Starting phenix.real_space_refine
on Mon Jun  9 01:31:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f6r_28889/06_2025/8f6r_28889.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f6r_28889/06_2025/8f6r_28889.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f6r_28889/06_2025/8f6r_28889.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f6r_28889/06_2025/8f6r_28889.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f6r_28889/06_2025/8f6r_28889.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f6r_28889/06_2025/8f6r_28889.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.003 sd=   0.057
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    6348      2.51       5
     N    1872      2.21       5
     O    2058      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10290
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1715
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 7, 'TRANS': 211}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 3.84, per 1000 atoms: 0.37
  Number of scatterers: 10290
  At special positions: 0
  Unit cell: (125.073, 129.349, 54.519, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O    2058      8.00
     N    1872      7.00
     C    6348      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=0, symmetry=0
  Time building additional restraints: 2.93
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      96.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 29
    Processing helix  chain 'A' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU A  43 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP A  54 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 85
    Processing helix  chain 'A' and resid 86 through 110
    Processing helix  chain 'A' and resid 113 through 141
    Processing helix  chain 'A' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN A 166 " --> pdb=" O   GLU A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 197
    Processing helix  chain 'A' and resid 198 through 220
      removed outlier: 3.940A  pdb=" N   ARG A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU A 218 " --> pdb=" O   GLU A 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 29
    Processing helix  chain 'B' and resid 30 through 54
      removed outlier: 4.073A  pdb=" N   LEU B  43 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP B  54 " --> pdb=" O   GLU B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 85
    Processing helix  chain 'B' and resid 86 through 110
    Processing helix  chain 'B' and resid 113 through 141
    Processing helix  chain 'B' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN B 166 " --> pdb=" O   GLU B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 197
    Processing helix  chain 'B' and resid 198 through 220
      removed outlier: 3.939A  pdb=" N   ARG B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 29
    Processing helix  chain 'C' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU C  43 " --> pdb=" O   GLU C  39 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP C  54 " --> pdb=" O   GLU C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 85
    Processing helix  chain 'C' and resid 86 through 110
    Processing helix  chain 'C' and resid 113 through 141
    Processing helix  chain 'C' and resid 142 through 166
      removed outlier: 3.543A  pdb=" N   ASN C 166 " --> pdb=" O   GLU C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 197
    Processing helix  chain 'C' and resid 198 through 220
      removed outlier: 3.940A  pdb=" N   ARG C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU C 218 " --> pdb=" O   GLU C 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 29
    Processing helix  chain 'D' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU D  43 " --> pdb=" O   GLU D  39 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP D  54 " --> pdb=" O   GLU D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 85
    Processing helix  chain 'D' and resid 86 through 110
    Processing helix  chain 'D' and resid 113 through 141
    Processing helix  chain 'D' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN D 166 " --> pdb=" O   GLU D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 197
    Processing helix  chain 'D' and resid 198 through 220
      removed outlier: 3.939A  pdb=" N   ARG D 202 " --> pdb=" O   ASP D 198 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU D 218 " --> pdb=" O   GLU D 214 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 4 through 29
    Processing helix  chain 'E' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU E  43 " --> pdb=" O   GLU E  39 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP E  54 " --> pdb=" O   GLU E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 57 through 85
    Processing helix  chain 'E' and resid 86 through 110
    Processing helix  chain 'E' and resid 113 through 141
    Processing helix  chain 'E' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN E 166 " --> pdb=" O   GLU E 162 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 169 through 197
    Processing helix  chain 'E' and resid 198 through 220
      removed outlier: 3.939A  pdb=" N   ARG E 202 " --> pdb=" O   ASP E 198 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU E 218 " --> pdb=" O   GLU E 214 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 29
    Processing helix  chain 'F' and resid 30 through 54
      removed outlier: 4.072A  pdb=" N   LEU F  43 " --> pdb=" O   GLU F  39 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP F  54 " --> pdb=" O   GLU F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 57 through 85
    Processing helix  chain 'F' and resid 86 through 110
    Processing helix  chain 'F' and resid 113 through 141
    Processing helix  chain 'F' and resid 142 through 166
      removed outlier: 3.542A  pdb=" N   ASN F 166 " --> pdb=" O   GLU F 162 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 169 through 197
    Processing helix  chain 'F' and resid 198 through 220
      removed outlier: 3.940A  pdb=" N   ARG F 202 " --> pdb=" O   ASP F 198 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU F 218 " --> pdb=" O   GLU F 214 " (cutoff:3.500A)

    1045 hydrogen bonds defined for protein.
    3135 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: 3.05

  Time building geometry restraints manager: 3.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3786
        1.34 -     1.46: 571
        1.46 -     1.57: 5987
        1.57 -     1.69: 0
        1.69 -     1.80: 24
  Bond restraints: 10368
  Sorted by residual:
  bond pdb=" CB  TRP C  52 "
       pdb=" CG  TRP C  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.447  0.051 3.10e-02 1.04e+03 2.67e+00
  bond pdb=" CB  TRP F  52 "
       pdb=" CG  TRP F  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.64e+00
  bond pdb=" CB  TRP B  52 "
       pdb=" CG  TRP B  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.62e+00
  bond pdb=" CB  TRP E  52 "
       pdb=" CG  TRP E  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.58e+00
  bond pdb=" CB  TRP A  52 "
       pdb=" CG  TRP A  52 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.57e+00
  ... (remaining 10363 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 13621
        1.78 -     3.55: 305
        3.55 -     5.33: 72
        5.33 -     7.11: 24
        7.11 -     8.88: 6
  Bond angle restraints: 14028
  Sorted by residual:
  angle pdb=" N   SER B  58 "
        pdb=" CA  SER B  58 "
        pdb=" C   SER B  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.16   -8.88 1.09e+00 8.42e-01 6.64e+01
  angle pdb=" N   SER A  58 "
        pdb=" CA  SER A  58 "
        pdb=" C   SER A  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.16   -8.88 1.09e+00 8.42e-01 6.63e+01
  angle pdb=" N   SER D  58 "
        pdb=" CA  SER D  58 "
        pdb=" C   SER D  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.14   -8.86 1.09e+00 8.42e-01 6.61e+01
  angle pdb=" N   SER C  58 "
        pdb=" CA  SER C  58 "
        pdb=" C   SER C  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.13   -8.85 1.09e+00 8.42e-01 6.59e+01
  angle pdb=" N   SER F  58 "
        pdb=" CA  SER F  58 "
        pdb=" C   SER F  58 "
      ideal   model   delta    sigma   weight residual
     111.28  120.12   -8.84 1.09e+00 8.42e-01 6.58e+01
  ... (remaining 14023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.27: 5694
       13.27 -    26.55: 690
       26.55 -    39.82: 198
       39.82 -    53.10: 42
       53.10 -    66.37: 18
  Dihedral angle restraints: 6642
    sinusoidal: 2754
      harmonic: 3888
  Sorted by residual:
  dihedral pdb=" CA  TRP E  52 "
           pdb=" C   TRP E  52 "
           pdb=" N   LEU E  53 "
           pdb=" CA  LEU E  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.09  -16.91     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  TRP A  52 "
           pdb=" C   TRP A  52 "
           pdb=" N   LEU A  53 "
           pdb=" CA  LEU A  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.12  -16.88     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  TRP F  52 "
           pdb=" C   TRP F  52 "
           pdb=" N   LEU F  53 "
           pdb=" CA  LEU F  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.14  -16.86     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1473
       0.061 -    0.122: 164
       0.122 -    0.183: 13
       0.183 -    0.244: 6
       0.244 -    0.305: 6
  Chirality restraints: 1662
  Sorted by residual:
  chirality pdb=" CA  SER B  58 "
            pdb=" N   SER B  58 "
            pdb=" C   SER B  58 "
            pdb=" CB  SER B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  SER F  58 "
            pdb=" N   SER F  58 "
            pdb=" C   SER F  58 "
            pdb=" CB  SER F  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  SER D  58 "
            pdb=" N   SER D  58 "
            pdb=" C   SER D  58 "
            pdb=" CB  SER D  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.31e+00
  ... (remaining 1659 not shown)

  Planarity restraints: 1884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  86 "    0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO C  87 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C  87 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  87 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E  86 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.12e+00
        pdb=" N   PRO E  87 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO E  87 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E  87 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  86 "   -0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A  87 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  87 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  87 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1881 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 42
        2.58 -     3.16: 9766
        3.16 -     3.74: 17399
        3.74 -     4.32: 20508
        4.32 -     4.90: 33156
  Nonbonded interactions: 80871
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU F  11 "
            pdb=" NH2 ARG F  15 "
     model   vdw
     1.997 3.120
  nonbonded pdb=" OE2 GLU B  11 "
            pdb=" NH2 ARG B  15 "
     model   vdw
     1.998 3.120
  nonbonded pdb=" OE2 GLU D  11 "
            pdb=" NH2 ARG D  15 "
     model   vdw
     1.998 3.120
  nonbonded pdb=" OE2 GLU C  11 "
            pdb=" NH2 ARG C  15 "
     model   vdw
     1.998 3.120
  nonbonded pdb=" OE2 GLU A  11 "
            pdb=" NH2 ARG A  15 "
     model   vdw
     1.998 3.120
  ... (remaining 80866 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  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:             0.560
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.850
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10368  Z= 0.240
  Angle     :  0.751   8.883  14028  Z= 0.474
  Chirality :  0.043   0.305   1662
  Planarity :  0.005   0.044   1884
  Dihedral  : 12.985  66.374   4062
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.20), residues: 1302
  helix: -0.69 (0.13), residues: 1248
  sheet:  None (None), residues: 0
  loop : -2.81 (0.56), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  52 
 PHE   0.002   0.000   PHE B 185 
 ARG   0.002   0.000   ARG F  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08566 ( 1045)
  hydrogen bonds       : angle       4.56979 ( 3135)
  covalent geometry    : bond        0.00505 (10368)
  covalent geometry    : angle       0.75089 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 364
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: A  110 ASN cc_start: 0.8677 (m110) cc_final: 0.8269 (t0)
REVERT: A  121 LYS cc_start: 0.9440 (mttt) cc_final: 0.9078 (mtpp)
REVERT: A  142 ASP cc_start: 0.8086 (t0) cc_final: 0.7856 (t0)
REVERT: A  183 ILE cc_start: 0.9127 (mt) cc_final: 0.8831 (tp)
REVERT: B  121 LYS cc_start: 0.9445 (mttt) cc_final: 0.9042 (mtpp)
REVERT: B  142 ASP cc_start: 0.8038 (t0) cc_final: 0.7561 (t0)
REVERT: B  185 PHE cc_start: 0.8784 (t80) cc_final: 0.8562 (t80)
REVERT: C  110 ASN cc_start: 0.8679 (m110) cc_final: 0.8089 (t0)
REVERT: C  121 LYS cc_start: 0.9417 (mttt) cc_final: 0.9041 (mtpt)
REVERT: C  142 ASP cc_start: 0.8128 (t0) cc_final: 0.7719 (t0)
REVERT: C  183 ILE cc_start: 0.9199 (mt) cc_final: 0.8981 (tp)
REVERT: C  185 PHE cc_start: 0.8818 (t80) cc_final: 0.8171 (t80)
REVERT: D   12 GLU cc_start: 0.8658 (tp30) cc_final: 0.8448 (tp30)
REVERT: D  110 ASN cc_start: 0.8653 (m110) cc_final: 0.8405 (m110)
REVERT: D  121 LYS cc_start: 0.9431 (mttt) cc_final: 0.9120 (mtpp)
REVERT: D  183 ILE cc_start: 0.9079 (mt) cc_final: 0.8811 (tp)
REVERT: D  185 PHE cc_start: 0.8747 (t80) cc_final: 0.8460 (t80)
REVERT: E  110 ASN cc_start: 0.8714 (m110) cc_final: 0.8275 (t0)
REVERT: E  121 LYS cc_start: 0.9412 (mttt) cc_final: 0.9132 (mtpp)
REVERT: E  142 ASP cc_start: 0.7971 (t0) cc_final: 0.7522 (t0)
REVERT: E  183 ILE cc_start: 0.9170 (mt) cc_final: 0.8923 (tp)
REVERT: F  110 ASN cc_start: 0.8649 (m110) cc_final: 0.8260 (t0)
REVERT: F  121 LYS cc_start: 0.9451 (mttt) cc_final: 0.9048 (mtpt)
REVERT: F  185 PHE cc_start: 0.9000 (t80) cc_final: 0.8268 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 364
  average time/residue: 0.2938
  time to fit residues: 144.6631
Evaluate side-chains
  205 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
B 117 ASN
B 173 ASN
** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 173 ASN
D 173 ASN
E 173 ASN
** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 173 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.100543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.077959 restraints weight = 24906.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.081371 restraints weight = 15464.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.083701 restraints weight = 11402.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10368  Z= 0.145
  Angle     :  0.609   9.680  14028  Z= 0.319
  Chirality :  0.040   0.345   1662
  Planarity :  0.005   0.034   1884
  Dihedral  :  3.452  13.250   1458
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.95 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.21), residues: 1302
  helix:  1.69 (0.13), residues: 1248
  sheet:  None (None), residues: 0
  loop : -3.75 (0.60), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 201 
 PHE   0.025   0.002   PHE A 185 
 ARG   0.004   0.000   ARG C 165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 ( 1045)
  hydrogen bonds       : angle       3.50180 ( 3135)
  covalent geometry    : bond        0.00347 (10368)
  covalent geometry    : angle       0.60945 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 278
  time to evaluate  : 1.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ASN cc_start: 0.8621 (m110) cc_final: 0.8051 (t0)
REVERT: A  121 LYS cc_start: 0.9396 (mttt) cc_final: 0.9108 (mtpp)
REVERT: A  142 ASP cc_start: 0.8283 (t0) cc_final: 0.7931 (t0)
REVERT: A  152 LEU cc_start: 0.9339 (pp) cc_final: 0.8879 (tp)
REVERT: A  190 LEU cc_start: 0.9272 (mt) cc_final: 0.8967 (mt)
REVERT: B  118 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7910 (mt-10)
REVERT: B  121 LYS cc_start: 0.9400 (mttt) cc_final: 0.9189 (mtpp)
REVERT: B  142 ASP cc_start: 0.7922 (t0) cc_final: 0.7635 (t0)
REVERT: B  164 GLN cc_start: 0.8420 (tt0) cc_final: 0.8144 (tt0)
REVERT: C  110 ASN cc_start: 0.8708 (m110) cc_final: 0.8015 (t0)
REVERT: C  121 LYS cc_start: 0.9372 (mttt) cc_final: 0.9097 (mtpt)
REVERT: C  142 ASP cc_start: 0.8179 (t0) cc_final: 0.7930 (t0)
REVERT: D   58 SER cc_start: 0.8714 (m) cc_final: 0.8313 (p)
REVERT: D  110 ASN cc_start: 0.8488 (m110) cc_final: 0.7884 (t0)
REVERT: D  121 LYS cc_start: 0.9397 (mttt) cc_final: 0.9114 (mtpp)
REVERT: D  152 LEU cc_start: 0.9296 (pp) cc_final: 0.8896 (tp)
REVERT: E  110 ASN cc_start: 0.8619 (m110) cc_final: 0.8079 (t0)
REVERT: E  142 ASP cc_start: 0.7997 (t0) cc_final: 0.7698 (t0)
REVERT: E  152 LEU cc_start: 0.9322 (pp) cc_final: 0.8850 (tp)
REVERT: E  164 GLN cc_start: 0.8460 (tt0) cc_final: 0.8258 (tt0)
REVERT: F  110 ASN cc_start: 0.8698 (m110) cc_final: 0.8059 (t0)
REVERT: F  121 LYS cc_start: 0.9395 (mttt) cc_final: 0.9088 (mtpt)
REVERT: F  142 ASP cc_start: 0.7811 (t0) cc_final: 0.7558 (t0)
REVERT: F  185 PHE cc_start: 0.8706 (t80) cc_final: 0.8215 (t80)
  outliers start: 29
  outliers final: 20
  residues processed: 293
  average time/residue: 0.2035
  time to fit residues: 85.2390
Evaluate side-chains
  238 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 218
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   59 ASP
Chi-restraints excluded: chain E residue  107 VAL
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  180 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
D 164 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.100798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.078189 restraints weight = 25298.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.081229 restraints weight = 16708.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.083445 restraints weight = 12705.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10368  Z= 0.130
  Angle     :  0.584  10.278  14028  Z= 0.303
  Chirality :  0.039   0.375   1662
  Planarity :  0.004   0.032   1884
  Dihedral  :  3.430  12.965   1458
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.24 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.22), residues: 1302
  helix:  2.13 (0.14), residues: 1248
  sheet:  None (None), residues: 0
  loop : -3.89 (0.64), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 201 
 PHE   0.017   0.003   PHE A 185 
 ARG   0.004   0.000   ARG D  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03380 ( 1045)
  hydrogen bonds       : angle       3.37297 ( 3135)
  covalent geometry    : bond        0.00306 (10368)
  covalent geometry    : angle       0.58401 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 234
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8310 (mm-30)
REVERT: A   58 SER cc_start: 0.8797 (m) cc_final: 0.8361 (p)
REVERT: A  110 ASN cc_start: 0.8621 (m110) cc_final: 0.7922 (t0)
REVERT: A  121 LYS cc_start: 0.9430 (mttt) cc_final: 0.9146 (mtpp)
REVERT: A  142 ASP cc_start: 0.8328 (t0) cc_final: 0.8057 (t0)
REVERT: A  178 LYS cc_start: 0.9285 (mttm) cc_final: 0.8914 (tppp)
REVERT: A  183 ILE cc_start: 0.8921 (mt) cc_final: 0.8721 (tp)
REVERT: B  142 ASP cc_start: 0.7932 (t0) cc_final: 0.7563 (t0)
REVERT: B  164 GLN cc_start: 0.8522 (tt0) cc_final: 0.8195 (tt0)
REVERT: C  110 ASN cc_start: 0.8806 (m110) cc_final: 0.7974 (t0)
REVERT: C  121 LYS cc_start: 0.9382 (mttt) cc_final: 0.9152 (mtpt)
REVERT: C  142 ASP cc_start: 0.8081 (t0) cc_final: 0.7809 (t0)
REVERT: C  152 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8918 (tt)
REVERT: D   58 SER cc_start: 0.8775 (m) cc_final: 0.8296 (p)
REVERT: D  121 LYS cc_start: 0.9419 (mttt) cc_final: 0.9145 (mtpp)
REVERT: D  188 MET cc_start: 0.9180 (mtp) cc_final: 0.8906 (mtp)
REVERT: E  110 ASN cc_start: 0.8600 (m110) cc_final: 0.8040 (t0)
REVERT: E  142 ASP cc_start: 0.7890 (t0) cc_final: 0.7591 (t0)
REVERT: E  164 GLN cc_start: 0.8481 (tt0) cc_final: 0.8254 (tt0)
REVERT: E  183 ILE cc_start: 0.9131 (mt) cc_final: 0.8779 (tp)
REVERT: F  110 ASN cc_start: 0.8704 (m110) cc_final: 0.7968 (t0)
REVERT: F  118 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7917 (mt-10)
REVERT: F  121 LYS cc_start: 0.9430 (mttt) cc_final: 0.9167 (mtpt)
REVERT: F  142 ASP cc_start: 0.7916 (t0) cc_final: 0.7587 (t0)
  outliers start: 35
  outliers final: 18
  residues processed: 254
  average time/residue: 0.2038
  time to fit residues: 74.1525
Evaluate side-chains
  232 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 213
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 95 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
E 164 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.100532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.077207 restraints weight = 25451.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.080363 restraints weight = 16858.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.082527 restraints weight = 12843.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10368  Z= 0.132
  Angle     :  0.585  11.105  14028  Z= 0.300
  Chirality :  0.037   0.367   1662
  Planarity :  0.004   0.028   1884
  Dihedral  :  3.409  13.219   1458
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.48 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.22), residues: 1302
  helix:  2.21 (0.14), residues: 1248
  sheet:  None (None), residues: 0
  loop : -3.97 (0.64), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 201 
 PHE   0.019   0.002   PHE F 185 
 ARG   0.004   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 ( 1045)
  hydrogen bonds       : angle       3.38270 ( 3135)
  covalent geometry    : bond        0.00317 (10368)
  covalent geometry    : angle       0.58543 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 235
  time to evaluate  : 1.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8195 (mm-30)
REVERT: A   58 SER cc_start: 0.8726 (m) cc_final: 0.8278 (p)
REVERT: A  121 LYS cc_start: 0.9456 (mttt) cc_final: 0.9202 (mtpp)
REVERT: A  142 ASP cc_start: 0.8292 (t0) cc_final: 0.7899 (t0)
REVERT: A  178 LYS cc_start: 0.9288 (mttm) cc_final: 0.8908 (tppp)
REVERT: A  183 ILE cc_start: 0.8990 (mt) cc_final: 0.8727 (tp)
REVERT: A  196 ILE cc_start: 0.9038 (tp) cc_final: 0.8755 (tp)
REVERT: B  142 ASP cc_start: 0.7871 (t0) cc_final: 0.7395 (t0)
REVERT: B  164 GLN cc_start: 0.8475 (tt0) cc_final: 0.8146 (tt0)
REVERT: C   79 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7682 (tm-30)
REVERT: C  110 ASN cc_start: 0.8767 (m110) cc_final: 0.8024 (t0)
REVERT: C  121 LYS cc_start: 0.9417 (mttt) cc_final: 0.9195 (mtpt)
REVERT: C  142 ASP cc_start: 0.8160 (t0) cc_final: 0.7883 (t0)
REVERT: D   58 SER cc_start: 0.8823 (m) cc_final: 0.8353 (p)
REVERT: D  121 LYS cc_start: 0.9443 (mttt) cc_final: 0.9200 (mtpp)
REVERT: D  188 MET cc_start: 0.9177 (mtp) cc_final: 0.8888 (mtp)
REVERT: E  142 ASP cc_start: 0.7913 (t0) cc_final: 0.7543 (t0)
REVERT: F  110 ASN cc_start: 0.8840 (m110) cc_final: 0.7936 (t0)
REVERT: F  121 LYS cc_start: 0.9475 (mttt) cc_final: 0.9189 (mtpp)
REVERT: F  142 ASP cc_start: 0.7576 (t0) cc_final: 0.7334 (t0)
REVERT: F  204 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8281 (ttm)
  outliers start: 36
  outliers final: 20
  residues processed: 261
  average time/residue: 0.2331
  time to fit residues: 87.3335
Evaluate side-chains
  234 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   45 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 120 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
D 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.099976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.076568 restraints weight = 25493.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.079620 restraints weight = 17113.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.081756 restraints weight = 13150.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10368  Z= 0.153
  Angle     :  0.657  13.033  14028  Z= 0.324
  Chirality :  0.040   0.385   1662
  Planarity :  0.004   0.025   1884
  Dihedral  :  3.407  13.615   1458
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.81 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.22), residues: 1302
  helix:  2.11 (0.14), residues: 1248
  sheet:  None (None), residues: 0
  loop : -4.00 (0.61), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 201 
 PHE   0.020   0.003   PHE F 185 
 ARG   0.003   0.000   ARG B  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 ( 1045)
  hydrogen bonds       : angle       3.54884 ( 3135)
  covalent geometry    : bond        0.00368 (10368)
  covalent geometry    : angle       0.65705 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 221
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 SER cc_start: 0.8824 (m) cc_final: 0.8405 (p)
REVERT: A  121 LYS cc_start: 0.9456 (mttt) cc_final: 0.9142 (mtpp)
REVERT: A  142 ASP cc_start: 0.8125 (t0) cc_final: 0.7811 (t0)
REVERT: A  178 LYS cc_start: 0.9317 (mttm) cc_final: 0.8929 (tppp)
REVERT: A  183 ILE cc_start: 0.9068 (mt) cc_final: 0.8723 (tp)
REVERT: B  121 LYS cc_start: 0.9337 (mtpp) cc_final: 0.9117 (mtpp)
REVERT: B  142 ASP cc_start: 0.7923 (t0) cc_final: 0.7596 (t0)
REVERT: B  164 GLN cc_start: 0.8468 (tt0) cc_final: 0.8087 (tt0)
REVERT: C   79 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7672 (tm-30)
REVERT: C  110 ASN cc_start: 0.8793 (m110) cc_final: 0.8062 (t0)
REVERT: C  121 LYS cc_start: 0.9418 (mttt) cc_final: 0.9154 (mtpt)
REVERT: C  142 ASP cc_start: 0.8022 (t0) cc_final: 0.7728 (t0)
REVERT: D   58 SER cc_start: 0.8858 (m) cc_final: 0.8392 (p)
REVERT: D  121 LYS cc_start: 0.9447 (mttt) cc_final: 0.9194 (mtpp)
REVERT: D  188 MET cc_start: 0.9190 (mtp) cc_final: 0.8876 (mtp)
REVERT: E  142 ASP cc_start: 0.8013 (t0) cc_final: 0.7562 (t0)
REVERT: E  181 LYS cc_start: 0.9481 (mmtp) cc_final: 0.9097 (mmtt)
REVERT: F  110 ASN cc_start: 0.8817 (m110) cc_final: 0.7891 (t0)
REVERT: F  121 LYS cc_start: 0.9465 (mttt) cc_final: 0.9160 (mtpt)
REVERT: F  142 ASP cc_start: 0.7457 (t0) cc_final: 0.7218 (t0)
  outliers start: 32
  outliers final: 25
  residues processed: 241
  average time/residue: 0.2039
  time to fit residues: 69.8740
Evaluate side-chains
  231 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   45 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  204 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 125 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 124 optimal weight:    6.9990
   chunk 122 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 102 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
C 164 GLN
F 164 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.100466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.077374 restraints weight = 25562.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.080473 restraints weight = 16893.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.082616 restraints weight = 12856.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10368  Z= 0.145
  Angle     :  0.669  12.646  14028  Z= 0.328
  Chirality :  0.042   0.401   1662
  Planarity :  0.004   0.023   1884
  Dihedral  :  3.421  13.789   1458
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.19 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.22), residues: 1302
  helix:  2.06 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.22 (0.67), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 201 
 PHE   0.021   0.003   PHE F 185 
 ARG   0.003   0.000   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 ( 1045)
  hydrogen bonds       : angle       3.51124 ( 3135)
  covalent geometry    : bond        0.00350 (10368)
  covalent geometry    : angle       0.66919 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 219
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 SER cc_start: 0.8919 (m) cc_final: 0.8527 (p)
REVERT: A  142 ASP cc_start: 0.8068 (t0) cc_final: 0.7757 (t0)
REVERT: A  183 ILE cc_start: 0.9061 (mt) cc_final: 0.8746 (tp)
REVERT: A  196 ILE cc_start: 0.8958 (tp) cc_final: 0.8646 (tp)
REVERT: B  121 LYS cc_start: 0.9362 (mtpp) cc_final: 0.8655 (mtmm)
REVERT: B  142 ASP cc_start: 0.7988 (t0) cc_final: 0.7610 (t70)
REVERT: B  164 GLN cc_start: 0.8482 (tt0) cc_final: 0.8102 (tt0)
REVERT: C   79 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: C  110 ASN cc_start: 0.8773 (m110) cc_final: 0.7982 (t0)
REVERT: C  142 ASP cc_start: 0.7785 (t0) cc_final: 0.7563 (t0)
REVERT: D   58 SER cc_start: 0.8845 (m) cc_final: 0.8366 (p)
REVERT: D  121 LYS cc_start: 0.9453 (mttt) cc_final: 0.9183 (mtpp)
REVERT: E  142 ASP cc_start: 0.7929 (t0) cc_final: 0.7633 (t0)
REVERT: E  181 LYS cc_start: 0.9461 (mmtp) cc_final: 0.9063 (mmtt)
REVERT: F  110 ASN cc_start: 0.8773 (m110) cc_final: 0.7859 (t0)
REVERT: F  118 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7837 (mt-10)
REVERT: F  142 ASP cc_start: 0.7521 (t0) cc_final: 0.7268 (t0)
  outliers start: 40
  outliers final: 26
  residues processed: 246
  average time/residue: 0.2187
  time to fit residues: 78.2577
Evaluate side-chains
  233 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   45 ILE
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain F residue  144 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 125 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    0.4980
   chunk 119 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 111 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   chunk 122 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
C 220 GLN
D 220 GLN
E 166 ASN
E 220 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.101840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.078233 restraints weight = 25811.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.081449 restraints weight = 17071.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.083712 restraints weight = 12962.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10368  Z= 0.129
  Angle     :  0.672  12.916  14028  Z= 0.327
  Chirality :  0.042   0.405   1662
  Planarity :  0.003   0.023   1884
  Dihedral  :  3.464  13.255   1458
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.33 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.22), residues: 1302
  helix:  2.18 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.13 (0.68), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 201 
 PHE   0.020   0.003   PHE F 185 
 ARG   0.002   0.000   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03377 ( 1045)
  hydrogen bonds       : angle       3.42477 ( 3135)
  covalent geometry    : bond        0.00300 (10368)
  covalent geometry    : angle       0.67172 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 227
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 SER cc_start: 0.8918 (m) cc_final: 0.8531 (p)
REVERT: A  142 ASP cc_start: 0.8056 (t0) cc_final: 0.7720 (t0)
REVERT: A  178 LYS cc_start: 0.9282 (mttm) cc_final: 0.8896 (tppp)
REVERT: A  183 ILE cc_start: 0.9020 (mt) cc_final: 0.8761 (tp)
REVERT: A  188 MET cc_start: 0.9032 (mtp) cc_final: 0.8771 (mtp)
REVERT: A  196 ILE cc_start: 0.8978 (tp) cc_final: 0.8684 (tp)
REVERT: B  121 LYS cc_start: 0.9387 (mtpp) cc_final: 0.8686 (mtmm)
REVERT: B  142 ASP cc_start: 0.7924 (t0) cc_final: 0.7560 (t0)
REVERT: B  164 GLN cc_start: 0.8471 (tt0) cc_final: 0.8136 (tt0)
REVERT: C   79 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: C  110 ASN cc_start: 0.8781 (m110) cc_final: 0.7937 (t0)
REVERT: C  142 ASP cc_start: 0.7890 (t0) cc_final: 0.7601 (t0)
REVERT: C  164 GLN cc_start: 0.8354 (tt0) cc_final: 0.8064 (mt0)
REVERT: D   58 SER cc_start: 0.8912 (m) cc_final: 0.8454 (p)
REVERT: D  121 LYS cc_start: 0.9431 (mttt) cc_final: 0.9225 (mtpp)
REVERT: E  142 ASP cc_start: 0.7939 (t0) cc_final: 0.7614 (t0)
REVERT: E  181 LYS cc_start: 0.9423 (mmtp) cc_final: 0.9002 (mmtt)
REVERT: F  110 ASN cc_start: 0.8813 (m110) cc_final: 0.7996 (t0)
REVERT: F  142 ASP cc_start: 0.7580 (t0) cc_final: 0.7288 (t0)
  outliers start: 27
  outliers final: 20
  residues processed: 241
  average time/residue: 0.1993
  time to fit residues: 71.1243
Evaluate side-chains
  227 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 207
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  215 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  144 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 113 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 122 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 103 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
B 166 ASN
C 166 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.102934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.079563 restraints weight = 25437.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.082890 restraints weight = 16604.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.085200 restraints weight = 12458.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10368  Z= 0.130
  Angle     :  0.693  13.456  14028  Z= 0.336
  Chirality :  0.043   0.403   1662
  Planarity :  0.003   0.025   1884
  Dihedral  :  3.459  13.779   1458
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 23.05 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.94 (0.22), residues: 1302
  helix:  2.16 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.13 (0.67), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 201 
 PHE   0.019   0.002   PHE F 185 
 ARG   0.002   0.000   ARG D  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 ( 1045)
  hydrogen bonds       : angle       3.44124 ( 3135)
  covalent geometry    : bond        0.00306 (10368)
  covalent geometry    : angle       0.69331 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 222
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 SER cc_start: 0.9002 (m) cc_final: 0.8594 (p)
REVERT: A  142 ASP cc_start: 0.8138 (t0) cc_final: 0.7764 (t0)
REVERT: A  178 LYS cc_start: 0.9280 (mttm) cc_final: 0.8916 (tppp)
REVERT: A  188 MET cc_start: 0.9012 (mtp) cc_final: 0.8757 (mtp)
REVERT: A  196 ILE cc_start: 0.8929 (tp) cc_final: 0.8637 (tp)
REVERT: B  121 LYS cc_start: 0.9371 (mtpp) cc_final: 0.8669 (mtmm)
REVERT: B  142 ASP cc_start: 0.7994 (t0) cc_final: 0.7558 (t0)
REVERT: B  164 GLN cc_start: 0.8493 (tt0) cc_final: 0.8137 (tt0)
REVERT: C   79 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: C  110 ASN cc_start: 0.8771 (m110) cc_final: 0.7879 (t0)
REVERT: C  142 ASP cc_start: 0.7925 (t0) cc_final: 0.7591 (t0)
REVERT: C  164 GLN cc_start: 0.8351 (tt0) cc_final: 0.8076 (mt0)
REVERT: D   58 SER cc_start: 0.9032 (m) cc_final: 0.8589 (p)
REVERT: D  121 LYS cc_start: 0.9410 (mttt) cc_final: 0.9205 (mtpp)
REVERT: E  142 ASP cc_start: 0.8106 (t0) cc_final: 0.7665 (t0)
REVERT: E  181 LYS cc_start: 0.9437 (mmtp) cc_final: 0.8971 (mmtt)
REVERT: F   79 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7689 (tm-30)
REVERT: F  110 ASN cc_start: 0.8771 (m110) cc_final: 0.7894 (t0)
REVERT: F  142 ASP cc_start: 0.7659 (t0) cc_final: 0.7320 (t0)
  outliers start: 21
  outliers final: 18
  residues processed: 234
  average time/residue: 0.1962
  time to fit residues: 66.5889
Evaluate side-chains
  230 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 212
  time to evaluate  : 1.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Chi-restraints excluded: chain F residue  144 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.102632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.079188 restraints weight = 25525.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.082447 restraints weight = 16666.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.084802 restraints weight = 12578.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089  10368  Z= 0.149
  Angle     :  0.708  13.360  14028  Z= 0.350
  Chirality :  0.044   0.412   1662
  Planarity :  0.003   0.023   1884
  Dihedral  :  3.459  13.863   1458
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 23.62 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.22), residues: 1302
  helix:  2.06 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.10 (0.66), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 201 
 PHE   0.022   0.003   PHE F 185 
 ARG   0.002   0.000   ARG F 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03545 ( 1045)
  hydrogen bonds       : angle       3.49562 ( 3135)
  covalent geometry    : bond        0.00364 (10368)
  covalent geometry    : angle       0.70780 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 220
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 SER cc_start: 0.8926 (m) cc_final: 0.8546 (p)
REVERT: A  142 ASP cc_start: 0.8140 (t0) cc_final: 0.7775 (t0)
REVERT: A  178 LYS cc_start: 0.9286 (mttm) cc_final: 0.8889 (tppp)
REVERT: A  196 ILE cc_start: 0.8960 (tp) cc_final: 0.8683 (tp)
REVERT: B  142 ASP cc_start: 0.8008 (t0) cc_final: 0.7629 (t0)
REVERT: B  164 GLN cc_start: 0.8592 (tt0) cc_final: 0.8192 (tt0)
REVERT: C  110 ASN cc_start: 0.8776 (m110) cc_final: 0.7902 (t0)
REVERT: C  125 ILE cc_start: 0.9197 (mm) cc_final: 0.8912 (mm)
REVERT: C  142 ASP cc_start: 0.7868 (t0) cc_final: 0.7569 (t0)
REVERT: C  164 GLN cc_start: 0.8313 (tt0) cc_final: 0.8040 (mt0)
REVERT: D   58 SER cc_start: 0.8963 (m) cc_final: 0.8525 (p)
REVERT: D  121 LYS cc_start: 0.9444 (mttt) cc_final: 0.9236 (mtpp)
REVERT: D  188 MET cc_start: 0.8913 (mtp) cc_final: 0.8583 (mtp)
REVERT: E  142 ASP cc_start: 0.8042 (t0) cc_final: 0.7679 (t0)
REVERT: E  181 LYS cc_start: 0.9429 (mmtp) cc_final: 0.9029 (mmtt)
REVERT: F   79 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: F  110 ASN cc_start: 0.8753 (m110) cc_final: 0.7873 (t0)
REVERT: F  142 ASP cc_start: 0.7667 (t0) cc_final: 0.7379 (t0)
  outliers start: 19
  outliers final: 18
  residues processed: 230
  average time/residue: 0.2184
  time to fit residues: 72.6607
Evaluate side-chains
  232 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 214
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 96 optimal weight:    0.8980
   chunk 113 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 89 optimal weight:    1.9990
   chunk 106 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
D 166 ASN
E 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.103488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.079978 restraints weight = 25365.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.083336 restraints weight = 16481.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.085675 restraints weight = 12370.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  10368  Z= 0.139
  Angle     :  0.712  14.134  14028  Z= 0.351
  Chirality :  0.044   0.414   1662
  Planarity :  0.003   0.025   1884
  Dihedral  :  3.483  14.328   1458
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 23.52 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.22), residues: 1302
  helix:  2.09 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.12 (0.68), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 201 
 PHE   0.022   0.002   PHE F 185 
 ARG   0.002   0.000   ARG E  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03453 ( 1045)
  hydrogen bonds       : angle       3.49068 ( 3135)
  covalent geometry    : bond        0.00335 (10368)
  covalent geometry    : angle       0.71185 (14028)

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

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

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2604 Ramachandran restraints generated.
    1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 221
  time to evaluate  : 1.529 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 SER cc_start: 0.9063 (m) cc_final: 0.8702 (p)
REVERT: A  142 ASP cc_start: 0.8203 (t0) cc_final: 0.7780 (t0)
REVERT: A  178 LYS cc_start: 0.9283 (mttm) cc_final: 0.8835 (tppp)
REVERT: A  188 MET cc_start: 0.9013 (mtp) cc_final: 0.8739 (mtp)
REVERT: A  196 ILE cc_start: 0.8885 (tp) cc_final: 0.8606 (tp)
REVERT: B  121 LYS cc_start: 0.9368 (mtpp) cc_final: 0.8638 (mtmm)
REVERT: B  142 ASP cc_start: 0.8041 (t0) cc_final: 0.7598 (t0)
REVERT: B  164 GLN cc_start: 0.8594 (tt0) cc_final: 0.8206 (tt0)
REVERT: B  182 LEU cc_start: 0.9408 (mt) cc_final: 0.8759 (tt)
REVERT: C  110 ASN cc_start: 0.8762 (m110) cc_final: 0.7854 (t0)
REVERT: C  125 ILE cc_start: 0.9187 (mm) cc_final: 0.8930 (mm)
REVERT: C  142 ASP cc_start: 0.7938 (t0) cc_final: 0.7573 (t0)
REVERT: C  164 GLN cc_start: 0.8325 (tt0) cc_final: 0.8054 (mt0)
REVERT: D   58 SER cc_start: 0.9069 (m) cc_final: 0.8640 (p)
REVERT: D  121 LYS cc_start: 0.9403 (mttt) cc_final: 0.9193 (mtpp)
REVERT: E  142 ASP cc_start: 0.8007 (t0) cc_final: 0.7618 (t0)
REVERT: E  181 LYS cc_start: 0.9464 (mmtp) cc_final: 0.8995 (mmtt)
REVERT: F   79 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7740 (tm-30)
REVERT: F  110 ASN cc_start: 0.8819 (m110) cc_final: 0.7838 (t0)
REVERT: F  142 ASP cc_start: 0.7606 (t0) cc_final: 0.7240 (t0)
  outliers start: 22
  outliers final: 19
  residues processed: 232
  average time/residue: 0.2392
  time to fit residues: 80.3345
Evaluate side-chains
  228 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 209
  time to evaluate  : 1.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  180 ILE
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain E residue   22 ILE
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue   53 LEU
Chi-restraints excluded: chain F residue   22 ILE
Chi-restraints excluded: chain F residue   51 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 105 optimal weight:    7.9990
   chunk 98 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
C 166 ASN
D 166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.103730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.080026 restraints weight = 25244.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.083374 restraints weight = 16545.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.085641 restraints weight = 12482.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.4545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  10368  Z= 0.142
  Angle     :  0.728  14.039  14028  Z= 0.360
  Chirality :  0.044   0.412   1662
  Planarity :  0.003   0.025   1884
  Dihedral  :  3.465  14.169   1458
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 23.62 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.90 (0.22), residues: 1302
  helix:  2.13 (0.14), residues: 1254
  sheet:  None (None), residues: 0
  loop : -4.11 (0.70), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 201 
 PHE   0.022   0.003   PHE F 185 
 ARG   0.008   0.000   ARG E  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03418 ( 1045)
  hydrogen bonds       : angle       3.44907 ( 3135)
  covalent geometry    : bond        0.00343 (10368)
  covalent geometry    : angle       0.72827 (14028)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3713.81 seconds
wall clock time: 68 minutes 27.93 seconds (4107.93 seconds total)