Starting phenix.real_space_refine
on Tue Feb  3 12:20:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hi8_52185/02_2026/9hi8_52185.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hi8_52185/02_2026/9hi8_52185.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hi8_52185/02_2026/9hi8_52185.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hi8_52185/02_2026/9hi8_52185.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hi8_52185/02_2026/9hi8_52185.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hi8_52185/02_2026/9hi8_52185.map"
  }
  resolution = 3.56
  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=   0.001
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
     C     462      2.51       5
     N     108      2.21       5
     O     120      1.98       5
     H     798      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1488
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 248
          Classifications: {'peptide': 16}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 15}
    Chain: "B"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 248
          Classifications: {'peptide': 16}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 15}
    Chain: "C"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 248
          Classifications: {'peptide': 16}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 15}
    Chain: "D"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 248
          Classifications: {'peptide': 16}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 15}
    Chain: "E"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 248
          Classifications: {'peptide': 16}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 15}
    Chain: "F"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 248
          Classifications: {'peptide': 16}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 15}
  Time building chain proxies: 0.27, per 1000 atoms: 0.18
  Number of scatterers: 1488
  At special positions: 0
  Unit cell: (64.295, 43.42, 37.575, 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)
     O     120      8.00
     N     108      7.00
     C     462      6.00
     H     798      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.13
  Conformation dependent library (CDL) restraints added in 37.8 milliseconds
  

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  156

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 3 sheets defined
      0.0% alpha, 72.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 53
      removed outlier: 6.934A  pdb=" N   ILE A  56 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   GLY F  57 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 53
      removed outlier: 6.453A  pdb=" N   ASP D  47 " --> pdb=" O   ILE F  48 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   LYS F  50 " --> pdb=" O   ASP D  47 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE D  49 " --> pdb=" O   LYS F  50 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   VAL F  52 " --> pdb=" O   ILE D  49 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   LYS D  51 " --> pdb=" O   VAL F  52 " (cutoff:3.500A)
      removed outlier: 8.462A  pdb=" N   SER F  54 " --> pdb=" O   LYS D  51 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ALA D  53 " --> pdb=" O   SER F  54 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ILE F  56 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   VAL D  55 " --> pdb=" O   ILE F  56 " (cutoff:3.500A)
      removed outlier: 8.878A  pdb=" N   GLY F  58 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY D  57 " --> pdb=" O   GLY F  58 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 53
      removed outlier: 6.454A  pdb=" N   ILE B  48 " --> pdb=" O   ILE C  49 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   LYS C  51 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   LYS B  50 " --> pdb=" O   LYS C  51 " (cutoff:3.500A)
      removed outlier: 8.238A  pdb=" N   ALA C  53 " --> pdb=" O   LYS B  50 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   VAL B  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ILE C  48 " --> pdb=" O   ILE E  49 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   LYS E  51 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LYS C  50 " --> pdb=" O   LYS E  51 " (cutoff:3.500A)
      removed outlier: 8.265A  pdb=" N   ALA E  53 " --> pdb=" O   LYS C  50 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL C  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    15 hydrogen bonds defined for protein.
    45 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: 0.27

  Time building geometry restraints manager: 0.20 seconds

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

  Histogram of bond lengths:
        0.66 -     0.84: 6
        0.84 -     1.02: 173
        1.02 -     1.20: 619
        1.20 -     1.38: 204
        1.38 -     1.56: 486
  Bond restraints: 1488
  Sorted by residual:
  bond pdb=" CG1 VAL D  52 "
       pdb="HG11 VAL D  52 "
    ideal  model  delta    sigma   weight residual
    0.970  0.659  0.311 2.00e-02 2.50e+03 2.41e+02
  bond pdb=" CG1 VAL D  52 "
       pdb="HG13 VAL D  52 "
    ideal  model  delta    sigma   weight residual
    0.970  0.679  0.291 2.00e-02 2.50e+03 2.12e+02
  bond pdb=" CG2 VAL C  55 "
       pdb="HG23 VAL C  55 "
    ideal  model  delta    sigma   weight residual
    0.970  0.716  0.254 2.00e-02 2.50e+03 1.61e+02
  bond pdb=" CG1 VAL D  52 "
       pdb="HG12 VAL D  52 "
    ideal  model  delta    sigma   weight residual
    0.970  0.777  0.193 2.00e-02 2.50e+03 9.32e+01
  bond pdb=" CG2 VAL C  55 "
       pdb="HG22 VAL C  55 "
    ideal  model  delta    sigma   weight residual
    0.970  0.779  0.191 2.00e-02 2.50e+03 9.11e+01
  ... (remaining 1483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.70: 2652
        6.70 -    13.40: 34
       13.40 -    20.10: 13
       20.10 -    26.79: 19
       26.79 -    33.49: 24
  Bond angle restraints: 2742
  Sorted by residual:
  angle pdb=" CA  VAL D  55 "
        pdb=" CB  VAL D  55 "
        pdb=" CG1 VAL D  55 "
      ideal   model   delta    sigma   weight residual
     110.40  134.85  -24.45 1.70e+00 3.46e-01 2.07e+02
  angle pdb=" CA  VAL C  55 "
        pdb=" CB  VAL C  55 "
        pdb=" CG1 VAL C  55 "
      ideal   model   delta    sigma   weight residual
     110.40  133.68  -23.28 1.70e+00 3.46e-01 1.88e+02
  angle pdb=" CA  VAL F  55 "
        pdb=" CB  VAL F  55 "
        pdb=" CG1 VAL F  55 "
      ideal   model   delta    sigma   weight residual
     110.40  133.34  -22.94 1.70e+00 3.46e-01 1.82e+02
  angle pdb=" CA  VAL A  55 "
        pdb=" CB  VAL A  55 "
        pdb=" CG1 VAL A  55 "
      ideal   model   delta    sigma   weight residual
     110.40  131.89  -21.49 1.70e+00 3.46e-01 1.60e+02
  angle pdb=" CA  VAL E  55 "
        pdb=" CB  VAL E  55 "
        pdb=" CG1 VAL E  55 "
      ideal   model   delta    sigma   weight residual
     110.40  131.30  -20.90 1.70e+00 3.46e-01 1.51e+02
  ... (remaining 2737 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 580
       17.82 -    35.64: 32
       35.64 -    53.47: 25
       53.47 -    71.29: 7
       71.29 -    89.11: 4
  Dihedral angle restraints: 648
    sinusoidal: 372
      harmonic: 276
  Sorted by residual:
  dihedral pdb=" CA  LEU A  45 "
           pdb=" C   LEU A  45 "
           pdb=" N   PHE A  46 "
           pdb=" CA  PHE A  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.53   29.47     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  LEU F  45 "
           pdb=" C   LEU F  45 "
           pdb=" N   PHE F  46 "
           pdb=" CA  PHE F  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.85   29.15     0      5.00e+00 4.00e-02 3.40e+01
  dihedral pdb=" CA  LEU D  45 "
           pdb=" C   LEU D  45 "
           pdb=" N   PHE D  46 "
           pdb=" CA  PHE D  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.57   28.43     0      5.00e+00 4.00e-02 3.23e+01
  ... (remaining 645 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.256: 100
       0.256 -    0.511: 8
       0.511 -    0.767: 0
       0.767 -    1.022: 4
       1.022 -    1.278: 8
  Chirality restraints: 120
  Sorted by residual:
  chirality pdb=" CB  VAL D  55 "
            pdb=" CA  VAL D  55 "
            pdb=" CG1 VAL D  55 "
            pdb=" CG2 VAL D  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.35   -1.28 2.00e-01 2.50e+01 4.08e+01
  chirality pdb=" CB  VAL B  52 "
            pdb=" CA  VAL B  52 "
            pdb=" CG1 VAL B  52 "
            pdb=" CG2 VAL B  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.46   -1.17 2.00e-01 2.50e+01 3.44e+01
  chirality pdb=" CB  VAL A  52 "
            pdb=" CA  VAL A  52 "
            pdb=" CG1 VAL A  52 "
            pdb=" CG2 VAL A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.46   -1.17 2.00e-01 2.50e+01 3.44e+01
  ... (remaining 117 not shown)

  Planarity restraints: 198
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  46 "    0.133 2.00e-02 2.50e+03   5.06e-02 7.69e+01
        pdb=" CG  PHE B  46 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  46 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  46 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  46 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  46 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  46 "    0.017 2.00e-02 2.50e+03
        pdb=" HD1 PHE B  46 "   -0.023 2.00e-02 2.50e+03
        pdb=" HD2 PHE B  46 "   -0.035 2.00e-02 2.50e+03
        pdb=" HE1 PHE B  46 "    0.003 2.00e-02 2.50e+03
        pdb=" HE2 PHE B  46 "    0.016 2.00e-02 2.50e+03
        pdb=" HZ  PHE B  46 "    0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  46 "    0.115 2.00e-02 2.50e+03   4.45e-02 5.93e+01
        pdb=" CG  PHE C  46 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  46 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  46 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  46 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  46 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  46 "    0.011 2.00e-02 2.50e+03
        pdb=" HD1 PHE C  46 "   -0.011 2.00e-02 2.50e+03
        pdb=" HD2 PHE C  46 "   -0.027 2.00e-02 2.50e+03
        pdb=" HE1 PHE C  46 "    0.011 2.00e-02 2.50e+03
        pdb=" HE2 PHE C  46 "    0.020 2.00e-02 2.50e+03
        pdb=" HZ  PHE C  46 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  46 "    0.099 2.00e-02 2.50e+03   3.80e-02 4.33e+01
        pdb=" CG  PHE A  46 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  46 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  46 "   -0.034 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  46 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  46 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  46 "    0.012 2.00e-02 2.50e+03
        pdb=" HD1 PHE A  46 "   -0.013 2.00e-02 2.50e+03
        pdb=" HD2 PHE A  46 "   -0.025 2.00e-02 2.50e+03
        pdb=" HE1 PHE A  46 "    0.005 2.00e-02 2.50e+03
        pdb=" HE2 PHE A  46 "    0.012 2.00e-02 2.50e+03
        pdb=" HZ  PHE A  46 "    0.041 2.00e-02 2.50e+03
  ... (remaining 195 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.25: 195
        2.25 -     2.81: 2707
        2.81 -     3.38: 3257
        3.38 -     3.94: 4605
        3.94 -     4.50: 6017
  Nonbonded interactions: 16781
  Sorted by model distance:
  nonbonded pdb=" O   LEU C  59 "
            pdb=" HZ2 LYS E  50 "
     model   vdw
     1.690 2.450
  nonbonded pdb=" HZ1 LYS D  50 "
            pdb=" OXT LEU E  59 "
     model   vdw
     1.713 2.450
  nonbonded pdb=" O   LEU B  59 "
            pdb=" HZ2 LYS C  50 "
     model   vdw
     1.731 2.450
  nonbonded pdb=" O   LEU A  59 "
            pdb=" HZ2 LYS F  50 "
     model   vdw
     1.737 2.450
  nonbonded pdb=" OXT LEU C  59 "
            pdb=" HZ1 LYS F  50 "
     model   vdw
     1.747 2.450
  ... (remaining 16776 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 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
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      :  0.011   0.030    690  Z= 0.590
  Angle     :  2.968  24.452    918  Z= 1.807
  Chirality :  0.366   1.278    120
  Planarity :  0.013   0.054    108
  Dihedral  : 11.625  36.314    246
  Min Nonbonded Distance : 2.689

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.10 %
    Favored  : 86.90 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  :  2.78 %
    Favored  : 94.44 %
  Cbeta Deviations :  2.56 %
  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: -1.98 (0.72), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.50 (0.55), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.088   0.030   PHE B  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.01073 (  690)
  covalent geometry    : angle       2.96785 (  918)
  hydrogen bonds       : bond        0.21557 (    8)
  hydrogen bonds       : angle       6.34965 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.026 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0459
  time to fit residues: 2.2878
Evaluate side-chains
  30 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.9990

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.100815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.084243 restraints weight = 5170.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.087030 restraints weight = 1621.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.088761 restraints weight = 887.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.090147 restraints weight = 613.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.091224 restraints weight = 468.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.7011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052    690  Z= 0.235
  Angle     :  1.741  11.356    918  Z= 0.896
  Chirality :  0.450   1.478    120
  Planarity :  0.003   0.011    108
  Dihedral  :  9.785  27.303     96
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 27.78 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.43 (0.68), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.52), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.026   0.005   PHE C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00692 (  690)
  covalent geometry    : angle       1.74121 (  918)
  hydrogen bonds       : bond        0.01521 (    8)
  hydrogen bonds       : angle       4.70087 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.045 
Fit side-chains
REVERT: B   45 LEU cc_start: 0.8832 (mp) cc_final: 0.8484 (mt)
REVERT: C   46 PHE cc_start: 0.8180 (p90) cc_final: 0.7765 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0386
  time to fit residues: 1.3729
Evaluate side-chains
  28 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    2.3320

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.095569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.082849 restraints weight = 5179.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.086097 restraints weight = 1516.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.088276 restraints weight = 751.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.089610 restraints weight = 474.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.090838 restraints weight = 347.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.8347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034    690  Z= 0.214
  Angle     :  1.706  11.032    918  Z= 0.879
  Chirality :  0.450   1.463    120
  Planarity :  0.002   0.014    108
  Dihedral  :  8.243  31.625     96
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 31.94 %
    Favored  : 65.28 %
  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: -2.16 (0.68), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.52), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.019   0.003   PHE E  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00582 (  690)
  covalent geometry    : angle       1.70591 (  918)
  hydrogen bonds       : bond        0.01311 (    8)
  hydrogen bonds       : angle       3.58551 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.026 
Fit side-chains
REVERT: C   59 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8517 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0347
  time to fit residues: 1.0771
Evaluate side-chains
  24 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   59 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.095019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.082221 restraints weight = 5322.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.085165 restraints weight = 1569.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.087213 restraints weight = 810.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.088647 restraints weight = 523.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.089583 restraints weight = 380.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.9061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034    690  Z= 0.208
  Angle     :  1.694  10.967    918  Z= 0.872
  Chirality :  0.451   1.489    120
  Planarity :  0.002   0.012    108
  Dihedral  :  7.931  28.927     96
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 34.72 %
    Favored  : 62.50 %
  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: -2.01 (0.69), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.53), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 (  690)
  covalent geometry    : angle       1.69441 (  918)
  hydrogen bonds       : bond        0.01175 (    8)
  hydrogen bonds       : angle       3.23508 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.027 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0389
  time to fit residues: 1.1870
Evaluate side-chains
  23 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    2.3323

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.101811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.090341 restraints weight = 5263.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.093299 restraints weight = 1523.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.095494 restraints weight = 741.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.097048 restraints weight = 461.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.098009 restraints weight = 316.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.9275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032    690  Z= 0.215
  Angle     :  1.702  10.988    918  Z= 0.872
  Chirality :  0.452   1.504    120
  Planarity :  0.002   0.009    108
  Dihedral  :  8.029  29.019     96
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 22.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 34.72 %
    Favored  : 63.89 %
  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: -1.79 (0.69), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.53), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.019   0.003   PHE C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 (  690)
  covalent geometry    : angle       1.70222 (  918)
  hydrogen bonds       : bond        0.01097 (    8)
  hydrogen bonds       : angle       3.08320 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.047 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 21
  average time/residue: 0.0404
  time to fit residues: 1.0627
Evaluate side-chains
  20 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.2987

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.114833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.102670 restraints weight = 4912.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.106083 restraints weight = 1514.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.108427 restraints weight = 756.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.109966 restraints weight = 462.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.111035 restraints weight = 318.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.9892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033    690  Z= 0.202
  Angle     :  1.697  10.892    918  Z= 0.872
  Chirality :  0.452   1.502    120
  Planarity :  0.002   0.014    108
  Dihedral  :  6.972  22.377     96
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 22.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 31.94 %
    Favored  : 63.89 %
  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: -1.20 (0.76), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.90 (0.58), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 (  690)
  covalent geometry    : angle       1.69696 (  918)
  hydrogen bonds       : bond        0.00988 (    8)
  hydrogen bonds       : angle       2.88464 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.047 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 19
  average time/residue: 0.0415
  time to fit residues: 0.9799
Evaluate side-chains
  20 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain D residue   55 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.1650

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.110335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.099754 restraints weight = 4973.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.103029 restraints weight = 1410.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.105178 restraints weight = 671.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.106492 restraints weight = 395.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.107556 restraints weight = 271.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.9898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033    690  Z= 0.199
  Angle     :  1.699  10.899    918  Z= 0.869
  Chirality :  0.454   1.505    120
  Planarity :  0.002   0.010    108
  Dihedral  :  6.207  18.034     96
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 22.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 31.94 %
    Favored  : 65.28 %
  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: -0.68 (0.83), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.51 (0.63), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.002   PHE C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 (  690)
  covalent geometry    : angle       1.69926 (  918)
  hydrogen bonds       : bond        0.01005 (    8)
  hydrogen bonds       : angle       2.89837 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.044 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 19
  average time/residue: 0.0394
  time to fit residues: 0.9430
Evaluate side-chains
  20 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain B residue   46 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.8320

-------------------------------------------------------------------------------
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 = 0.3958 r_free = 0.3958 target = 0.101296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.089645 restraints weight = 5082.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.092553 restraints weight = 1488.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.094395 restraints weight = 740.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.096145 restraints weight = 484.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.097198 restraints weight = 328.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          1.0259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033    690  Z= 0.204
  Angle     :  1.696  10.967    918  Z= 0.867
  Chirality :  0.454   1.503    120
  Planarity :  0.002   0.009    108
  Dihedral  :  6.756  23.653     96
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 20.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 31.94 %
    Favored  : 65.28 %
  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: -0.23 (0.91), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.16 (0.70), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE F  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 (  690)
  covalent geometry    : angle       1.69595 (  918)
  hydrogen bonds       : bond        0.01058 (    8)
  hydrogen bonds       : angle       2.82811 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.038 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 18
  average time/residue: 0.0390
  time to fit residues: 0.8933
Evaluate side-chains
  18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    2.3323

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.109553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.099756 restraints weight = 5105.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.102854 restraints weight = 1367.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.104993 restraints weight = 647.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.106511 restraints weight = 379.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.107360 restraints weight = 231.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          1.0438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033    690  Z= 0.213
  Angle     :  1.707  11.009    918  Z= 0.869
  Chirality :  0.453   1.486    120
  Planarity :  0.002   0.008    108
  Dihedral  :  7.317  28.868     96
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 22.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 29.17 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.91), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.18 (0.69), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 (  690)
  covalent geometry    : angle       1.70739 (  918)
  hydrogen bonds       : bond        0.00899 (    8)
  hydrogen bonds       : angle       2.85026 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.045 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 18
  average time/residue: 0.0429
  time to fit residues: 0.9657
Evaluate side-chains
  19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   46 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0870
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.9947

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.113393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.102713 restraints weight = 4906.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.106145 restraints weight = 1440.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.108375 restraints weight = 679.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.109842 restraints weight = 394.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.110727 restraints weight = 250.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          1.0679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032    690  Z= 0.193
  Angle     :  1.698  10.920    918  Z= 0.866
  Chirality :  0.454   1.483    120
  Planarity :  0.002   0.008    108
  Dihedral  :  6.010  20.426     96
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 20.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 29.17 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.94), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.03 (0.72), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 (  690)
  covalent geometry    : angle       1.69808 (  918)
  hydrogen bonds       : bond        0.00886 (    8)
  hydrogen bonds       : angle       2.74653 (   45)

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

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

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  168 Ramachandran restraints generated.
    84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.027 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 18
  average time/residue: 0.0242
  time to fit residues: 0.5669
Evaluate side-chains
  20 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain B residue   46 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 6
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.3320

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.112350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.102325 restraints weight = 4937.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.105680 restraints weight = 1416.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.107909 restraints weight = 649.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.109276 restraints weight = 363.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.110204 restraints weight = 229.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          1.0698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.031    690  Z= 0.200
  Angle     :  1.701  10.936    918  Z= 0.867
  Chirality :  0.453   1.490    120
  Planarity :  0.002   0.007    108
  Dihedral  :  5.772  18.919     96
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 19.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 30.56 %
    Favored  : 65.28 %
  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:  0.10 (0.93), residues: 84
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.09 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE C  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 (  690)
  covalent geometry    : angle       1.70065 (  918)
  hydrogen bonds       : bond        0.00821 (    8)
  hydrogen bonds       : angle       2.69279 (   45)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 585.36 seconds
wall clock time: 10 minutes 29.51 seconds (629.51 seconds total)