Starting phenix.real_space_refine
on Wed Mar  4 01:14:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zxq_15014/03_2026/7zxq_15014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxq_15014/03_2026/7zxq_15014.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxq_15014/03_2026/7zxq_15014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxq_15014/03_2026/7zxq_15014.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxq_15014/03_2026/7zxq_15014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxq_15014/03_2026/7zxq_15014.map"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      90      5.16       5
     C    6558      2.51       5
     N    1656      2.21       5
     O    1626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9930
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1655
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 1.19, per 1000 atoms: 0.12
  Number of scatterers: 9930
  At special positions: 0
  Unit cell: (100.062, 100.062, 92.214, 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      90     16.00
     O    1626      8.00
     N    1656      7.00
     C    6558      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  53 " - pdb=" SG  CYS E 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  53 " - pdb=" SG  CYS F 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  60 " - pdb=" SG  CYS E 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  60 " - pdb=" SG  CYS F 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  64 " - pdb=" SG  CYS D 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  64 " - pdb=" SG  CYS F 168 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 345.5 milliseconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      73.8% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR A   7 " --> pdb=" O   TRP A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 42
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 107
      Proline residue:  A  87  - end of helix
    Processing helix  chain 'A' and resid 123 through 157
    Processing helix  chain 'A' and resid 183 through 220
    Processing helix  chain 'B' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR B   7 " --> pdb=" O   TRP B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 42
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 107
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 123 through 157
    Processing helix  chain 'B' and resid 183 through 220
    Processing helix  chain 'C' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR C   7 " --> pdb=" O   TRP C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 42
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 107
      Proline residue:  C  87  - end of helix
    Processing helix  chain 'C' and resid 123 through 157
    Processing helix  chain 'C' and resid 183 through 220
    Processing helix  chain 'D' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR D   7 " --> pdb=" O   TRP D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 42
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 107
      Proline residue:  D  87  - end of helix
    Processing helix  chain 'D' and resid 123 through 157
    Processing helix  chain 'D' and resid 183 through 220
    Processing helix  chain 'E' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR E   7 " --> pdb=" O   TRP E   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 42
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 107
      Proline residue:  E  87  - end of helix
    Processing helix  chain 'E' and resid 123 through 157
    Processing helix  chain 'E' and resid 183 through 220
    Processing helix  chain 'F' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR F   7 " --> pdb=" O   TRP F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 42
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 107
      Proline residue:  F  87  - end of helix
    Processing helix  chain 'F' and resid 123 through 157
    Processing helix  chain 'F' and resid 183 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53
      removed outlier: 4.123A  pdb=" N   ILE A  52 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE A 180 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE B  52 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE C  52 " --> pdb=" O   PHE C 180 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE C 180 " --> pdb=" O   ILE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE D  52 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE E  52 " --> pdb=" O   PHE E 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE E 180 " --> pdb=" O   ILE E  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE F  52 " --> pdb=" O   PHE F 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE F 180 " --> pdb=" O   ILE F  52 " (cutoff:3.500A)

    756 hydrogen bonds defined for protein.
    2268 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: 1.73

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2994
        1.35 -     1.47: 2716
        1.47 -     1.59: 4358
        1.59 -     1.71: 0
        1.71 -     1.83: 132
  Bond restraints: 10200
  Sorted by residual:
  bond pdb=" CG  PRO E  58 "
       pdb=" CD  PRO E  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.77e+00
  bond pdb=" CG  PRO B  58 "
       pdb=" CD  PRO B  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.75e+00
  bond pdb=" CG  PRO A  58 "
       pdb=" CD  PRO A  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  bond pdb=" CG  PRO D  58 "
       pdb=" CD  PRO D  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  bond pdb=" CG  PRO C  58 "
       pdb=" CD  PRO C  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  ... (remaining 10195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 13556
        1.88 -     3.75: 286
        3.75 -     5.63: 36
        5.63 -     7.51: 12
        7.51 -     9.38: 6
  Bond angle restraints: 13896
  Sorted by residual:
  angle pdb=" C   ASN B  14 "
        pdb=" CA  ASN B  14 "
        pdb=" CB  ASN B  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN E  14 "
        pdb=" CA  ASN E  14 "
        pdb=" CB  ASN E  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN D  14 "
        pdb=" CA  ASN D  14 "
        pdb=" CB  ASN D  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN A  14 "
        pdb=" CA  ASN A  14 "
        pdb=" CB  ASN A  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.75    6.59 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN F  14 "
        pdb=" CA  ASN F  14 "
        pdb=" CB  ASN F  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.75    6.59 1.40e+00 5.10e-01 2.21e+01
  ... (remaining 13891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.52: 5179
       13.52 -    27.03: 548
       27.03 -    40.55: 171
       40.55 -    54.07: 48
       54.07 -    67.58: 12
  Dihedral angle restraints: 5958
    sinusoidal: 2316
      harmonic: 3642
  Sorted by residual:
  dihedral pdb=" CB  CYS D  64 "
           pdb=" SG  CYS D  64 "
           pdb=" SG  CYS D 168 "
           pdb=" CB  CYS D 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.33  -50.33     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CB  CYS A  64 "
           pdb=" SG  CYS A  64 "
           pdb=" SG  CYS A 168 "
           pdb=" CB  CYS A 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.32  -50.32     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CB  CYS C  64 "
           pdb=" SG  CYS C  64 "
           pdb=" SG  CYS C 168 "
           pdb=" CB  CYS C 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.31  -50.31     1      1.00e+01 1.00e-02 3.47e+01
  ... (remaining 5955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1051
       0.033 -    0.066: 399
       0.066 -    0.099: 127
       0.099 -    0.133: 55
       0.133 -    0.166: 6
  Chirality restraints: 1638
  Sorted by residual:
  chirality pdb=" CA  ILE F  20 "
            pdb=" N   ILE F  20 "
            pdb=" C   ILE F  20 "
            pdb=" CB  ILE F  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CA  ILE C  20 "
            pdb=" N   ILE C  20 "
            pdb=" C   ILE C  20 "
            pdb=" CB  ILE C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CA  ILE A  20 "
            pdb=" N   ILE A  20 "
            pdb=" C   ILE A  20 "
            pdb=" CB  ILE A  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 1635 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  57 "   -0.050 5.00e-02 4.00e+02   7.56e-02 9.15e+00
        pdb=" N   PRO B  58 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B  58 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B  58 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  57 "    0.050 5.00e-02 4.00e+02   7.55e-02 9.12e+00
        pdb=" N   PRO A  58 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A  58 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A  58 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  57 "   -0.050 5.00e-02 4.00e+02   7.54e-02 9.10e+00
        pdb=" N   PRO C  58 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO C  58 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C  58 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 84
        2.60 -     3.18: 8797
        3.18 -     3.75: 16284
        3.75 -     4.33: 18793
        4.33 -     4.90: 33420
  Nonbonded interactions: 77378
  Sorted by model distance:
  nonbonded pdb=" O   ILE D  71 "
            pdb=" OH  TYR D 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE E  71 "
            pdb=" OH  TYR E 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE B  71 "
            pdb=" OH  TYR B 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE C  71 "
            pdb=" OH  TYR C 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE F  71 "
            pdb=" OH  TYR F 157 "
     model   vdw
     2.027 3.040
  ... (remaining 77373 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     8.800
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
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      :  0.003   0.045  10218  Z= 0.151
  Angle     :  0.667   9.385  13932  Z= 0.365
  Chirality :  0.041   0.166   1638
  Planarity :  0.006   0.076   1662
  Dihedral  : 12.725  67.582   3540
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.24), residues: 1212
  helix:  3.25 (0.16), residues: 852
  sheet: -0.01 (0.73), residues: 60
  loop : -3.28 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 183 
 TYR   0.011   0.001   TYR A 151 
 PHE   0.007   0.001   PHE B 190 
 TRP   0.005   0.001   TRP A  44 
 HIS   0.003   0.001   HIS C  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10200)
  covalent geometry    : angle       0.66236 (13896)
  SS BOND              : bond        0.00653 (   18)
  SS BOND              : angle       1.67906 (   36)
  hydrogen bonds       : bond        0.12449 (  756)
  hydrogen bonds       : angle       4.49650 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.372 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1169
  time to fit residues: 26.1481
Evaluate side-chains
  106 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    4.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.066738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.051417 restraints weight = 47818.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.052811 restraints weight = 26312.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.053552 restraints weight = 18945.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.054174 restraints weight = 16024.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.054351 restraints weight = 14384.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10218  Z= 0.200
  Angle     :  0.607   7.258  13932  Z= 0.313
  Chirality :  0.042   0.173   1638
  Planarity :  0.004   0.040   1662
  Dihedral  :  4.007  23.792   1344
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  6.34 %
    Favored  : 92.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.24), residues: 1212
  helix:  3.17 (0.16), residues: 870
  sheet:  0.31 (0.78), residues: 60
  loop : -2.91 (0.30), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  75 
 TYR   0.013   0.002   TYR A 151 
 PHE   0.012   0.001   PHE F 180 
 TRP   0.007   0.001   TRP A  77 
 HIS   0.003   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (10200)
  covalent geometry    : angle       0.60177 (13896)
  SS BOND              : bond        0.00626 (   18)
  SS BOND              : angle       1.67188 (   36)
  hydrogen bonds       : bond        0.04143 (  756)
  hydrogen bonds       : angle       3.90130 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A   93 MET cc_start: 0.8846 (mtm) cc_final: 0.8642 (mtm)
REVERT: B   93 MET cc_start: 0.8804 (mtm) cc_final: 0.8332 (mtm)
REVERT: D   93 MET cc_start: 0.8840 (mtm) cc_final: 0.8640 (mtm)
  outliers start: 17
  outliers final: 5
  residues processed: 131
  average time/residue: 0.1055
  time to fit residues: 19.3286
Evaluate side-chains
  109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain F residue   41 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 71 optimal weight:   20.0000
   chunk 56 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.067079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.051621 restraints weight = 47796.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.053007 restraints weight = 26251.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.053906 restraints weight = 18884.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.054251 restraints weight = 15728.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.054513 restraints weight = 14474.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10218  Z= 0.146
  Angle     :  0.541   9.607  13932  Z= 0.278
  Chirality :  0.040   0.168   1638
  Planarity :  0.004   0.031   1662
  Dihedral  :  3.818  22.787   1344
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  9.24 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.93 (0.24), residues: 1212
  helix:  3.35 (0.16), residues: 864
  sheet:  0.26 (0.79), residues: 60
  loop : -2.49 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  75 
 TYR   0.013   0.001   TYR A 171 
 PHE   0.010   0.001   PHE B 180 
 TRP   0.005   0.001   TRP A   3 
 HIS   0.002   0.001   HIS F  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10200)
  covalent geometry    : angle       0.53707 (13896)
  SS BOND              : bond        0.00580 (   18)
  SS BOND              : angle       1.41573 (   36)
  hydrogen bonds       : bond        0.03696 (  756)
  hydrogen bonds       : angle       3.69386 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.318 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8309 (ttm)
REVERT: E  162 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8311 (ttm)
  outliers start: 28
  outliers final: 20
  residues processed: 126
  average time/residue: 0.0980
  time to fit residues: 17.2286
Evaluate side-chains
  125 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9990
   chunk 105 optimal weight:   20.0000
   chunk 100 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
B  80 GLN
E  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.066971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.051423 restraints weight = 48946.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.052861 restraints weight = 26334.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.053749 restraints weight = 18809.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.054090 restraints weight = 15615.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.054209 restraints weight = 14379.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10218  Z= 0.132
  Angle     :  0.528   7.454  13932  Z= 0.269
  Chirality :  0.039   0.165   1638
  Planarity :  0.003   0.028   1662
  Dihedral  :  3.676  20.974   1344
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.41 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.98 (0.24), residues: 1212
  helix:  3.41 (0.16), residues: 864
  sheet:  0.05 (0.84), residues: 60
  loop : -2.49 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  75 
 TYR   0.009   0.001   TYR A 151 
 PHE   0.009   0.001   PHE D  68 
 TRP   0.004   0.001   TRP A  77 
 HIS   0.002   0.001   HIS D  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10200)
  covalent geometry    : angle       0.52395 (13896)
  SS BOND              : bond        0.00543 (   18)
  SS BOND              : angle       1.32022 (   36)
  hydrogen bonds       : bond        0.03499 (  756)
  hydrogen bonds       : angle       3.56290 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.348 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8339 (ttm)
REVERT: E  162 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8335 (ttm)
  outliers start: 26
  outliers final: 14
  residues processed: 132
  average time/residue: 0.1001
  time to fit residues: 18.4317
Evaluate side-chains
  120 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0370
   chunk 90 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0770
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.2222

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

Flipped N/Q/H residues before XYZ refinement:
C  80 GLN
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 GLN
** F  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.068290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.052961 restraints weight = 48271.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.054401 restraints weight = 25987.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.055052 restraints weight = 18489.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.055694 restraints weight = 15709.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.055847 restraints weight = 14127.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10218  Z= 0.098
  Angle     :  0.491   7.622  13932  Z= 0.247
  Chirality :  0.038   0.156   1638
  Planarity :  0.003   0.024   1662
  Dihedral  :  3.423  18.322   1344
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.95 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.18 (0.24), residues: 1212
  helix:  3.57 (0.16), residues: 870
  sheet: -0.34 (0.80), residues: 60
  loop : -2.51 (0.31), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  75 
 TYR   0.005   0.001   TYR A   7 
 PHE   0.006   0.001   PHE E  31 
 TRP   0.004   0.000   TRP D   3 
 HIS   0.002   0.000   HIS F  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (10200)
  covalent geometry    : angle       0.48796 (13896)
  SS BOND              : bond        0.00482 (   18)
  SS BOND              : angle       1.09622 (   36)
  hydrogen bonds       : bond        0.03020 (  756)
  hydrogen bonds       : angle       3.35703 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 TYR cc_start: 0.9004 (t80) cc_final: 0.8729 (t80)
REVERT: B  162 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8406 (ttm)
REVERT: C  171 TYR cc_start: 0.8983 (t80) cc_final: 0.8706 (t80)
REVERT: D  171 TYR cc_start: 0.8996 (t80) cc_final: 0.8721 (t80)
REVERT: E  162 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8400 (ttm)
REVERT: F  171 TYR cc_start: 0.8980 (t80) cc_final: 0.8700 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 132
  average time/residue: 0.0919
  time to fit residues: 17.3698
Evaluate side-chains
  125 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 113 optimal weight:    9.9990
   chunk 119 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 105 optimal weight:    9.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.066256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.050902 restraints weight = 48712.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.052225 restraints weight = 26701.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.053055 restraints weight = 19269.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.053356 restraints weight = 16152.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.053751 restraints weight = 14950.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10218  Z= 0.152
  Angle     :  0.521   7.618  13932  Z= 0.268
  Chirality :  0.039   0.161   1638
  Planarity :  0.003   0.023   1662
  Dihedral  :  3.564  19.015   1344
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.04 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.24), residues: 1212
  helix:  3.44 (0.16), residues: 876
  sheet: -0.45 (0.78), residues: 60
  loop : -2.64 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  75 
 TYR   0.017   0.001   TYR E 171 
 PHE   0.010   0.001   PHE D 180 
 TRP   0.005   0.001   TRP C  44 
 HIS   0.002   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10200)
  covalent geometry    : angle       0.51795 (13896)
  SS BOND              : bond        0.00505 (   18)
  SS BOND              : angle       1.29226 (   36)
  hydrogen bonds       : bond        0.03513 (  756)
  hydrogen bonds       : angle       3.43796 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  162 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8290 (ttm)
REVERT: E  162 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8294 (ttm)
  outliers start: 27
  outliers final: 19
  residues processed: 127
  average time/residue: 0.0909
  time to fit residues: 16.7435
Evaluate side-chains
  119 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 112 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 82 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 96 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.064684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.049455 restraints weight = 48858.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.050746 restraints weight = 26963.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.051595 restraints weight = 19413.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.051891 restraints weight = 16213.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.052005 restraints weight = 15005.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10218  Z= 0.200
  Angle     :  0.574   7.226  13932  Z= 0.299
  Chirality :  0.041   0.167   1638
  Planarity :  0.004   0.025   1662
  Dihedral  :  3.875  22.894   1344
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.40 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.24), residues: 1212
  helix:  3.24 (0.16), residues: 876
  sheet: -0.48 (0.79), residues: 60
  loop : -2.65 (0.32), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 107 
 TYR   0.015   0.002   TYR A 151 
 PHE   0.013   0.001   PHE F  68 
 TRP   0.007   0.001   TRP F  44 
 HIS   0.003   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (10200)
  covalent geometry    : angle       0.56803 (13896)
  SS BOND              : bond        0.00662 (   18)
  SS BOND              : angle       1.69974 (   36)
  hydrogen bonds       : bond        0.03970 (  756)
  hydrogen bonds       : angle       3.62962 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 TYR cc_start: 0.9110 (t80) cc_final: 0.8840 (t80)
REVERT: B  162 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8396 (ttm)
REVERT: B  171 TYR cc_start: 0.9071 (t80) cc_final: 0.8740 (t80)
REVERT: C  171 TYR cc_start: 0.9048 (t80) cc_final: 0.8815 (t80)
REVERT: D  171 TYR cc_start: 0.9114 (t80) cc_final: 0.8840 (t80)
REVERT: E  162 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8391 (ttm)
REVERT: E  171 TYR cc_start: 0.9076 (t80) cc_final: 0.8751 (t80)
REVERT: F  171 TYR cc_start: 0.9043 (t80) cc_final: 0.8810 (t80)
  outliers start: 27
  outliers final: 24
  residues processed: 121
  average time/residue: 0.0865
  time to fit residues: 15.5366
Evaluate side-chains
  115 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 116 optimal weight:    0.9990
   chunk 91 optimal weight:    9.9990
   chunk 110 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 80 optimal weight:    0.0020
   chunk 118 optimal weight:    5.9990
   chunk 90 optimal weight:    8.9990
   chunk 101 optimal weight:    0.0770
   overall best weight:    1.3550

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

Flipped N/Q/H residues before XYZ refinement:
** C  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.066737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.051653 restraints weight = 48707.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.053058 restraints weight = 25803.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.053933 restraints weight = 18252.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.054229 restraints weight = 15139.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.054457 restraints weight = 13993.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10218  Z= 0.105
  Angle     :  0.507   8.069  13932  Z= 0.258
  Chirality :  0.038   0.155   1638
  Planarity :  0.003   0.026   1662
  Dihedral  :  3.559  20.939   1344
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.58 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.14 (0.24), residues: 1212
  helix:  3.54 (0.16), residues: 876
  sheet: -0.62 (0.78), residues: 60
  loop : -2.57 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  75 
 TYR   0.005   0.001   TYR D   7 
 PHE   0.006   0.001   PHE F  68 
 TRP   0.005   0.000   TRP E   3 
 HIS   0.001   0.000   HIS E 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10200)
  covalent geometry    : angle       0.50343 (13896)
  SS BOND              : bond        0.00640 (   18)
  SS BOND              : angle       1.34345 (   36)
  hydrogen bonds       : bond        0.03121 (  756)
  hydrogen bonds       : angle       3.36515 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 TYR cc_start: 0.9124 (t80) cc_final: 0.8882 (t80)
REVERT: B  171 TYR cc_start: 0.9106 (t80) cc_final: 0.8864 (t80)
REVERT: C  171 TYR cc_start: 0.9061 (t80) cc_final: 0.8834 (t80)
REVERT: D  171 TYR cc_start: 0.9120 (t80) cc_final: 0.8875 (t80)
REVERT: E  171 TYR cc_start: 0.9099 (t80) cc_final: 0.8847 (t80)
REVERT: F  171 TYR cc_start: 0.9053 (t80) cc_final: 0.8798 (t80)
  outliers start: 26
  outliers final: 24
  residues processed: 122
  average time/residue: 0.0690
  time to fit residues: 13.0390
Evaluate side-chains
  120 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 114 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
D  80 GLN
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 205 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.064820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.049564 restraints weight = 49281.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.050883 restraints weight = 27038.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.051525 restraints weight = 19417.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.052116 restraints weight = 16464.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.052258 restraints weight = 14857.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10218  Z= 0.179
  Angle     :  0.561   7.903  13932  Z= 0.288
  Chirality :  0.040   0.165   1638
  Planarity :  0.004   0.025   1662
  Dihedral  :  3.712  21.561   1344
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.39 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.24), residues: 1212
  helix:  3.42 (0.16), residues: 876
  sheet: -0.47 (0.78), residues: 60
  loop : -2.54 (0.32), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 107 
 TYR   0.013   0.001   TYR A 151 
 PHE   0.012   0.001   PHE C  68 
 TRP   0.007   0.001   TRP F 132 
 HIS   0.003   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (10200)
  covalent geometry    : angle       0.55643 (13896)
  SS BOND              : bond        0.00610 (   18)
  SS BOND              : angle       1.52366 (   36)
  hydrogen bonds       : bond        0.03684 (  756)
  hydrogen bonds       : angle       3.50266 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 TYR cc_start: 0.9134 (t80) cc_final: 0.8862 (t80)
REVERT: B  162 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8352 (ttm)
REVERT: B  171 TYR cc_start: 0.9105 (t80) cc_final: 0.8805 (t80)
REVERT: C  171 TYR cc_start: 0.9071 (t80) cc_final: 0.8799 (t80)
REVERT: D  171 TYR cc_start: 0.9136 (t80) cc_final: 0.8862 (t80)
REVERT: E  162 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8383 (ttm)
REVERT: E  171 TYR cc_start: 0.9114 (t80) cc_final: 0.8811 (t80)
REVERT: F  171 TYR cc_start: 0.9068 (t80) cc_final: 0.8797 (t80)
  outliers start: 27
  outliers final: 25
  residues processed: 118
  average time/residue: 0.0716
  time to fit residues: 13.0269
Evaluate side-chains
  117 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   93 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 21 optimal weight:   20.0000
   chunk 75 optimal weight:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.065188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.050211 restraints weight = 48470.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.051489 restraints weight = 27284.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.052100 restraints weight = 19872.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.052668 restraints weight = 17025.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.052700 restraints weight = 15400.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.4480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10218  Z= 0.146
  Angle     :  0.543   8.689  13932  Z= 0.276
  Chirality :  0.039   0.163   1638
  Planarity :  0.003   0.026   1662
  Dihedral  :  3.644  21.364   1344
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.39 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.07 (0.24), residues: 1212
  helix:  3.45 (0.16), residues: 876
  sheet: -0.54 (0.78), residues: 60
  loop : -2.48 (0.32), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 107 
 TYR   0.009   0.001   TYR D 151 
 PHE   0.009   0.001   PHE C  68 
 TRP   0.007   0.001   TRP F 132 
 HIS   0.002   0.001   HIS D  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10200)
  covalent geometry    : angle       0.53870 (13896)
  SS BOND              : bond        0.00603 (   18)
  SS BOND              : angle       1.39806 (   36)
  hydrogen bonds       : bond        0.03441 (  756)
  hydrogen bonds       : angle       3.44826 ( 2268)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.2237 (mtt) cc_final: 0.1902 (mtp)
REVERT: A  171 TYR cc_start: 0.9137 (t80) cc_final: 0.8894 (t80)
REVERT: B  162 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8386 (ttm)
REVERT: B  171 TYR cc_start: 0.9094 (t80) cc_final: 0.8826 (t80)
REVERT: C  171 TYR cc_start: 0.9075 (t80) cc_final: 0.8841 (t80)
REVERT: D  105 MET cc_start: 0.2243 (mtt) cc_final: 0.1895 (mtp)
REVERT: E  162 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8372 (ttm)
REVERT: E  171 TYR cc_start: 0.9106 (t80) cc_final: 0.8830 (t80)
REVERT: F  171 TYR cc_start: 0.9069 (t80) cc_final: 0.8835 (t80)
  outliers start: 27
  outliers final: 25
  residues processed: 123
  average time/residue: 0.0742
  time to fit residues: 14.1758
Evaluate side-chains
  120 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   93 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 63 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0670
   chunk 111 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0170
   chunk 92 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    1.1160

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  80 GLN
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 GLN
** E  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  61 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.066605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.051735 restraints weight = 49206.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.053093 restraints weight = 26035.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.053898 restraints weight = 18531.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.054202 restraints weight = 15470.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.054470 restraints weight = 14314.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10218  Z= 0.102
  Angle     :  0.521   8.866  13932  Z= 0.262
  Chirality :  0.038   0.152   1638
  Planarity :  0.003   0.027   1662
  Dihedral  :  3.492  19.946   1344
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.75 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.23 (0.24), residues: 1212
  helix:  3.54 (0.16), residues: 882
  sheet: -0.64 (0.77), residues: 60
  loop : -2.42 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  75 
 TYR   0.005   0.001   TYR D 135 
 PHE   0.006   0.001   PHE B 149 
 TRP   0.005   0.000   TRP C   3 
 HIS   0.002   0.000   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (10200)
  covalent geometry    : angle       0.51769 (13896)
  SS BOND              : bond        0.00558 (   18)
  SS BOND              : angle       1.18872 (   36)
  hydrogen bonds       : bond        0.02978 (  756)
  hydrogen bonds       : angle       3.30381 ( 2268)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1409.76 seconds
wall clock time: 25 minutes 11.08 seconds (1511.08 seconds total)