Starting phenix.real_space_refine
on Fri Aug 22 15:00:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ccw_45460/08_2025/9ccw_45460.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ccw_45460/08_2025/9ccw_45460.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ccw_45460/08_2025/9ccw_45460.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ccw_45460/08_2025/9ccw_45460.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ccw_45460/08_2025/9ccw_45460.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ccw_45460/08_2025/9ccw_45460.map"
  }
  resolution = 3.69
  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=   0.018
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      17      5.16       5
     C    2868      2.51       5
     N     760      2.21       5
     O     912      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4557
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1227
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 10, 'TRANS': 153}
    Chain: "B"
      Number of atoms: 1645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1645
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 205}
    Chain: "C"
      Number of atoms: 1685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1685
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 211}
  Time building chain proxies: 1.02, per 1000 atoms: 0.22
  Number of scatterers: 4557
  At special positions: 0
  Unit cell: (78.144, 66.304, 111.296, 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      17     16.00
     O     912      8.00
     N     760      7.00
     C    2868      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   3 " - pdb=" SG  CYS A  44 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 139 " - pdb=" SG  CYS B 199 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  27 " - pdb=" SG  CYS C 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 153 " - pdb=" SG  CYS C 209 " 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: 0.27
  Conformation dependent library (CDL) restraints added in 183.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1108

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 14 sheets defined
      5.8% alpha, 33.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 40
      removed outlier: 3.533A  pdb=" N   THR A  40 " --> pdb=" O   ASP A  37 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 37 through 40'
    Processing helix  chain 'B' and resid 55 through 57
      No H-bonds generated for 'chain 'B' and resid 55 through 57'
    Processing helix  chain 'B' and resid 127 through 132
      removed outlier: 4.327A  pdb=" N   LYS B 131 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 192
    Processing helix  chain 'C' and resid 33 through 37
      removed outlier: 3.542A  pdb=" N   SER C  36 " --> pdb=" O   THR C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 171
    Processing helix  chain 'C' and resid 199 through 205
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 21
      removed outlier: 3.625A  pdb=" N   GLY A  16 " --> pdb=" O   GLN A 143 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   PHE A 142 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN A 133 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA A 127 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   ILE A 126 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ALA A  63 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL A 128 " --> pdb=" O   GLY A  61 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLY A  61 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ILE A 130 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75
    Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 10
    Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 17
      removed outlier: 3.730A  pdb=" N   GLU B 110 " --> pdb=" O   MET B  16 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   GLN B  42 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   VAL B  51 " --> pdb=" O   GLN B  42 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 123
      removed outlier: 3.619A  pdb=" N   SER B 119 " --> pdb=" O   ASN B 142 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   TYR B 178 " --> pdb=" O   ASN B 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 155
    Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 12
      removed outlier: 3.607A  pdb=" N   CYS C  27 " --> pdb=" O   LEU C  84 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   THR C  83 " --> pdb=" O   ASP C  78 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ASP C  78 " --> pdb=" O   THR C  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 15 through 17
      removed outlier: 4.146A  pdb=" N   GLY C  15 " --> pdb=" O   THR C 121 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   THR C 123 " --> pdb=" O   GLY C  15 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   MET C  39 " --> pdb=" O   TYR C  55 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   TYR C  55 " --> pdb=" O   MET C  39 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   TRP C  41 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TYR C  64 " --> pdb=" O   TYR C  55 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 15 through 17
      removed outlier: 4.146A  pdb=" N   GLY C  15 " --> pdb=" O   THR C 121 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   THR C 123 " --> pdb=" O   GLY C  15 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   VAL C 115 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 133 through 136
      removed outlier: 5.980A  pdb=" N   TYR C 189 " --> pdb=" O   ASP C 157 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 148 through 151
    Processing sheet with id=AB5, first strand: chain 'C' and resid 208 through 213

    140 hydrogen bonds defined for protein.
    345 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: 0.63

  Time building geometry restraints manager: 0.40 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: 1456
        1.34 -     1.47: 1190
        1.47 -     1.59: 1993
        1.59 -     1.71: 0
        1.71 -     1.83: 22
  Bond restraints: 4661
  Sorted by residual:
  bond pdb=" CA  CYS B 199 "
       pdb=" CB  CYS B 199 "
    ideal  model  delta    sigma   weight residual
    1.528  1.581 -0.053 2.61e-02 1.47e+03 4.15e+00
  bond pdb=" C   PHE A  84 "
       pdb=" N   PRO A  85 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.034 2.34e-02 1.83e+03 2.06e+00
  bond pdb=" CA  ASN C 210 "
       pdb=" CB  ASN C 210 "
    ideal  model  delta    sigma   weight residual
    1.532  1.550 -0.019 1.74e-02 3.30e+03 1.17e+00
  bond pdb=" CB  ASN C 210 "
       pdb=" CG  ASN C 210 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.10e+00
  bond pdb=" CA  LYS C 214 "
       pdb=" C   LYS C 214 "
    ideal  model  delta    sigma   weight residual
    1.521  1.532 -0.012 1.14e-02 7.69e+03 1.04e+00
  ... (remaining 4656 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 6281
        2.87 -     5.75: 62
        5.75 -     8.62: 6
        8.62 -    11.50: 1
       11.50 -    14.37: 1
  Bond angle restraints: 6351
  Sorted by residual:
  angle pdb=" CB  MET B   9 "
        pdb=" CG  MET B   9 "
        pdb=" SD  MET B   9 "
      ideal   model   delta    sigma   weight residual
     112.70  127.07  -14.37 3.00e+00 1.11e-01 2.30e+01
  angle pdb=" N   MET B   9 "
        pdb=" CA  MET B   9 "
        pdb=" C   MET B   9 "
      ideal   model   delta    sigma   weight residual
     109.71  104.38    5.33 1.41e+00 5.03e-01 1.43e+01
  angle pdb=" CA  LEU B 101 "
        pdb=" CB  LEU B 101 "
        pdb=" CG  LEU B 101 "
      ideal   model   delta    sigma   weight residual
     116.30  127.72  -11.42 3.50e+00 8.16e-02 1.06e+01
  angle pdb=" C   PRO B 124 "
        pdb=" N   PRO B 125 "
        pdb=" CA  PRO B 125 "
      ideal   model   delta    sigma   weight residual
     121.65  118.43    3.22 1.01e+00 9.80e-01 1.02e+01
  angle pdb=" N   VAL C 182 "
        pdb=" CA  VAL C 182 "
        pdb=" C   VAL C 182 "
      ideal   model   delta    sigma   weight residual
     109.34  115.52   -6.18 2.08e+00 2.31e-01 8.82e+00
  ... (remaining 6346 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 2357
       17.60 -    35.20: 310
       35.20 -    52.80: 82
       52.80 -    70.40: 10
       70.40 -    88.00: 7
  Dihedral angle restraints: 2766
    sinusoidal: 1029
      harmonic: 1737
  Sorted by residual:
  dihedral pdb=" CA  PHE A  84 "
           pdb=" C   PHE A  84 "
           pdb=" N   PRO A  85 "
           pdb=" CA  PRO A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -129.74  -50.26     0      5.00e+00 4.00e-02 1.01e+02
  dihedral pdb=" CA  GLU C 161 "
           pdb=" C   GLU C 161 "
           pdb=" N   PRO C 162 "
           pdb=" CA  PRO C 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.67   24.33     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  VAL C 163 "
           pdb=" C   VAL C 163 "
           pdb=" N   THR C 164 "
           pdb=" CA  THR C 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.13   22.87     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 2763 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 519
       0.049 -    0.098: 148
       0.098 -    0.146: 51
       0.146 -    0.195: 6
       0.195 -    0.244: 2
  Chirality restraints: 726
  Sorted by residual:
  chirality pdb=" CB  ILE C  63 "
            pdb=" CA  ILE C  63 "
            pdb=" CG1 ILE C  63 "
            pdb=" CG2 ILE C  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CB  VAL C 165 "
            pdb=" CA  VAL C 165 "
            pdb=" CG1 VAL C 165 "
            pdb=" CG2 VAL C 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  VAL C 109 "
            pdb=" N   VAL C 109 "
            pdb=" C   VAL C 109 "
            pdb=" CB  VAL C 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.17 2.00e-01 2.50e+01 7.58e-01
  ... (remaining 723 not shown)

  Planarity restraints: 813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  84 "    0.047 5.00e-02 4.00e+02   7.17e-02 8.22e+00
        pdb=" N   PRO A  85 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A  85 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  85 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 101 "    0.044 5.00e-02 4.00e+02   6.74e-02 7.27e+00
        pdb=" N   PRO A 102 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 156 "   -0.043 5.00e-02 4.00e+02   6.50e-02 6.77e+00
        pdb=" N   PRO A 157 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 157 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 157 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 810 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 88
        2.64 -     3.21: 4086
        3.21 -     3.77: 7000
        3.77 -     4.34: 9423
        4.34 -     4.90: 15338
  Nonbonded interactions: 35935
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 105 "
            pdb=" O   SER C 110 "
     model   vdw
     2.078 3.040
  nonbonded pdb=" OD1 ASP C  95 "
            pdb=" OH  TYR C  99 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OH  TYR B  41 "
            pdb=" O   TYR C 112 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OH  TYR C 100 "
            pdb=" O   GLY C 117 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   TYR B 191 "
            pdb=" OH  TYR B 197 "
     model   vdw
     2.231 3.040
  ... (remaining 35930 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.420
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.050
  Find NCS groups from input model:        0.020
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5783
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      :  0.004   0.053   4666  Z= 0.173
  Angle     :  0.811  14.374   6361  Z= 0.438
  Chirality :  0.051   0.244    726
  Planarity :  0.007   0.072    813
  Dihedral  : 17.064  87.996   1643
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 11.43 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 26.16 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.02 (0.32), residues: 595
  helix: -1.31 (1.92), residues: 6
  sheet: -1.41 (0.36), residues: 191
  loop : -2.47 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  98 
 TYR   0.013   0.001   TYR C 189 
 PHE   0.027   0.002   PHE B  67 
 TRP   0.007   0.001   TRP B  40 
 HIS   0.003   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4661)
  covalent geometry    : angle       0.80978 ( 6351)
  SS BOND              : bond        0.00492 (    5)
  SS BOND              : angle       1.55047 (   10)
  hydrogen bonds       : bond        0.15090 (  135)
  hydrogen bonds       : angle       9.79470 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.180 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0521
  time to fit residues: 5.2250
Evaluate side-chains
  74 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.4450 r_free = 0.4450 target = 0.189639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.172440 restraints weight = 7397.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.176615 restraints weight = 4323.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.179430 restraints weight = 2763.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.181352 restraints weight = 1899.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.182614 restraints weight = 1396.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5876
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4666  Z= 0.219
  Angle     :  0.729   9.112   6361  Z= 0.392
  Chirality :  0.049   0.163    726
  Planarity :  0.007   0.072    813
  Dihedral  :  6.393  44.621    647
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.94 %
    Favored  : 86.72 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 22.48 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.29 (0.32), residues: 595
  helix: -1.78 (1.34), residues: 12
  sheet: -1.82 (0.33), residues: 215
  loop : -2.53 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  77 
 TYR   0.017   0.002   TYR B  54 
 PHE   0.022   0.002   PHE C 159 
 TRP   0.016   0.002   TRP C 116 
 HIS   0.005   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 4661)
  covalent geometry    : angle       0.72739 ( 6351)
  SS BOND              : bond        0.00627 (    5)
  SS BOND              : angle       1.47441 (   10)
  hydrogen bonds       : bond        0.03762 (  135)
  hydrogen bonds       : angle       9.13778 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  151 ASN cc_start: 0.6528 (t0) cc_final: 0.6184 (t0)
REVERT: C  100 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7317 (t80)
REVERT: C  113 PHE cc_start: 0.6914 (m-80) cc_final: 0.6534 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 95
  average time/residue: 0.0595
  time to fit residues: 7.5041
Evaluate side-chains
  99 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain B residue   14 LYS
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  163 VAL
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  212 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 7 optimal weight:    0.1980
   chunk 19 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0030
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** 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 = 0.4485 r_free = 0.4485 target = 0.192763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.175318 restraints weight = 7317.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.179520 restraints weight = 4261.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.182404 restraints weight = 2742.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.184493 restraints weight = 1882.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.185923 restraints weight = 1358.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.4411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5796
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4666  Z= 0.137
  Angle     :  0.649   8.700   6361  Z= 0.346
  Chirality :  0.047   0.187    726
  Planarity :  0.006   0.067    813
  Dihedral  :  5.997  46.378    647
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 10.76 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 24.22 %
    Favored  : 70.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.18 (0.32), residues: 595
  helix: -1.53 (1.40), residues: 12
  sheet: -1.64 (0.34), residues: 213
  loop : -2.52 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  77 
 TYR   0.013   0.001   TYR B  54 
 PHE   0.013   0.001   PHE C 159 
 TRP   0.010   0.001   TRP C 116 
 HIS   0.002   0.001   HIS A  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4661)
  covalent geometry    : angle       0.64817 ( 6351)
  SS BOND              : bond        0.00204 (    5)
  SS BOND              : angle       1.22766 (   10)
  hydrogen bonds       : bond        0.03029 (  135)
  hydrogen bonds       : angle       8.35451 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  137 TYR cc_start: 0.7378 (t80) cc_final: 0.7023 (t80)
REVERT: A  151 ASN cc_start: 0.6728 (t0) cc_final: 0.6244 (t0)
REVERT: B   87 ASP cc_start: 0.7492 (m-30) cc_final: 0.7264 (m-30)
REVERT: C  100 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.7167 (t80)
REVERT: C  113 PHE cc_start: 0.6887 (m-80) cc_final: 0.6501 (m-80)
  outliers start: 27
  outliers final: 17
  residues processed: 98
  average time/residue: 0.0565
  time to fit residues: 7.2949
Evaluate side-chains
  98 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain B residue   14 LYS
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  104 ASP
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  212 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.188837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.171654 restraints weight = 7278.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.175860 restraints weight = 4242.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.178782 restraints weight = 2714.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.180789 restraints weight = 1856.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.182117 restraints weight = 1342.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5884
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4666  Z= 0.196
  Angle     :  0.696   8.048   6361  Z= 0.374
  Chirality :  0.048   0.220    726
  Planarity :  0.007   0.069    813
  Dihedral  :  6.275  45.519    647
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 14.62 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 25.58 %
    Favored  : 68.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.30 (0.32), residues: 595
  helix: -1.99 (1.35), residues: 12
  sheet: -1.81 (0.33), residues: 209
  loop : -2.54 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  77 
 TYR   0.013   0.002   TYR B  54 
 PHE   0.011   0.002   PHE C 159 
 TRP   0.014   0.002   TRP C 116 
 HIS   0.005   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 4661)
  covalent geometry    : angle       0.69287 ( 6351)
  SS BOND              : bond        0.00330 (    5)
  SS BOND              : angle       1.86773 (   10)
  hydrogen bonds       : bond        0.03454 (  135)
  hydrogen bonds       : angle       8.56259 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  151 ASN cc_start: 0.6929 (t0) cc_final: 0.6356 (t0)
REVERT: B  172 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6249 (t70)
REVERT: C   61 ASP cc_start: 0.6023 (p0) cc_final: 0.5589 (p0)
REVERT: C  100 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7187 (t80)
REVERT: C  111 ARG cc_start: 0.6483 (mtt90) cc_final: 0.5997 (mtt90)
REVERT: C  113 PHE cc_start: 0.6897 (m-80) cc_final: 0.6543 (m-80)
  outliers start: 31
  outliers final: 25
  residues processed: 105
  average time/residue: 0.0629
  time to fit residues: 8.6374
Evaluate side-chains
  111 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain B residue   14 LYS
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  172 ASP
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  104 ASP
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  212 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.187110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.170256 restraints weight = 7308.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.174382 restraints weight = 4273.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.177229 restraints weight = 2736.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.179217 restraints weight = 1876.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.180529 restraints weight = 1354.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5932
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4666  Z= 0.228
  Angle     :  0.728  10.536   6361  Z= 0.393
  Chirality :  0.050   0.253    726
  Planarity :  0.007   0.071    813
  Dihedral  :  6.567  46.922    647
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 14.62 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 26.55 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.35 (0.32), residues: 595
  helix: -2.20 (1.36), residues: 12
  sheet: -1.89 (0.34), residues: 196
  loop : -2.53 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  77 
 TYR   0.013   0.002   TYR B  54 
 PHE   0.011   0.002   PHE B  67 
 TRP   0.013   0.002   TRP C 116 
 HIS   0.006   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 4661)
  covalent geometry    : angle       0.72551 ( 6351)
  SS BOND              : bond        0.00356 (    5)
  SS BOND              : angle       1.74337 (   10)
  hydrogen bonds       : bond        0.03626 (  135)
  hydrogen bonds       : angle       8.81946 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 88
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  151 ASN cc_start: 0.7024 (t0) cc_final: 0.6527 (t0)
REVERT: B  172 ASP cc_start: 0.6551 (OUTLIER) cc_final: 0.6293 (t70)
REVERT: B  177 THR cc_start: 0.7686 (p) cc_final: 0.7403 (t)
REVERT: C   61 ASP cc_start: 0.6053 (p0) cc_final: 0.5656 (p0)
REVERT: C  100 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7162 (t80)
REVERT: C  111 ARG cc_start: 0.6715 (mtt90) cc_final: 0.6347 (mtt90)
REVERT: C  113 PHE cc_start: 0.6965 (m-80) cc_final: 0.6548 (m-80)
  outliers start: 33
  outliers final: 22
  residues processed: 109
  average time/residue: 0.0604
  time to fit residues: 8.5381
Evaluate side-chains
  112 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  172 ASP
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  104 ASP
Chi-restraints excluded: chain C residue  212 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.187010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.170103 restraints weight = 7361.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.174239 restraints weight = 4313.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.177081 restraints weight = 2775.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.178884 restraints weight = 1902.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.180306 restraints weight = 1401.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.4341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5939
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4666  Z= 0.219
  Angle     :  0.739  12.300   6361  Z= 0.398
  Chirality :  0.050   0.237    726
  Planarity :  0.007   0.070    813
  Dihedral  :  6.654  46.920    647
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 14.62 %
    Favored  : 85.04 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 26.36 %
    Favored  : 66.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.41 (0.32), residues: 595
  helix: -2.32 (1.07), residues: 18
  sheet: -1.92 (0.33), residues: 200
  loop : -2.57 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  77 
 TYR   0.014   0.002   TYR C 189 
 PHE   0.017   0.002   PHE A 142 
 TRP   0.012   0.002   TRP C 116 
 HIS   0.005   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 4661)
  covalent geometry    : angle       0.73694 ( 6351)
  SS BOND              : bond        0.00312 (    5)
  SS BOND              : angle       1.56504 (   10)
  hydrogen bonds       : bond        0.03554 (  135)
  hydrogen bonds       : angle       8.78320 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 90
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 ASN cc_start: 0.7067 (t0) cc_final: 0.6651 (t0)
REVERT: B   88 LEU cc_start: 0.7287 (mp) cc_final: 0.7006 (mp)
REVERT: B  172 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6273 (t70)
REVERT: C   61 ASP cc_start: 0.6049 (p0) cc_final: 0.5646 (p0)
REVERT: C  100 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7095 (t80)
REVERT: C  113 PHE cc_start: 0.6971 (m-80) cc_final: 0.6483 (m-80)
REVERT: C  219 LYS cc_start: 0.6401 (OUTLIER) cc_final: 0.6073 (mmtt)
REVERT: C  223 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5952 (tmmt)
  outliers start: 37
  outliers final: 28
  residues processed: 114
  average time/residue: 0.0593
  time to fit residues: 8.8756
Evaluate side-chains
  117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 85
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   45 HIS
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain B residue   14 LYS
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  172 ASP
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  104 ASP
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  212 ASN
Chi-restraints excluded: chain C residue  219 LYS
Chi-restraints excluded: chain C residue  223 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.186322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.169026 restraints weight = 7372.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.173315 restraints weight = 4269.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.176188 restraints weight = 2726.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.178267 restraints weight = 1866.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.179640 restraints weight = 1343.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5960
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4666  Z= 0.229
  Angle     :  0.744  11.436   6361  Z= 0.404
  Chirality :  0.051   0.208    726
  Planarity :  0.007   0.070    813
  Dihedral  :  6.784  47.232    647
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 18.71
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 16.30 %
    Favored  : 83.36 %
  Rotamer:
    Outliers :  6.98 %
    Allowed  : 27.71 %
    Favored  : 65.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.53 (0.32), residues: 595
  helix: -2.24 (1.04), residues: 18
  sheet: -1.91 (0.34), residues: 198
  loop : -2.72 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  77 
 TYR   0.013   0.002   TYR C 189 
 PHE   0.013   0.002   PHE A 142 
 TRP   0.011   0.002   TRP B  40 
 HIS   0.005   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 4661)
  covalent geometry    : angle       0.74275 ( 6351)
  SS BOND              : bond        0.00202 (    5)
  SS BOND              : angle       1.35502 (   10)
  hydrogen bonds       : bond        0.03685 (  135)
  hydrogen bonds       : angle       8.88477 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 83
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 ASN cc_start: 0.6035 (p0) cc_final: 0.5742 (p0)
REVERT: A  151 ASN cc_start: 0.7062 (t0) cc_final: 0.6629 (t0)
REVERT: B   88 LEU cc_start: 0.7198 (mp) cc_final: 0.6938 (mp)
REVERT: B  172 ASP cc_start: 0.6537 (OUTLIER) cc_final: 0.6297 (t70)
REVERT: C   44 GLN cc_start: 0.4868 (OUTLIER) cc_final: 0.3072 (tm-30)
REVERT: C   61 ASP cc_start: 0.6062 (p0) cc_final: 0.5655 (p0)
REVERT: C  100 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7129 (t80)
REVERT: C  113 PHE cc_start: 0.7174 (m-80) cc_final: 0.6648 (m-80)
REVERT: C  223 LYS cc_start: 0.6318 (OUTLIER) cc_final: 0.5916 (tmmt)
  outliers start: 36
  outliers final: 27
  residues processed: 106
  average time/residue: 0.0665
  time to fit residues: 9.0127
Evaluate side-chains
  113 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain B residue   14 LYS
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  172 ASP
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   44 GLN
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  104 ASP
Chi-restraints excluded: chain C residue  111 ARG
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  212 ASN
Chi-restraints excluded: chain C residue  223 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** 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 = 0.4408 r_free = 0.4408 target = 0.185873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.168541 restraints weight = 7305.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.172783 restraints weight = 4215.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.175754 restraints weight = 2696.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.177778 restraints weight = 1838.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.179220 restraints weight = 1332.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5978
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4666  Z= 0.244
  Angle     :  0.766  11.863   6361  Z= 0.416
  Chirality :  0.052   0.205    726
  Planarity :  0.007   0.071    813
  Dihedral  :  6.915  46.359    647
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 15.80 %
    Favored  : 83.87 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 28.10 %
    Favored  : 65.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.59 (0.32), residues: 595
  helix: -2.13 (1.05), residues: 18
  sheet: -1.80 (0.36), residues: 180
  loop : -2.86 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  77 
 TYR   0.014   0.002   TYR C 107 
 PHE   0.017   0.002   PHE A 142 
 TRP   0.011   0.002   TRP B  40 
 HIS   0.005   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 4661)
  covalent geometry    : angle       0.76382 ( 6351)
  SS BOND              : bond        0.00240 (    5)
  SS BOND              : angle       1.54647 (   10)
  hydrogen bonds       : bond        0.03754 (  135)
  hydrogen bonds       : angle       9.11123 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  136 ASN cc_start: 0.6108 (p0) cc_final: 0.5839 (p0)
REVERT: A  151 ASN cc_start: 0.7066 (t0) cc_final: 0.6642 (t0)
REVERT: B   88 LEU cc_start: 0.7260 (mp) cc_final: 0.6999 (mp)
REVERT: B  172 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6309 (t70)
REVERT: C   61 ASP cc_start: 0.6070 (p0) cc_final: 0.5697 (p0)
REVERT: C  100 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7117 (t80)
REVERT: C  113 PHE cc_start: 0.7123 (m-80) cc_final: 0.6495 (m-80)
REVERT: C  223 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5877 (tmmt)
  outliers start: 31
  outliers final: 23
  residues processed: 104
  average time/residue: 0.0707
  time to fit residues: 9.3593
Evaluate side-chains
  107 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  172 ASP
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  104 ASP
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  212 ASN
Chi-restraints excluded: chain C residue  223 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 43 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 42 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** 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 = 0.4421 r_free = 0.4421 target = 0.187088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.169743 restraints weight = 7217.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.174047 restraints weight = 4183.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.176989 restraints weight = 2668.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.178985 restraints weight = 1820.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.180398 restraints weight = 1323.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5936
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4666  Z= 0.192
  Angle     :  0.722  11.022   6361  Z= 0.392
  Chirality :  0.050   0.182    726
  Planarity :  0.007   0.070    813
  Dihedral  :  6.665  48.241    647
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 17.82
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 15.13 %
    Favored  : 84.54 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 28.68 %
    Favored  : 65.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.46 (0.32), residues: 595
  helix: -2.22 (1.05), residues: 18
  sheet: -1.71 (0.36), residues: 186
  loop : -2.76 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 111 
 TYR   0.015   0.002   TYR B  54 
 PHE   0.011   0.002   PHE B  67 
 TRP   0.011   0.002   TRP B  40 
 HIS   0.004   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 4661)
  covalent geometry    : angle       0.72045 ( 6351)
  SS BOND              : bond        0.00169 (    5)
  SS BOND              : angle       1.33874 (   10)
  hydrogen bonds       : bond        0.03455 (  135)
  hydrogen bonds       : angle       8.76262 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 ASN cc_start: 0.6097 (p0) cc_final: 0.5841 (p0)
REVERT: A  137 TYR cc_start: 0.7593 (t80) cc_final: 0.7055 (t80)
REVERT: A  151 ASN cc_start: 0.7191 (t0) cc_final: 0.6711 (t0)
REVERT: B   88 LEU cc_start: 0.7194 (mp) cc_final: 0.6935 (mp)
REVERT: C   61 ASP cc_start: 0.6273 (p0) cc_final: 0.5826 (p0)
REVERT: C  100 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7056 (t80)
REVERT: C  113 PHE cc_start: 0.7046 (m-80) cc_final: 0.6537 (m-80)
REVERT: C  223 LYS cc_start: 0.6253 (OUTLIER) cc_final: 0.5790 (tmmt)
  outliers start: 29
  outliers final: 24
  residues processed: 104
  average time/residue: 0.0533
  time to fit residues: 7.2662
Evaluate side-chains
  109 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  104 ASP
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  212 ASN
Chi-restraints excluded: chain C residue  223 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 41 optimal weight:    0.3980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** 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 = 0.4413 r_free = 0.4413 target = 0.186413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.169635 restraints weight = 7285.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.173737 restraints weight = 4266.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.176601 restraints weight = 2729.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.178349 restraints weight = 1867.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.179793 restraints weight = 1380.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5960
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4666  Z= 0.216
  Angle     :  0.755   9.832   6361  Z= 0.410
  Chirality :  0.051   0.182    726
  Planarity :  0.007   0.070    813
  Dihedral  :  6.795  47.300    647
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 16.13 %
    Favored  : 83.53 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 28.68 %
    Favored  : 65.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.50 (0.32), residues: 595
  helix: -2.26 (1.04), residues: 18
  sheet: -1.78 (0.35), residues: 186
  loop : -2.77 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 111 
 TYR   0.012   0.002   TYR C 189 
 PHE   0.013   0.002   PHE B  67 
 TRP   0.012   0.002   TRP B  40 
 HIS   0.004   0.001   HIS B  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 4661)
  covalent geometry    : angle       0.75479 ( 6351)
  SS BOND              : bond        0.00306 (    5)
  SS BOND              : angle       1.00983 (   10)
  hydrogen bonds       : bond        0.03605 (  135)
  hydrogen bonds       : angle       9.03709 (  345)

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

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

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1190 Ramachandran restraints generated.
    595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  136 ASN cc_start: 0.6026 (p0) cc_final: 0.5752 (p0)
REVERT: A  137 TYR cc_start: 0.7564 (t80) cc_final: 0.7026 (t80)
REVERT: A  151 ASN cc_start: 0.7217 (t0) cc_final: 0.6791 (t0)
REVERT: C   61 ASP cc_start: 0.6069 (p0) cc_final: 0.5674 (p0)
REVERT: C  100 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.7134 (t80)
REVERT: C  223 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5790 (tmmt)
  outliers start: 28
  outliers final: 24
  residues processed: 100
  average time/residue: 0.0735
  time to fit residues: 9.3740
Evaluate side-chains
  108 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  219 CYS
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue   89 SER
Chi-restraints excluded: chain C residue   98 MET
Chi-restraints excluded: chain C residue  100 TYR
Chi-restraints excluded: chain C residue  104 ASP
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  212 ASN
Chi-restraints excluded: chain C residue  223 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0370
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** 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 = 0.4436 r_free = 0.4436 target = 0.188399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.171330 restraints weight = 7391.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.175514 restraints weight = 4275.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.178438 restraints weight = 2725.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.180460 restraints weight = 1856.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.181816 restraints weight = 1334.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5925
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4666  Z= 0.183
  Angle     :  0.718   8.205   6361  Z= 0.390
  Chirality :  0.050   0.183    726
  Planarity :  0.007   0.070    813
  Dihedral  :  6.596  47.091    647
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 14.12 %
    Favored  : 85.55 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 29.46 %
    Favored  : 65.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.34 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    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 aren not related in a simple way.
  whole: -3.46 (0.32), residues: 595
  helix: -2.11 (1.06), residues: 18
  sheet: -1.79 (0.35), residues: 192
  loop : -2.72 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 111 
 TYR   0.015   0.002   TYR C 107 
 PHE   0.012   0.002   PHE B  67 
 TRP   0.011   0.002   TRP B  40 
 HIS   0.004   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 4661)
  covalent geometry    : angle       0.71770 ( 6351)
  SS BOND              : bond        0.00293 (    5)
  SS BOND              : angle       0.98367 (   10)
  hydrogen bonds       : bond        0.03363 (  135)
  hydrogen bonds       : angle       8.76256 (  345)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 829.79 seconds
wall clock time: 15 minutes 1.29 seconds (901.29 seconds total)