Starting phenix.real_space_refine
on Tue Aug  4 11:43:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pef_71560/08_2026/9pef_71560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pef_71560/08_2026/9pef_71560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pef_71560/08_2026/9pef_71560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pef_71560/08_2026/9pef_71560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pef_71560/08_2026/9pef_71560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pef_71560/08_2026/9pef_71560.cif"
  }
  resolution = 3.7
  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=   0.007
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: 3
    Type Number    sf(0)   Gaussians
     C     456      2.51       5
     N      88      2.21       5
     O      88      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 632
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "J"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "J"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "K"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "K"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "L"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "M"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "N"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "N"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "O"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "O"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'TRANS': 7}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.14, per 1000 atoms: 0.22
  Number of scatterers: 632
  At special positions: 0
  Unit cell: (55.61, 64.74, 40.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O      88      8.00
     N      88      7.00
     C     456      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=8, symmetry=0
  Number of additional bonds: simple=8, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.08
  Conformation dependent library (CDL) restraints added in 13.5 milliseconds
  

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  112

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 4 sheets defined
      0.0% alpha, 40.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.01
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'J' and resid 3 through 5
      removed outlier: 6.229A  pdb=" N   GLU J   4 " --> pdb=" O   PHE B   5 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'K' and resid 2 through 6
    Processing sheet with id=AA3, first strand: chain 'M' and resid 2 through 6
    Processing sheet with id=AA4, first strand: chain 'O' and resid 3 through 6
      removed outlier: 6.331A  pdb=" N   GLU O   4 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    12 hydrogen bonds defined for protein.
    24 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: 0.03

  Time building geometry restraints manager: 0.06 seconds

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

  Histogram of bond lengths:
        1.18 -     1.25: 80
        1.25 -     1.32: 8
        1.32 -     1.39: 240
        1.39 -     1.46: 78
        1.46 -     1.53: 242
  Bond restraints: 648
  Sorted by residual:
  bond pdb=" C   PHE N   7 "
       pdb=" N   GLY N   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.24e+01
  bond pdb=" C   PHE J   7 "
       pdb=" N   GLY J   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.18e+01
  bond pdb=" C   PHE K   7 "
       pdb=" N   GLY K   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.17e+01
  bond pdb=" C   PHE O   7 "
       pdb=" N   GLY O   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.17e+01
  bond pdb=" C   PHE B   7 "
       pdb=" N   GLY B   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.16e+01
  ... (remaining 643 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.60: 786
        5.60 -    11.20: 32
       11.20 -    16.81: 5
       16.81 -    22.41: 3
       22.41 -    28.01: 6
  Bond angle restraints: 832
  Sorted by residual:
  angle pdb=" O   PHE K   7 "
        pdb=" C   PHE K   7 "
        pdb=" N   GLY K   8 "
      ideal   model   delta    sigma   weight residual
     122.59   98.38   24.21 1.33e+00 5.65e-01 3.31e+02
  angle pdb=" C   PHE M   7 "
        pdb=" N   GLY M   8 "
        pdb=" CA  GLY M   8 "
      ideal   model   delta    sigma   weight residual
     121.70  149.71  -28.01 1.80e+00 3.09e-01 2.42e+02
  angle pdb=" C   PHE B   7 "
        pdb=" N   GLY B   8 "
        pdb=" CA  GLY B   8 "
      ideal   model   delta    sigma   weight residual
     121.70  145.99  -24.29 1.80e+00 3.09e-01 1.82e+02
  angle pdb=" C   PHE N   7 "
        pdb=" N   GLY N   8 "
        pdb=" CA  GLY N   8 "
      ideal   model   delta    sigma   weight residual
     121.70   97.60   24.10 1.80e+00 3.09e-01 1.79e+02
  angle pdb=" O   PHE M   7 "
        pdb=" C   PHE M   7 "
        pdb=" N   GLY M   8 "
      ideal   model   delta    sigma   weight residual
     122.34   98.54   23.80 1.80e+00 3.09e-01 1.75e+02
  ... (remaining 827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    35.99: 316
       35.99 -    71.98: 12
       71.98 -   107.97: 0
      107.97 -   143.96: 0
      143.96 -   179.95: 8
  Dihedral angle restraints: 336
    sinusoidal: 168
      harmonic: 168
  Sorted by residual:
  dihedral pdb=" CH3 ACE L   0 "
           pdb=" C   ACE L   0 "
           pdb=" N   PHE L   1 "
           pdb=" CA  PHE L   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00   -0.05 -179.95     1      5.00e+00 4.00e-02 7.68e+02
  dihedral pdb=" CH3 ACE B   0 "
           pdb=" C   ACE B   0 "
           pdb=" N   PHE B   1 "
           pdb=" CA  PHE B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00   -0.16 -179.84     1      5.00e+00 4.00e-02 7.68e+02
  dihedral pdb=" CH3 ACE O   0 "
           pdb=" C   ACE O   0 "
           pdb=" N   PHE O   1 "
           pdb=" CA  PHE O   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00   -0.24 -179.76     1      5.00e+00 4.00e-02 7.68e+02
  ... (remaining 333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.011: 12
       0.011 -    0.021: 15
       0.021 -    0.032: 16
       0.032 -    0.042: 8
       0.042 -    0.052: 5
  Chirality restraints: 56
  Sorted by residual:
  chirality pdb=" CA  LYS L   6 "
            pdb=" N   LYS L   6 "
            pdb=" C   LYS L   6 "
            pdb=" CB  LYS L   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.56   -0.05 2.00e-01 2.50e+01 6.88e-02
  chirality pdb=" CA  PHE C   1 "
            pdb=" N   PHE C   1 "
            pdb=" C   PHE C   1 "
            pdb=" CB  PHE C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.46    0.05 2.00e-01 2.50e+01 5.36e-02
  chirality pdb=" CA  PHE N   1 "
            pdb=" N   PHE N   1 "
            pdb=" C   PHE N   1 "
            pdb=" CB  PHE N   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.47    0.05 2.00e-01 2.50e+01 5.14e-02
  ... (remaining 53 not shown)

  Planarity restraints: 104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE L   7 "   -0.063 2.00e-02 2.50e+03   1.06e-01 1.13e+02
        pdb=" C   PHE L   7 "    0.184 2.00e-02 2.50e+03
        pdb=" O   PHE L   7 "   -0.064 2.00e-02 2.50e+03
        pdb=" N   GLY L   8 "   -0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE K   7 "   -0.048 2.00e-02 2.50e+03   7.58e-02 5.74e+01
        pdb=" C   PHE K   7 "    0.131 2.00e-02 2.50e+03
        pdb=" O   PHE K   7 "   -0.040 2.00e-02 2.50e+03
        pdb=" N   GLY K   8 "   -0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE J   7 "   -0.037 2.00e-02 2.50e+03   6.58e-02 4.33e+01
        pdb=" C   PHE J   7 "    0.114 2.00e-02 2.50e+03
        pdb=" O   PHE J   7 "   -0.040 2.00e-02 2.50e+03
        pdb=" N   GLY J   8 "   -0.036 2.00e-02 2.50e+03
  ... (remaining 101 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 328
        3.01 -     3.48: 474
        3.48 -     3.95: 750
        3.95 -     4.43: 921
        4.43 -     4.90: 1465
  Nonbonded interactions: 3938
  Sorted by model distance:
  nonbonded pdb=" O   PHE N   7 "
            pdb=" CA  GLY N   8 "
     model   vdw
     2.535 2.752
  nonbonded pdb=" O   PHE J   7 "
            pdb=" CA  GLY J   8 "
     model   vdw
     2.570 2.752
  nonbonded pdb=" O   PHE L   7 "
            pdb=" CA  GLY L   8 "
     model   vdw
     2.621 2.752
  nonbonded pdb=" CG  LYS J   2 "
            pdb=" NZ  LYS J   2 "
     model   vdw
     2.638 2.816
  nonbonded pdb=" CG  LYS B   2 "
            pdb=" NZ  LYS B   2 "
     model   vdw
     2.639 2.816
  ... (remaining 3933 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.680
  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:             0.000
  Extract box with map and model:          0.020
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     1.770
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
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      :  0.020   0.135    656  Z= 1.172
  Angle     :  3.129  28.011    832  Z= 1.824
  Chirality :  0.026   0.052     56
  Planarity :  0.015   0.106    104
  Dihedral  : 37.697 179.950    224
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 12.50 %
    Favored  : 85.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.07 %
    Favored  : 83.93 %
  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: -4.60 (0.81), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.62), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE M   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.02011 /  1.15 (  648)
  covalent geometry    : angle       3.12874 /  1.82 (  832)
  hydrogen bonds       : bond        0.25559 / 13.12 (   12)
  hydrogen bonds       : angle      21.15051 / 11.33 (   24)
  Misc. bond           : bond        0.02164 /  1.15 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  4 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 4
  time to evaluate  : 0.014 
Fit side-chains
REVERT: N    2 LYS cc_start: 0.7664 (mttt) cc_final: 0.6824 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1173
  time to fit residues: 0.4986
Evaluate side-chains
  3 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 3
  time to evaluate  : 0.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.5980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.079103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.068445 restraints weight = 1710.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.069517 restraints weight = 1227.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.070364 restraints weight = 981.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.070959 restraints weight = 822.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.071235 restraints weight = 719.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8821
moved from start:          0.9211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.137   0.399    656  Z= 5.775
  Angle     :  4.471  29.583    832  Z= 2.436
  Chirality :  0.344   0.886     56
  Planarity :  0.029   0.069    104
  Dihedral  : 12.793  28.651     72
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 152.90
  Ramachandran Plot:
    Outliers : 22.92 %
    Allowed  : 52.08 %
    Favored  : 25.00 %
  Rotamer:
    Outliers : 28.57 %
    Allowed  : 30.36 %
    Favored  : 41.07 %
  Cbeta Deviations : 25.00 %
  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: -9.93 (0.44), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.57 (0.33), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.119   0.022   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13830 /  5.81 (  648)
  covalent geometry    : angle       4.47099 /  2.44 (  832)
  hydrogen bonds       : bond        0.41694 / 21.70 (   12)
  hydrogen bonds       : angle      22.24458 / 11.70 (   24)
  Misc. bond           : bond        0.00423 /  0.22 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 14
  time to evaluate  : 0.018 
Fit side-chains
REVERT: J    4 GLU cc_start: 0.8966 (tt0) cc_final: 0.7855 (tm-30)
REVERT: M    6 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8307 (mtmt)
REVERT: N    2 LYS cc_start: 0.8272 (mttt) cc_final: 0.7932 (mttm)
  outliers start: 16
  outliers final: 11
  residues processed: 28
  average time/residue: 0.0569
  time to fit residues: 1.6659
Evaluate side-chains
  26 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 14
  time to evaluate  : 0.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain J residue    7 PHE
Chi-restraints excluded: chain K residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain M residue    6 LYS
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain C residue    7 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.079318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.068231 restraints weight = 1821.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.069472 restraints weight = 1264.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.070336 restraints weight = 979.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.071001 restraints weight = 816.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.071443 restraints weight = 705.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.9653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.137   0.401    656  Z= 5.743
  Angle     :  4.559  29.693    832  Z= 2.489
  Chirality :  0.345   0.892     56
  Planarity :  0.028   0.054    104
  Dihedral  : 13.689  28.116     72
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 156.05
  Ramachandran Plot:
    Outliers : 16.67 %
    Allowed  : 60.42 %
    Favored  : 22.92 %
  Rotamer:
    Outliers : 33.93 %
    Allowed  : 30.36 %
    Favored  : 35.71 %
  Cbeta Deviations : 30.36 %
  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: -10.01 (0.40), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.63 (0.30), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.115   0.018   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13746 /  5.78 (  648)
  covalent geometry    : angle       4.55923 /  2.49 (  832)
  hydrogen bonds       : bond        0.40951 / 21.32 (   12)
  hydrogen bonds       : angle      21.55806 / 11.29 (   24)
  Misc. bond           : bond        0.00337 /  0.17 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 14
  time to evaluate  : 0.018 
Fit side-chains
  outliers start: 19
  outliers final: 14
  residues processed: 30
  average time/residue: 0.0613
  time to fit residues: 1.9147
Evaluate side-chains
  28 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 14
  time to evaluate  : 0.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    3 PHE
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain O residue    6 LYS
Chi-restraints excluded: chain C residue    1 PHE
Chi-restraints excluded: chain C residue    3 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.077138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.065344 restraints weight = 1991.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.066531 restraints weight = 1446.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.067473 restraints weight = 1153.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.068002 restraints weight = 966.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.068225 restraints weight = 866.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.9767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.137   0.402    656  Z= 5.746
  Angle     :  4.531  26.211    832  Z= 2.486
  Chirality :  0.340   0.803     56
  Planarity :  0.027   0.054    104
  Dihedral  : 13.945  32.255     72
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 157.68
  Ramachandran Plot:
    Outliers : 14.58 %
    Allowed  : 66.67 %
    Favored  : 18.75 %
  Rotamer:
    Outliers : 39.29 %
    Allowed  : 28.57 %
    Favored  : 32.14 %
  Cbeta Deviations : 28.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.79 %

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: -10.05 (0.38), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.65 (0.29), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.115   0.017   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13752 /  5.78 (  648)
  covalent geometry    : angle       4.53061 /  2.49 (  832)
  hydrogen bonds       : bond        0.41437 / 21.51 (   12)
  hydrogen bonds       : angle      21.51437 / 11.28 (   24)
  Misc. bond           : bond        0.00344 /  0.18 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 14
  time to evaluate  : 0.016 
Fit side-chains
REVERT: B    2 LYS cc_start: 0.8950 (tttm) cc_final: 0.7874 (tmtt)
REVERT: K    1 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8517 (t80)
REVERT: L    6 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7647 (tttp)
  outliers start: 22
  outliers final: 16
  residues processed: 33
  average time/residue: 0.0595
  time to fit residues: 2.0904
Evaluate side-chains
  32 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 14
  time to evaluate  : 0.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    3 PHE
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain J residue    7 PHE
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain K residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain O residue    6 LYS
Chi-restraints excluded: chain C residue    1 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.076225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.065193 restraints weight = 1671.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.066144 restraints weight = 1273.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.066926 restraints weight = 1055.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.067456 restraints weight = 904.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.067482 restraints weight = 810.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.9801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.137   0.401    656  Z= 5.746
  Angle     :  4.536  26.219    832  Z= 2.490
  Chirality :  0.340   0.806     56
  Planarity :  0.027   0.056    104
  Dihedral  : 14.138  33.828     72
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 157.68
  Ramachandran Plot:
    Outliers : 14.58 %
    Allowed  : 62.50 %
    Favored  : 22.92 %
  Rotamer:
    Outliers : 41.07 %
    Allowed  : 30.36 %
    Favored  : 28.57 %
  Cbeta Deviations : 28.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.79 %

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: -10.01 (0.37), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.62 (0.29), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.114   0.017   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13753 /  5.78 (  648)
  covalent geometry    : angle       4.53586 /  2.49 (  832)
  hydrogen bonds       : bond        0.41627 / 21.59 (   12)
  hydrogen bonds       : angle      21.53795 / 11.29 (   24)
  Misc. bond           : bond        0.00355 /  0.18 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 15
  time to evaluate  : 0.015 
Fit side-chains
REVERT: B    2 LYS cc_start: 0.8934 (tttm) cc_final: 0.7815 (tmtt)
REVERT: K    1 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8527 (t80)
REVERT: L    4 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7405 (tt0)
REVERT: L    6 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7618 (tttp)
  outliers start: 23
  outliers final: 17
  residues processed: 34
  average time/residue: 0.0602
  time to fit residues: 2.1325
Evaluate side-chains
  35 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 15
  time to evaluate  : 0.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    3 PHE
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain J residue    7 PHE
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain B residue    6 LYS
Chi-restraints excluded: chain K residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    4 GLU
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain O residue    6 LYS
Chi-restraints excluded: chain C residue    1 PHE
Chi-restraints excluded: chain C residue    3 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

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 = 0.078047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.066633 restraints weight = 2341.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.067869 restraints weight = 1627.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.068812 restraints weight = 1254.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.069279 restraints weight = 1042.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.069822 restraints weight = 933.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.9822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.403    656  Z= 5.732
  Angle     :  4.525  26.250    832  Z= 2.490
  Chirality :  0.339   0.805     56
  Planarity :  0.027   0.053    104
  Dihedral  : 14.215  35.173     72
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 157.68
  Ramachandran Plot:
    Outliers : 14.58 %
    Allowed  : 62.50 %
    Favored  : 22.92 %
  Rotamer:
    Outliers : 44.64 %
    Allowed  : 28.57 %
    Favored  : 26.79 %
  Cbeta Deviations : 28.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.79 %

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: -9.96 (0.39), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.59 (0.30), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.115   0.017   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13712 /  5.77 (  648)
  covalent geometry    : angle       4.52471 /  2.49 (  832)
  hydrogen bonds       : bond        0.41862 / 21.70 (   12)
  hydrogen bonds       : angle      21.49780 / 11.29 (   24)
  Misc. bond           : bond        0.00355 /  0.18 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 15
  time to evaluate  : 0.017 
Fit side-chains
REVERT: B    2 LYS cc_start: 0.8951 (tttm) cc_final: 0.7810 (tmtt)
REVERT: B    3 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8389 (m-10)
REVERT: K    1 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8523 (t80)
REVERT: L    6 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7717 (tttp)
REVERT: M    6 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8347 (mtmt)
  outliers start: 25
  outliers final: 18
  residues processed: 35
  average time/residue: 0.0696
  time to fit residues: 2.5503
Evaluate side-chains
  37 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 15
  time to evaluate  : 0.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    3 PHE
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain J residue    7 PHE
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain B residue    6 LYS
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain K residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain M residue    6 LYS
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain O residue    6 LYS
Chi-restraints excluded: chain C residue    1 PHE
Chi-restraints excluded: chain C residue    3 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.078175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.067592 restraints weight = 1841.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.068576 restraints weight = 1368.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.069364 restraints weight = 1114.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.069959 restraints weight = 955.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.070037 restraints weight = 844.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.9851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.404    656  Z= 5.735
  Angle     :  4.529  26.182    832  Z= 2.491
  Chirality :  0.338   0.803     56
  Planarity :  0.027   0.053    104
  Dihedral  : 14.309  35.218     72
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 155.23
  Ramachandran Plot:
    Outliers : 16.67 %
    Allowed  : 60.42 %
    Favored  : 22.92 %
  Rotamer:
    Outliers : 42.86 %
    Allowed  : 33.93 %
    Favored  : 23.21 %
  Cbeta Deviations : 26.79 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.79 %

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: -9.82 (0.48), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.48 (0.36), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.116   0.018   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13720 /  5.77 (  648)
  covalent geometry    : angle       4.52870 /  2.49 (  832)
  hydrogen bonds       : bond        0.41746 / 21.63 (   12)
  hydrogen bonds       : angle      21.45219 / 11.26 (   24)
  Misc. bond           : bond        0.00354 /  0.18 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 15
  time to evaluate  : 0.030 
Fit side-chains
REVERT: B    2 LYS cc_start: 0.8955 (tttm) cc_final: 0.7828 (tmtt)
REVERT: B    3 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8369 (m-10)
REVERT: K    1 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8510 (t80)
REVERT: L    6 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7744 (tttp)
REVERT: M    6 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8357 (mtmt)
  outliers start: 24
  outliers final: 18
  residues processed: 35
  average time/residue: 0.0953
  time to fit residues: 3.4630
Evaluate side-chains
  37 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 15
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    3 PHE
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain J residue    7 PHE
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain B residue    6 LYS
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain K residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain M residue    6 LYS
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain O residue    6 LYS
Chi-restraints excluded: chain C residue    1 PHE
Chi-restraints excluded: chain C residue    3 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.075118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.063821 restraints weight = 1691.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.064813 restraints weight = 1296.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.065445 restraints weight = 1076.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.065703 restraints weight = 945.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.066227 restraints weight = 886.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start:          0.9998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.402    656  Z= 5.733
  Angle     :  4.495  26.278    832  Z= 2.477
  Chirality :  0.340   0.803     56
  Planarity :  0.028   0.053    104
  Dihedral  : 14.399  36.283     72
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 155.23
  Ramachandran Plot:
    Outliers : 16.67 %
    Allowed  : 60.42 %
    Favored  : 22.92 %
  Rotamer:
    Outliers : 41.07 %
    Allowed  : 33.93 %
    Favored  : 25.00 %
  Cbeta Deviations : 28.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.79 %

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: -9.62 (0.62), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.33 (0.47), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.114   0.018   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13711 /  5.77 (  648)
  covalent geometry    : angle       4.49518 /  2.48 (  832)
  hydrogen bonds       : bond        0.42436 / 21.97 (   12)
  hydrogen bonds       : angle      21.67783 / 11.42 (   24)
  Misc. bond           : bond        0.00352 /  0.18 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 15
  time to evaluate  : 0.016 
Fit side-chains
REVERT: B    2 LYS cc_start: 0.8930 (tttm) cc_final: 0.7790 (tmtt)
REVERT: B    3 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8340 (m-10)
REVERT: K    1 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8512 (t80)
REVERT: L    6 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7681 (tttp)
REVERT: M    6 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8373 (mtmt)
  outliers start: 23
  outliers final: 18
  residues processed: 34
  average time/residue: 0.0610
  time to fit residues: 2.1618
Evaluate side-chains
  37 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 15
  time to evaluate  : 0.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    3 PHE
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain J residue    7 PHE
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain B residue    6 LYS
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain K residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain M residue    6 LYS
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain O residue    6 LYS
Chi-restraints excluded: chain C residue    1 PHE
Chi-restraints excluded: chain C residue    3 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.075223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.063730 restraints weight = 1824.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.064794 restraints weight = 1363.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.065560 restraints weight = 1115.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.065908 restraints weight = 955.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.066336 restraints weight = 878.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start:          1.0002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.400    656  Z= 5.737
  Angle     :  4.500  26.334    832  Z= 2.481
  Chirality :  0.339   0.804     56
  Planarity :  0.028   0.053    104
  Dihedral  : 14.423  36.360     72
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 153.59
  Ramachandran Plot:
    Outliers : 16.67 %
    Allowed  : 60.42 %
    Favored  : 22.92 %
  Rotamer:
    Outliers : 39.29 %
    Allowed  : 35.71 %
    Favored  : 25.00 %
  Cbeta Deviations : 28.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.79 %

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: -9.53 (0.68), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.26 (0.52), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.115   0.018   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13718 /  5.77 (  648)
  covalent geometry    : angle       4.50028 /  2.48 (  832)
  hydrogen bonds       : bond        0.42376 / 21.93 (   12)
  hydrogen bonds       : angle      21.61230 / 11.38 (   24)
  Misc. bond           : bond        0.00352 /  0.18 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 15
  time to evaluate  : 0.017 
Fit side-chains
REVERT: B    2 LYS cc_start: 0.8934 (tttm) cc_final: 0.7794 (tmtt)
REVERT: B    3 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8342 (m-10)
REVERT: K    1 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8508 (t80)
REVERT: L    6 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7694 (tttp)
REVERT: M    6 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8362 (mtmt)
  outliers start: 22
  outliers final: 17
  residues processed: 33
  average time/residue: 0.0792
  time to fit residues: 2.7142
Evaluate side-chains
  36 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 15
  time to evaluate  : 0.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    3 PHE
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain J residue    7 PHE
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain B residue    6 LYS
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain K residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain M residue    6 LYS
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain O residue    6 LYS
Chi-restraints excluded: chain C residue    1 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.076984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.065640 restraints weight = 1902.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.066802 restraints weight = 1361.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.067626 restraints weight = 1082.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.067723 restraints weight = 912.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.067723 restraints weight = 889.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8856
moved from start:          0.9998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.401    656  Z= 5.738
  Angle     :  4.499  26.300    832  Z= 2.481
  Chirality :  0.339   0.802     56
  Planarity :  0.028   0.053    104
  Dihedral  : 14.498  37.030     72
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 152.78
  Ramachandran Plot:
    Outliers : 16.67 %
    Allowed  : 62.50 %
    Favored  : 20.83 %
  Rotamer:
    Outliers : 37.50 %
    Allowed  : 37.50 %
    Favored  : 25.00 %
  Cbeta Deviations : 28.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.79 %

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: -9.52 (0.69), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.25 (0.53), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.115   0.018   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13717 /  5.77 (  648)
  covalent geometry    : angle       4.49906 /  2.48 (  832)
  hydrogen bonds       : bond        0.42270 / 21.89 (   12)
  hydrogen bonds       : angle      21.65236 / 11.40 (   24)
  Misc. bond           : bond        0.00352 /  0.18 (    8)

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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 14
  time to evaluate  : 0.027 
Fit side-chains
REVERT: B    2 LYS cc_start: 0.8933 (tttm) cc_final: 0.7792 (tmtt)
REVERT: B    3 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8343 (m-10)
REVERT: K    1 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8514 (t80)
REVERT: L    6 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7687 (tttp)
REVERT: M    6 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8369 (mtmt)
  outliers start: 21
  outliers final: 17
  residues processed: 31
  average time/residue: 0.1052
  time to fit residues: 3.3857
Evaluate side-chains
  35 residues out of total 56 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 14
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    3 PHE
Chi-restraints excluded: chain J residue    5 PHE
Chi-restraints excluded: chain J residue    6 LYS
Chi-restraints excluded: chain J residue    7 PHE
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain B residue    6 LYS
Chi-restraints excluded: chain B residue    7 PHE
Chi-restraints excluded: chain K residue    1 PHE
Chi-restraints excluded: chain L residue    3 PHE
Chi-restraints excluded: chain L residue    5 PHE
Chi-restraints excluded: chain L residue    6 LYS
Chi-restraints excluded: chain L residue    7 PHE
Chi-restraints excluded: chain M residue    3 PHE
Chi-restraints excluded: chain M residue    6 LYS
Chi-restraints excluded: chain N residue    1 PHE
Chi-restraints excluded: chain O residue    1 PHE
Chi-restraints excluded: chain O residue    3 PHE
Chi-restraints excluded: chain O residue    5 PHE
Chi-restraints excluded: chain O residue    6 LYS
Chi-restraints excluded: chain C residue    1 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.076899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.065633 restraints weight = 1824.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.066703 restraints weight = 1326.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.067498 restraints weight = 1069.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.068044 restraints weight = 908.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.068516 restraints weight = 812.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.9999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.136   0.401    656  Z= 5.735
  Angle     :  4.498  26.335    832  Z= 2.481
  Chirality :  0.338   0.802     56
  Planarity :  0.028   0.053    104
  Dihedral  : 14.503  37.376     72
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 156.05
  Ramachandran Plot:
    Outliers : 16.67 %
    Allowed  : 60.42 %
    Favored  : 22.92 %
  Rotamer:
    Outliers : 37.50 %
    Allowed  : 37.50 %
    Favored  : 25.00 %
  Cbeta Deviations : 28.57 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.79 %

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: -9.53 (0.69), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.26 (0.53), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.115   0.018   PHE L   5 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.13710 /  5.77 (  648)
  covalent geometry    : angle       4.49755 /  2.48 (  832)
  hydrogen bonds       : bond        0.42331 / 21.91 (   12)
  hydrogen bonds       : angle      21.64310 / 11.40 (   24)
  Misc. bond           : bond        0.00354 /  0.18 (    8)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 243.14 seconds
wall clock time: 4 minutes 56.56 seconds (296.56 seconds total)