' and resid 32 through 34
    Processing sheet with id=AA4, first strand: chain 'AB' and resid 37 through 38
      removed outlier: 6.350A  pdb=" N   TYRAA  37 " --> pdb=" O   ARGAB  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'AB' and resid 46 through 49
      removed outlier: 9.089A  pdb=" N   LYSAA  46 " --> pdb=" O   VALAB  47 " (cutoff:3.500A)
      removed outlier: 9.833A  pdb=" N   ILEAB  49 " --> pdb=" O   LYSAA  46 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   LEUAA  48 " --> pdb=" O   ILEAB  49 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VALAA  47 " --> pdb=" O   LYSAC  46 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   LEUAC  48 " --> pdb=" O   VALAA  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'AB' and resid 53 through 54
      removed outlier: 6.650A  pdb=" N   ASNAA  53 " --> pdb=" O   TYRAB  54 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'AB' and resid 74 through 80
      removed outlier: 6.305A  pdb=" N   ALAAA  75 " --> pdb=" O   ILEAB  76 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   GLYAB  78 " --> pdb=" O   ALAAA  75 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   SERAA  77 " --> pdb=" O   GLYAB  78 " (cutoff:3.500A)
      removed outlier: 8.481A  pdb=" N   GLNAB  80 " --> pdb=" O   SERAA  77 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEUAA  79 " --> pdb=" O   GLNAB  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'AB' and resid 86 through 88
      removed outlier: 6.485A  pdb=" N   ASPAA  86 " --> pdb=" O   TYRAC  87 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'AB' and resid 106 through 108
      removed outlier: 6.443A  pdb=" N   GLNAA 106 " --> pdb=" O   LEUAB 107 " (cutoff:3.500A)

    23 hydrogen bonds defined for protein.
    69 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: 0.32

  Time building geometry restraints manager: 0.24 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: 756
        1.34 -     1.45: 406
        1.45 -     1.57: 1154
        1.57 -     1.68: 0
        1.68 -     1.80: 6
  Bond restraints: 2322
  Sorted by residual:
  bond pdb=" C   LEUAB  40 "
       pdb=" N   PROAB  41 "
    ideal  model  delta    sigma   weight residual
    1.334  1.317  0.017 8.40e-03 1.42e+04 3.88e+00
  bond pdb=" C   LEUAA  40 "
       pdb=" N   PROAA  41 "
    ideal  model  delta    sigma   weight residual
    1.334  1.317  0.016 8.40e-03 1.42e+04 3.86e+00
  bond pdb=" C   LEUAC  40 "
       pdb=" N   PROAC  41 "
    ideal  model  delta    sigma   weight residual
    1.334  1.318  0.016 8.40e-03 1.42e+04 3.50e+00
  bond pdb=" N   THRAB  13 "
       pdb=" CA  THRAB  13 "
    ideal  model  delta    sigma   weight residual
    1.464  1.451  0.013 9.80e-03 1.04e+04 1.77e+00
  bond pdb=" C   THRAB  13 "
       pdb=" N   PROAB  14 "
    ideal  model  delta    sigma   weight residual
    1.334  1.319  0.015 1.11e-02 8.12e+03 1.77e+00
  ... (remaining 2317 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 2902
        1.40 -     2.81: 222
        2.81 -     4.21: 32
        4.21 -     5.62: 6
        5.62 -     7.02: 6
  Bond angle restraints: 3168
  Sorted by residual:
  angle pdb=" C   SERAA  81 "
        pdb=" N   GLUAA  82 "
        pdb=" CA  GLUAA  82 "
      ideal   model   delta    sigma   weight residual
     122.42  116.68    5.74 1.55e+00 4.16e-01 1.37e+01
  angle pdb=" C   SERAC  81 "
        pdb=" N   GLUAC  82 "
        pdb=" CA  GLUAC  82 "
      ideal   model   delta    sigma   weight residual
     122.42  116.69    5.73 1.55e+00 4.16e-01 1.37e+01
  angle pdb=" C   SERAB  81 "
        pdb=" N   GLUAB  82 "
        pdb=" CA  GLUAB  82 "
      ideal   model   delta    sigma   weight residual
     122.42  116.72    5.70 1.55e+00 4.16e-01 1.35e+01
  angle pdb=" CG1 VALAB  59 "
        pdb=" CB  VALAB  59 "
        pdb=" CG2 VALAB  59 "
      ideal   model   delta    sigma   weight residual
     110.80  103.78    7.02 2.20e+00 2.07e-01 1.02e+01
  angle pdb=" CG1 VALAC  59 "
        pdb=" CB  VALAC  59 "
        pdb=" CG2 VALAC  59 "
      ideal   model   delta    sigma   weight residual
     110.80  103.78    7.02 2.20e+00 2.07e-01 1.02e+01
  ... (remaining 3163 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.05: 1276
       18.05 -    36.10: 83
       36.10 -    54.15: 3
       54.15 -    72.20: 3
       72.20 -    90.25: 3
  Dihedral angle restraints: 1368
    sinusoidal: 507
      harmonic: 861
  Sorted by residual:
  dihedral pdb=" CA  SERAB  81 "
           pdb=" C   SERAB  81 "
           pdb=" N   GLUAB  82 "
           pdb=" CA  GLUAB  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.00   20.00     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  SERAA  81 "
           pdb=" C   SERAA  81 "
           pdb=" N   GLUAA  82 "
           pdb=" CA  GLUAA  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.06   19.94     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  SERAC  81 "
           pdb=" C   SERAC  81 "
           pdb=" N   GLUAC  82 "
           pdb=" CA  GLUAC  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.11   19.89     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 1365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 182
       0.027 -    0.053: 94
       0.053 -    0.080: 23
       0.080 -    0.107: 34
       0.107 -    0.134: 12
  Chirality restraints: 345
  Sorted by residual:
  chirality pdb=" CA  VALAB  47 "
            pdb=" N   VALAB  47 "
            pdb=" C   VALAB  47 "
            pdb=" CB  VALAB  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  VALAA  47 "
            pdb=" N   VALAA  47 "
            pdb=" C   VALAA  47 "
            pdb=" CB  VALAA  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  VALAC  47 "
            pdb=" N   VALAC  47 "
            pdb=" C   VALAC  47 "
            pdb=" CB  VALAC  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 342 not shown)

  Planarity restraints: 417
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLYAB  98 "    0.046 5.00e-02 4.00e+02   6.98e-02 7.81e+00
        pdb=" N   PROAB  99 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PROAB  99 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PROAB  99 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLYAA  98 "    0.046 5.00e-02 4.00e+02   6.96e-02 7.76e+00
        pdb=" N   PROAA  99 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PROAA  99 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PROAA  99 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLYAC  98 "    0.046 5.00e-02 4.00e+02   6.95e-02 7.73e+00
        pdb=" N   PROAC  99 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PROAC  99 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PROAC  99 "    0.038 5.00e-02 4.00e+02
  ... (remaining 414 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 716
        2.83 -     3.35: 1910
        3.35 -     3.86: 3787
        3.86 -     4.38: 4275
        4.38 -     4.90: 8162
  Nonbonded interactions: 18850
  Sorted by model distance:
  nonbonded pdb=" O   SERAB  68 "
            pdb=" OG  SERAB  68 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   SERAA  68 "
            pdb=" OG  SERAA  68 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   SERAC  68 "
            pdb=" OG  SERAC  68 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" N   GLUAA  82 "
            pdb=" O   GLUAC  82 "
     model   vdw
     2.443 3.120
  nonbonded pdb=" O   GLUAA  82 "
            pdb=" N   GLUAB  82 "
     model   vdw
     2.489 3.120
  ... (remaining 18845 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'AA'
  selection = chain 'AB'
  selection = chain 'AC'
}

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:             4.310
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.740
  Find NCS groups from input model:        0.020
  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:1.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
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      :  0.007   0.036   2325  Z= 0.331
  Angle     :  0.841   7.022   3174  Z= 0.512
  Chirality :  0.047   0.134    345
  Planarity :  0.010   0.070    417
  Dihedral  : 11.863  90.251    819
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.51 (0.27), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.19 (0.20), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARGAC  58 
 TYR   0.015   0.002   TYRAB  88 
 PHE   0.005   0.002   PHEAA 101 
 TRP   0.005   0.001   TRPAC  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 ( 2322)
  covalent geometry    : angle       0.84110 ( 3168)
  SS BOND              : bond        0.00529 (    3)
  SS BOND              : angle       0.88597 (    6)
  hydrogen bonds       : bond        0.15960 (   23)
  hydrogen bonds       : angle       7.37504 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.083 
Fit side-chains
REVERT: AA   55 ARG cc_start: 0.7736 (ttm170) cc_final: 0.7492 (ttp-170)
REVERT: AC   62 ARG cc_start: 0.6442 (ptp-170) cc_final: 0.4750 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0869
  time to fit residues: 4.9223
Evaluate side-chains
  43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0980
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
AA  35 ASN
AA  80 GLN
AA 106 GLN
AB  35 ASN
AB  80 GLN
AB 106 GLN
AC  80 GLN
AC 106 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.141489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.120617 restraints weight = 3171.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 2.81
r_work: 0.3848 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2325  Z= 0.103
  Angle     :  0.503   5.116   3174  Z= 0.267
  Chirality :  0.042   0.120    345
  Planarity :  0.008   0.070    417
  Dihedral  :  4.271  17.205    336
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.04 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -5.14 (0.30), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.91 (0.23), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAC  38 
 TYR   0.017   0.001   TYRAA  88 
 PHE   0.006   0.001   PHEAB 101 
 TRP   0.004   0.001   TRPAB  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2322)
  covalent geometry    : angle       0.50282 ( 3168)
  SS BOND              : bond        0.00111 (    3)
  SS BOND              : angle       0.48000 (    6)
  hydrogen bonds       : bond        0.02473 (   23)
  hydrogen bonds       : angle       5.63135 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.081 
Fit side-chains
REVERT: AC   62 ARG cc_start: 0.6454 (ptp-170) cc_final: 0.4688 (tpm170)
REVERT: AC   82 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6833 (tt0)
  outliers start: 6
  outliers final: 4
  residues processed: 45
  average time/residue: 0.0822
  time to fit residues: 4.2246
Evaluate side-chains
  44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AA residue   82 GLU
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 26 optimal weight:    0.4980
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0870
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.3164

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.138197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.117262 restraints weight = 3265.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 2.88
r_work: 0.3805 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2325  Z= 0.140
  Angle     :  0.502   5.318   3174  Z= 0.267
  Chirality :  0.042   0.123    345
  Planarity :  0.007   0.061    417
  Dihedral  :  4.203  17.564    336
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.84 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.89 (0.32), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.25), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAC  38 
 TYR   0.019   0.002   TYRAA  88 
 PHE   0.005   0.001   PHEAB 101 
 TRP   0.005   0.001   TRPAB  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 2322)
  covalent geometry    : angle       0.50160 ( 3168)
  SS BOND              : bond        0.00278 (    3)
  SS BOND              : angle       0.55581 (    6)
  hydrogen bonds       : bond        0.02188 (   23)
  hydrogen bonds       : angle       5.16942 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.054 
Fit side-chains
REVERT: AC   62 ARG cc_start: 0.6398 (ptp-170) cc_final: 0.4570 (tpm170)
REVERT: AC   82 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6959 (mp0)
  outliers start: 3
  outliers final: 3
  residues processed: 39
  average time/residue: 0.0700
  time to fit residues: 3.0893
Evaluate side-chains
  42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
AA  80 GLN
AB  80 GLN
AC  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.141305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.120577 restraints weight = 3186.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 2.83
r_work: 0.3858 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2325  Z= 0.107
  Angle     :  0.474   4.962   3174  Z= 0.250
  Chirality :  0.042   0.119    345
  Planarity :  0.007   0.064    417
  Dihedral  :  3.920  16.860    336
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.05 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.70 (0.34), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.26), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAC  38 
 TYR   0.018   0.002   TYRAA  88 
 PHE   0.005   0.001   PHEAB 101 
 TRP   0.004   0.001   TRPAA  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 2322)
  covalent geometry    : angle       0.47413 ( 3168)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       0.39965 (    6)
  hydrogen bonds       : bond        0.01977 (   23)
  hydrogen bonds       : angle       4.98935 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.051 
Fit side-chains
REVERT: AA   62 ARG cc_start: 0.6783 (ptm-80) cc_final: 0.6539 (ptm-80)
REVERT: AC   62 ARG cc_start: 0.6400 (ptp-170) cc_final: 0.4604 (tpm170)
REVERT: AC   82 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7153 (tt0)
  outliers start: 5
  outliers final: 5
  residues processed: 39
  average time/residue: 0.0550
  time to fit residues: 2.4528
Evaluate side-chains
  44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AA residue   61 ASP
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Chi-restraints excluded: chain AC residue   64 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 15 optimal weight:    0.0000
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 20 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
AC  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.144523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.123667 restraints weight = 3165.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 2.85
r_work: 0.3909 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2325  Z= 0.092
  Angle     :  0.458   4.802   3174  Z= 0.240
  Chirality :  0.041   0.123    345
  Planarity :  0.007   0.060    417
  Dihedral  :  3.660  15.474    336
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 14.46 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.60 (0.35), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB  58 
 TYR   0.014   0.001   TYRAA  88 
 PHE   0.007   0.001   PHEAB 101 
 TRP   0.003   0.001   TRPAB  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 2322)
  covalent geometry    : angle       0.45773 ( 3168)
  SS BOND              : bond        0.00120 (    3)
  SS BOND              : angle       0.32943 (    6)
  hydrogen bonds       : bond        0.01805 (   23)
  hydrogen bonds       : angle       4.78900 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.082 
Fit side-chains
REVERT: AA   62 ARG cc_start: 0.6776 (ptm-80) cc_final: 0.6519 (ptm-80)
REVERT: AC   62 ARG cc_start: 0.6432 (ptp-170) cc_final: 0.4630 (tpm170)
REVERT: AC   82 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7127 (tt0)
  outliers start: 3
  outliers final: 3
  residues processed: 42
  average time/residue: 0.0867
  time to fit residues: 4.1378
Evaluate side-chains
  43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
AA  80 GLN
AB  80 GLN
AC  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.136753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.115843 restraints weight = 3280.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 2.86
r_work: 0.3786 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2325  Z= 0.169
  Angle     :  0.505   5.016   3174  Z= 0.270
  Chirality :  0.042   0.127    345
  Planarity :  0.007   0.061    417
  Dihedral  :  4.108  16.570    336
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.86 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.59 (0.35), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.26), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB  55 
 TYR   0.019   0.002   TYRAA  88 
 PHE   0.004   0.001   PHEAB  63 
 TRP   0.007   0.001   TRPAA  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 2322)
  covalent geometry    : angle       0.50483 ( 3168)
  SS BOND              : bond        0.00356 (    3)
  SS BOND              : angle       0.61659 (    6)
  hydrogen bonds       : bond        0.02174 (   23)
  hydrogen bonds       : angle       4.72061 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.055 
Fit side-chains
REVERT: AC   62 ARG cc_start: 0.6426 (ptp-170) cc_final: 0.4538 (tpm170)
REVERT: AC   82 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7217 (mp0)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0504
  time to fit residues: 2.2268
Evaluate side-chains
  41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Chi-restraints excluded: chain AC residue   39 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0070
   chunk 19 optimal weight:    0.0050
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.2016

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

Flipped N/Q/H residues before XYZ refinement:
AC  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.139343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.118463 restraints weight = 3235.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 2.86
r_work: 0.3829 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2325  Z= 0.128
  Angle     :  0.483   4.770   3174  Z= 0.256
  Chirality :  0.042   0.126    345
  Planarity :  0.007   0.062    417
  Dihedral  :  3.944  16.771    336
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.26 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.53 (0.35), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.45 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAA  38 
 TYR   0.020   0.002   TYRAA  88 
 PHE   0.004   0.001   PHEAB 101 
 TRP   0.004   0.001   TRPAA  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2322)
  covalent geometry    : angle       0.48260 ( 3168)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       0.49326 (    6)
  hydrogen bonds       : bond        0.02055 (   23)
  hydrogen bonds       : angle       4.69226 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.052 
Fit side-chains
REVERT: AA   62 ARG cc_start: 0.6769 (ptm-80) cc_final: 0.6546 (ptm-80)
REVERT: AC   62 ARG cc_start: 0.6413 (ptp-170) cc_final: 0.4534 (tpm170)
  outliers start: 4
  outliers final: 4
  residues processed: 39
  average time/residue: 0.0532
  time to fit residues: 2.4011
Evaluate side-chains
  42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Chi-restraints excluded: chain AC residue   61 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
AA  80 GLN
AC  80 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.138648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.118231 restraints weight = 3229.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 2.83
r_work: 0.3826 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2325  Z= 0.140
  Angle     :  0.489   5.231   3174  Z= 0.260
  Chirality :  0.042   0.127    345
  Planarity :  0.007   0.061    417
  Dihedral  :  3.997  16.107    336
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.26 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.54 (0.35), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.46 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB  38 
 TYR   0.021   0.002   TYRAA  88 
 PHE   0.004   0.001   PHEAB 101 
 TRP   0.005   0.001   TRPAC  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2322)
  covalent geometry    : angle       0.48911 ( 3168)
  SS BOND              : bond        0.00275 (    3)
  SS BOND              : angle       0.56355 (    6)
  hydrogen bonds       : bond        0.02083 (   23)
  hydrogen bonds       : angle       4.66465 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.065 
Fit side-chains
REVERT: AA   62 ARG cc_start: 0.6785 (ptm-80) cc_final: 0.6544 (ptm-80)
REVERT: AC   62 ARG cc_start: 0.6392 (ptp-170) cc_final: 0.4505 (tpm170)
  outliers start: 5
  outliers final: 5
  residues processed: 37
  average time/residue: 0.0485
  time to fit residues: 2.0787
Evaluate side-chains
  40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Chi-restraints excluded: chain AC residue   39 GLN
Chi-restraints excluded: chain AC residue   61 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
AC  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.140163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.120003 restraints weight = 3243.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.83
r_work: 0.3849 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2325  Z= 0.118
  Angle     :  0.477   5.257   3174  Z= 0.252
  Chirality :  0.042   0.132    345
  Planarity :  0.007   0.062    417
  Dihedral  :  3.852  15.926    336
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.66 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.52 (0.36), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.44 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB  38 
 TYR   0.020   0.002   TYRAA  88 
 PHE   0.005   0.001   PHEAB 101 
 TRP   0.004   0.001   TRPAC  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 2322)
  covalent geometry    : angle       0.47710 ( 3168)
  SS BOND              : bond        0.00197 (    3)
  SS BOND              : angle       0.45065 (    6)
  hydrogen bonds       : bond        0.01992 (   23)
  hydrogen bonds       : angle       4.60346 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.098 
Fit side-chains
REVERT: AA   62 ARG cc_start: 0.6780 (ptm-80) cc_final: 0.6532 (ptm-80)
REVERT: AC   62 ARG cc_start: 0.6403 (ptp-170) cc_final: 0.4516 (tpm170)
  outliers start: 5
  outliers final: 5
  residues processed: 41
  average time/residue: 0.0519
  time to fit residues: 2.4827
Evaluate side-chains
  42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Chi-restraints excluded: chain AC residue   39 GLN
Chi-restraints excluded: chain AC residue   61 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
AA  80 GLN
AC  80 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.139187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.119710 restraints weight = 3259.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 2.67
r_work: 0.3798 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2325  Z= 0.163
  Angle     :  0.505   5.431   3174  Z= 0.269
  Chirality :  0.043   0.135    345
  Planarity :  0.007   0.059    417
  Dihedral  :  4.048  15.929    336
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.06 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.57 (0.36), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB  38 
 TYR   0.025   0.002   TYRAA  88 
 PHE   0.004   0.001   PHEAB 101 
 TRP   0.006   0.001   TRPAC  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 2322)
  covalent geometry    : angle       0.50456 ( 3168)
  SS BOND              : bond        0.00336 (    3)
  SS BOND              : angle       0.66088 (    6)
  hydrogen bonds       : bond        0.02116 (   23)
  hydrogen bonds       : angle       4.65628 (   69)

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

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

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  600 Ramachandran restraints generated.
    300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.050 
Fit side-chains
REVERT: AA   62 ARG cc_start: 0.7030 (ptm-80) cc_final: 0.6772 (ptm-80)
REVERT: AC   62 ARG cc_start: 0.6638 (ptp-170) cc_final: 0.4640 (tpm170)
  outliers start: 5
  outliers final: 5
  residues processed: 38
  average time/residue: 0.0478
  time to fit residues: 2.1077
Evaluate side-chains
  41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue   13 THR
Chi-restraints excluded: chain AB residue   13 THR
Chi-restraints excluded: chain AC residue   13 THR
Chi-restraints excluded: chain AC residue   39 GLN
Chi-restraints excluded: chain AC residue   61 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 14 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0170
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0270
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
AC  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.142418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.123542 restraints weight = 3319.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 2.74
r_work: 0.3882 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3772 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   2325  Z= 0.088
  Angle     :  0.463   5.329   3174  Z= 0.241
  Chirality :  0.042   0.131    345
  Planarity :  0.007   0.063    417
  Dihedral  :  3.533  14.604    336
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.06 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.48 (0.36), residues: 300
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAA  38 
 TYR   0.016   0.001   TYRAA  88 
 PHE   0.008   0.001   PHEAB 101 
 TRP   0.003   0.001   TRPAB  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 2322)
  covalent geometry    : angle       0.46324 ( 3168)
  SS BOND              : bond        0.00047 (    3)
  SS BOND              : angle       0.27988 (    6)
  hydrogen bonds       : bond        0.01907 (   23)
  hydrogen bonds       : angle       4.56475 (   69)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 669.33 seconds
wall clock time: 12 minutes 7.31 seconds (727.31 seconds total)