Starting phenix.real_space_refine
on Wed Mar  5 14:17:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kew_37170/03_2025/8kew_37170.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kew_37170/03_2025/8kew_37170.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kew_37170/03_2025/8kew_37170.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kew_37170/03_2025/8kew_37170.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kew_37170/03_2025/8kew_37170.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kew_37170/03_2025/8kew_37170.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C     978      2.51       5
     N     252      2.21       5
     O     264      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 1500
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
  Restraints were copied for chains:
    C, B, D, G, F
  Time building chain proxies: 0.87, per 1000 atoms: 0.58
  Number of scatterers: 1500
  At special positions: 0
  Unit cell: (68.89, 68.89, 36.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     264      8.00
     N     252      7.00
     C     978      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 182.9 milliseconds
  

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  336

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 29.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'F' and resid 12 through 13
      removed outlier: 6.392A  pdb=" N   VAL F  12 " --> pdb=" O   HIS A  13 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL A  12 " --> pdb=" O   HIS B  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'F' and resid 16 through 17
    Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 25
      removed outlier: 6.397A  pdb=" N   VAL F  24 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A  24 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'F' and resid 30 through 36
      removed outlier: 6.909A  pdb=" N   ILE A  31 " --> pdb=" O   ALA F  30 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ILE F  32 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   GLY A  33 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE B  31 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ILE A  32 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   GLY B  33 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 40 through 41
    Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 13
      removed outlier: 6.413A  pdb=" N   VAL G  12 " --> pdb=" O   HIS C  13 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   VAL C  12 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 16 through 17
    Processing sheet with id=AA8, first strand: chain 'G' and resid 24 through 25
      removed outlier: 6.410A  pdb=" N   VAL G  24 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   VAL C  24 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 30 through 36
      removed outlier: 6.914A  pdb=" N   ILE C  31 " --> pdb=" O   ALA G  30 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ILE G  32 " --> pdb=" O   ILE C  31 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   GLY C  33 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ILE D  31 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ILE C  32 " --> pdb=" O   ILE D  31 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   GLY D  33 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 40 through 41

    20 hydrogen bonds defined for protein.
    60 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.39

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 486
        1.34 -     1.45: 181
        1.45 -     1.56: 845
        1.56 -     1.68: 0
        1.68 -     1.79: 12
  Bond restraints: 1524
  Sorted by residual:
  bond pdb=" CG  LEU F  34 "
       pdb=" CD1 LEU F  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.64e+00
  bond pdb=" CG  LEU G  34 "
       pdb=" CD1 LEU G  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.64e+00
  bond pdb=" CG  LEU B  34 "
       pdb=" CD1 LEU B  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.62e+00
  bond pdb=" CG  LEU A  34 "
       pdb=" CD1 LEU A  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.61e+00
  bond pdb=" CG  LEU C  34 "
       pdb=" CD1 LEU C  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.59e+00
  ... (remaining 1519 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.88: 1617
        0.88 -     1.75: 313
        1.75 -     2.63: 80
        2.63 -     3.50: 30
        3.50 -     4.38: 6
  Bond angle restraints: 2046
  Sorted by residual:
  angle pdb=" N   GLU C  22 "
        pdb=" CA  GLU C  22 "
        pdb=" C   GLU C  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.83   -4.38 1.26e+00 6.30e-01 1.21e+01
  angle pdb=" N   GLU F  22 "
        pdb=" CA  GLU F  22 "
        pdb=" C   GLU F  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.81   -4.36 1.26e+00 6.30e-01 1.20e+01
  angle pdb=" N   GLU A  22 "
        pdb=" CA  GLU A  22 "
        pdb=" C   GLU A  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.81   -4.36 1.26e+00 6.30e-01 1.20e+01
  angle pdb=" N   GLU B  22 "
        pdb=" CA  GLU B  22 "
        pdb=" C   GLU B  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.81   -4.36 1.26e+00 6.30e-01 1.19e+01
  angle pdb=" N   GLU D  22 "
        pdb=" CA  GLU D  22 "
        pdb=" C   GLU D  22 "
      ideal   model   delta    sigma   weight residual
     108.45  112.79   -4.34 1.26e+00 6.30e-01 1.19e+01
  ... (remaining 2041 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    12.24: 708
       12.24 -    24.48: 96
       24.48 -    36.71: 24
       36.71 -    48.95: 12
       48.95 -    61.18: 6
  Dihedral angle restraints: 846
    sinusoidal: 306
      harmonic: 540
  Sorted by residual:
  dihedral pdb=" CA  HIS F  14 "
           pdb=" C   HIS F  14 "
           pdb=" N   GLN F  15 "
           pdb=" CA  GLN F  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  167.19   12.81     0      5.00e+00 4.00e-02 6.56e+00
  dihedral pdb=" CA  HIS D  14 "
           pdb=" C   HIS D  14 "
           pdb=" N   GLN D  15 "
           pdb=" CA  GLN D  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  167.21   12.79     0      5.00e+00 4.00e-02 6.55e+00
  dihedral pdb=" CA  HIS G  14 "
           pdb=" C   HIS G  14 "
           pdb=" N   GLN G  15 "
           pdb=" CA  GLN G  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  167.21   12.79     0      5.00e+00 4.00e-02 6.54e+00
  ... (remaining 843 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 79
       0.029 -    0.058: 53
       0.058 -    0.087: 42
       0.087 -    0.116: 24
       0.116 -    0.145: 36
  Chirality restraints: 234
  Sorted by residual:
  chirality pdb=" CA  VAL F  39 "
            pdb=" N   VAL F  39 "
            pdb=" C   VAL F  39 "
            pdb=" CB  VAL F  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  VAL C  39 "
            pdb=" N   VAL C  39 "
            pdb=" C   VAL C  39 "
            pdb=" CB  VAL C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  VAL D  39 "
            pdb=" N   VAL D  39 "
            pdb=" C   VAL D  39 "
            pdb=" CB  VAL D  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.18e-01
  ... (remaining 231 not shown)

  Planarity restraints: 258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  20 "    0.006 2.00e-02 2.50e+03   4.74e-03 3.94e-01
        pdb=" CG  PHE A  20 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  20 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  20 "    0.006 2.00e-02 2.50e+03   4.71e-03 3.88e-01
        pdb=" CG  PHE G  20 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  20 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  20 "    0.006 2.00e-02 2.50e+03   4.67e-03 3.82e-01
        pdb=" CG  PHE D  20 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  20 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  20 "    0.001 2.00e-02 2.50e+03
  ... (remaining 255 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 585
        2.89 -     3.39: 1237
        3.39 -     3.89: 2379
        3.89 -     4.40: 2364
        4.40 -     4.90: 4769
  Nonbonded interactions: 11334
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  27 "
            pdb=" N   LYS B  28 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" OD1 ASN C  27 "
            pdb=" N   LYS C  28 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" OD1 ASN D  27 "
            pdb=" N   LYS D  28 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" OD1 ASN G  27 "
            pdb=" N   LYS G  28 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" OD1 ASN F  27 "
            pdb=" N   LYS F  28 "
     model   vdw
     2.388 3.120
  ... (remaining 11329 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'G'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.300
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
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      :  0.010   0.045   1524  Z= 0.628
  Angle     :  0.841   4.375   2046  Z= 0.523
  Chirality :  0.070   0.145    234
  Planarity :  0.003   0.006    258
  Dihedral  : 14.456  61.184    510
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.87 (0.44), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.34), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS D  14 
 PHE   0.011   0.002   PHE A  20 
 TYR   0.001   0.000   TYR A  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.171 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8178 (mm-30) cc_final: 0.6816 (pt0)
REVERT: F   26 SER cc_start: 0.8743 (m) cc_final: 0.8178 (t)
REVERT: G   22 GLU cc_start: 0.8267 (mm-30) cc_final: 0.6727 (pt0)
REVERT: G   26 SER cc_start: 0.8773 (m) cc_final: 0.8178 (t)
REVERT: A   10 TYR cc_start: 0.7392 (m-80) cc_final: 0.7077 (m-80)
REVERT: A   26 SER cc_start: 0.8559 (m) cc_final: 0.8005 (t)
REVERT: A   27 ASN cc_start: 0.8853 (t0) cc_final: 0.8608 (t0)
REVERT: C   22 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7965 (mm-30)
REVERT: C   26 SER cc_start: 0.8652 (m) cc_final: 0.7983 (t)
REVERT: B   26 SER cc_start: 0.8779 (m) cc_final: 0.8287 (t)
REVERT: D   14 HIS cc_start: 0.8287 (m90) cc_final: 0.7996 (m90)
REVERT: D   26 SER cc_start: 0.8757 (m) cc_final: 0.8231 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1719
  time to fit residues: 6.1586
Evaluate side-chains
  25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.119679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.090146 restraints weight = 1701.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 3.24
r_work: 0.3174 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1524  Z= 0.148
  Angle     :  0.459   2.302   2046  Z= 0.271
  Chirality :  0.062   0.130    234
  Planarity :  0.001   0.007    258
  Dihedral  :  4.697  11.025    204
  Min Nonbonded Distance : 2.672

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.47), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.36), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C  13 
 PHE   0.004   0.001   PHE B  20 
 TYR   0.001   0.000   TYR F  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.175 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8353 (mm-30) cc_final: 0.6799 (pt0)
REVERT: F   26 SER cc_start: 0.8261 (m) cc_final: 0.7746 (t)
REVERT: G   22 GLU cc_start: 0.8344 (mm-30) cc_final: 0.6699 (pt0)
REVERT: G   26 SER cc_start: 0.8285 (m) cc_final: 0.7797 (t)
REVERT: A   10 TYR cc_start: 0.7436 (m-80) cc_final: 0.7118 (m-80)
REVERT: A   14 HIS cc_start: 0.8064 (m90) cc_final: 0.7627 (m90)
REVERT: A   26 SER cc_start: 0.7789 (m) cc_final: 0.7303 (t)
REVERT: C   22 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7737 (mm-30)
REVERT: C   26 SER cc_start: 0.7964 (m) cc_final: 0.7415 (t)
REVERT: B   26 SER cc_start: 0.8170 (m) cc_final: 0.7675 (t)
REVERT: D   14 HIS cc_start: 0.8207 (m90) cc_final: 0.7926 (m90)
REVERT: D   26 SER cc_start: 0.8155 (m) cc_final: 0.7646 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0949
  time to fit residues: 3.3804
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0370
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.1262

-------------------------------------------------------------------------------
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 = 0.3890 r_free = 0.3890 target = 0.128710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100833 restraints weight = 1600.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 3.05
r_work: 0.3169 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   1524  Z= 0.178
  Angle     :  0.450   2.261   2046  Z= 0.265
  Chirality :  0.061   0.129    234
  Planarity :  0.001   0.006    258
  Dihedral  :  4.433  10.372    204
  Min Nonbonded Distance : 2.670

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.00 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.48), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.37), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C  14 
 PHE   0.006   0.001   PHE A  20 
 TYR   0.002   0.000   TYR F  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.164 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8377 (mm-30) cc_final: 0.6763 (pt0)
REVERT: F   26 SER cc_start: 0.8273 (m) cc_final: 0.7767 (t)
REVERT: G   22 GLU cc_start: 0.8261 (mm-30) cc_final: 0.6786 (pt0)
REVERT: G   26 SER cc_start: 0.8224 (m) cc_final: 0.7715 (t)
REVERT: A   10 TYR cc_start: 0.7440 (m-80) cc_final: 0.7144 (m-80)
REVERT: A   14 HIS cc_start: 0.8093 (m90) cc_final: 0.7892 (m90)
REVERT: A   22 GLU cc_start: 0.8055 (tp30) cc_final: 0.7733 (mm-30)
REVERT: A   26 SER cc_start: 0.7849 (m) cc_final: 0.7314 (t)
REVERT: C   22 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7777 (mm-30)
REVERT: C   26 SER cc_start: 0.7962 (m) cc_final: 0.7455 (t)
REVERT: B   26 SER cc_start: 0.8162 (m) cc_final: 0.7633 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1057
  time to fit residues: 3.6327
Evaluate side-chains
  26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.126978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.095633 restraints weight = 1615.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 3.28
r_work: 0.3333 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   1524  Z= 0.335
  Angle     :  0.556   3.387   2046  Z= 0.321
  Chirality :  0.063   0.150    234
  Planarity :  0.002   0.006    258
  Dihedral  :  5.046  11.384    204
  Min Nonbonded Distance : 2.662

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.49), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.38), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  14 
 PHE   0.013   0.002   PHE G  20 
 TYR   0.002   0.000   TYR F  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.167 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8425 (mm-30) cc_final: 0.6798 (pt0)
REVERT: F   26 SER cc_start: 0.8414 (m) cc_final: 0.7905 (t)
REVERT: G   22 GLU cc_start: 0.8302 (mm-30) cc_final: 0.6800 (pt0)
REVERT: G   26 SER cc_start: 0.8333 (m) cc_final: 0.7849 (t)
REVERT: A   10 TYR cc_start: 0.7513 (m-80) cc_final: 0.7276 (m-80)
REVERT: A   14 HIS cc_start: 0.8209 (m90) cc_final: 0.8007 (m90)
REVERT: A   22 GLU cc_start: 0.8248 (tp30) cc_final: 0.7879 (mm-30)
REVERT: A   26 SER cc_start: 0.8110 (m) cc_final: 0.7561 (t)
REVERT: C   22 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7958 (mm-30)
REVERT: C   26 SER cc_start: 0.8137 (m) cc_final: 0.7589 (t)
REVERT: B   26 SER cc_start: 0.8244 (m) cc_final: 0.7718 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0940
  time to fit residues: 3.3966
Evaluate side-chains
  27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.118432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.089350 restraints weight = 1734.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 3.26
r_work: 0.3311 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   1524  Z= 0.273
  Angle     :  0.514   2.602   2046  Z= 0.299
  Chirality :  0.063   0.145    234
  Planarity :  0.002   0.006    258
  Dihedral  :  4.887  11.157    204
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.00 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.51), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS G  14 
 PHE   0.008   0.001   PHE G  20 
 TYR   0.001   0.000   TYR F  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.163 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8422 (mm-30) cc_final: 0.6830 (pt0)
REVERT: F   26 SER cc_start: 0.8297 (m) cc_final: 0.7762 (t)
REVERT: G   22 GLU cc_start: 0.8305 (mm-30) cc_final: 0.6812 (pt0)
REVERT: G   26 SER cc_start: 0.8356 (m) cc_final: 0.7897 (t)
REVERT: G   31 ILE cc_start: 0.8763 (mt) cc_final: 0.8528 (mt)
REVERT: A   10 TYR cc_start: 0.7458 (m-80) cc_final: 0.7249 (m-80)
REVERT: A   22 GLU cc_start: 0.8225 (tp30) cc_final: 0.7808 (mm-30)
REVERT: A   26 SER cc_start: 0.7974 (m) cc_final: 0.7404 (t)
REVERT: C   22 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7912 (mm-30)
REVERT: C   26 SER cc_start: 0.7957 (m) cc_final: 0.7387 (t)
REVERT: B   22 GLU cc_start: 0.8185 (tp30) cc_final: 0.7830 (tp30)
REVERT: B   26 SER cc_start: 0.8216 (m) cc_final: 0.7680 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0816
  time to fit residues: 2.9731
Evaluate side-chains
  28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0470
   overall best weight:    2.2086

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.104095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.077251 restraints weight = 2008.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 3.41
r_work: 0.3299 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   1524  Z= 0.310
  Angle     :  0.533   2.727   2046  Z= 0.310
  Chirality :  0.064   0.145    234
  Planarity :  0.002   0.005    258
  Dihedral  :  5.070  11.759    204
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.33 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.53), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.26 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS G  14 
 PHE   0.010   0.002   PHE G  20 
 TYR   0.001   0.000   TYR F  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.166 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8387 (mm-30) cc_final: 0.6863 (pt0)
REVERT: F   26 SER cc_start: 0.8312 (m) cc_final: 0.7774 (t)
REVERT: G   22 GLU cc_start: 0.8300 (mm-30) cc_final: 0.6844 (pt0)
REVERT: G   31 ILE cc_start: 0.8696 (mt) cc_final: 0.8468 (mt)
REVERT: A   10 TYR cc_start: 0.7450 (m-80) cc_final: 0.7202 (m-80)
REVERT: A   26 SER cc_start: 0.7951 (m) cc_final: 0.7407 (t)
REVERT: C   22 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7928 (mm-30)
REVERT: C   26 SER cc_start: 0.7929 (m) cc_final: 0.7317 (t)
REVERT: B   22 GLU cc_start: 0.8278 (tp30) cc_final: 0.8022 (tp30)
REVERT: B   26 SER cc_start: 0.8220 (m) cc_final: 0.7693 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0831
  time to fit residues: 2.9315
Evaluate side-chains
  27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.130596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.099003 restraints weight = 1607.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 3.30
r_work: 0.3206 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1524  Z= 0.196
  Angle     :  0.470   2.446   2046  Z= 0.274
  Chirality :  0.062   0.147    234
  Planarity :  0.001   0.007    258
  Dihedral  :  4.547  12.144    204
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.00 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.55), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.03 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS G  14 
 PHE   0.004   0.001   PHE G  20 
 TYR   0.001   0.000   TYR D  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.165 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8307 (mm-30) cc_final: 0.6820 (pt0)
REVERT: F   26 SER cc_start: 0.8203 (m) cc_final: 0.7650 (t)
REVERT: G   31 ILE cc_start: 0.8713 (mt) cc_final: 0.8504 (mt)
REVERT: A   10 TYR cc_start: 0.7418 (m-80) cc_final: 0.7157 (m-80)
REVERT: A   22 GLU cc_start: 0.8097 (tp30) cc_final: 0.7718 (mm-30)
REVERT: A   26 SER cc_start: 0.7774 (m) cc_final: 0.7224 (t)
REVERT: C   22 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7954 (mm-30)
REVERT: C   26 SER cc_start: 0.7763 (m) cc_final: 0.7190 (t)
REVERT: B   26 SER cc_start: 0.8088 (m) cc_final: 0.7539 (t)
REVERT: D   23 ASP cc_start: 0.7237 (t70) cc_final: 0.7031 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0769
  time to fit residues: 2.5599
Evaluate side-chains
  26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.119462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.090290 restraints weight = 1735.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 3.29
r_work: 0.3372 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1524  Z= 0.236
  Angle     :  0.510   3.626   2046  Z= 0.295
  Chirality :  0.062   0.140    234
  Planarity :  0.002   0.017    258
  Dihedral  :  4.632  11.950    204
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.33 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.57), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.93 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS G  14 
 PHE   0.006   0.001   PHE G  20 
 TYR   0.001   0.000   TYR G  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.165 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8186 (mm-30) cc_final: 0.6809 (pt0)
REVERT: F   26 SER cc_start: 0.8222 (m) cc_final: 0.7645 (t)
REVERT: G   26 SER cc_start: 0.8343 (m) cc_final: 0.7837 (t)
REVERT: G   31 ILE cc_start: 0.8739 (mt) cc_final: 0.8524 (mt)
REVERT: A   10 TYR cc_start: 0.7380 (m-80) cc_final: 0.7119 (m-80)
REVERT: A   22 GLU cc_start: 0.8087 (tp30) cc_final: 0.7678 (mm-30)
REVERT: A   26 SER cc_start: 0.7778 (m) cc_final: 0.7204 (t)
REVERT: C   22 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7942 (mm-30)
REVERT: C   26 SER cc_start: 0.7799 (m) cc_final: 0.7213 (t)
REVERT: B   22 GLU cc_start: 0.8135 (tp30) cc_final: 0.7632 (mm-30)
REVERT: B   26 SER cc_start: 0.8132 (m) cc_final: 0.7578 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0798
  time to fit residues: 3.0171
Evaluate side-chains
  29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0770
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7942

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.134490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.102618 restraints weight = 1579.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 3.32
r_work: 0.3424 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   1524  Z= 0.139
  Angle     :  0.478   4.328   2046  Z= 0.279
  Chirality :  0.061   0.140    234
  Planarity :  0.001   0.017    258
  Dihedral  :  4.226  12.250    204
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.33 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.57), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.84 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS G  14 
 PHE   0.002   0.000   PHE B  19 
 TYR   0.002   0.000   TYR D  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.8048 (tp30) cc_final: 0.7687 (mm-30)
REVERT: C   22 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7997 (mm-30)
REVERT: B   22 GLU cc_start: 0.8046 (tp30) cc_final: 0.7582 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0961
  time to fit residues: 3.1997
Evaluate side-chains
  26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0980
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4048 r_free = 0.4048 target = 0.139560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.107942 restraints weight = 1563.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 3.33
r_work: 0.3318 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   1524  Z= 0.129
  Angle     :  0.460   3.328   2046  Z= 0.266
  Chirality :  0.061   0.134    234
  Planarity :  0.002   0.016    258
  Dihedral  :  4.164  11.786    204
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.33 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.57), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.80 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS G  14 
 PHE   0.002   0.000   PHE B  19 
 TYR   0.011   0.001   TYR A  10 

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

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

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  384 Ramachandran restraints generated.
    192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.8053 (tp30) cc_final: 0.7779 (mm-30)
REVERT: C   22 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7959 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0793
  time to fit residues: 2.6356
Evaluate side-chains
  26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.124864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.094493 restraints weight = 1744.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 3.43
r_work: 0.3462 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   1524  Z= 0.172
  Angle     :  0.475   3.294   2046  Z= 0.276
  Chirality :  0.061   0.138    234
  Planarity :  0.002   0.017    258
  Dihedral  :  4.166  11.282    204
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 24.00 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.57), residues: 192
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.78 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS G  14 
 PHE   0.003   0.001   PHE G  20 
 TYR   0.010   0.001   TYR A  10 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1230.69 seconds
wall clock time: 21 minutes 51.35 seconds (1311.35 seconds total)