Starting phenix.real_space_refine
on Wed Mar 12 23:44:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8crb_16807/03_2025/8crb_16807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8crb_16807/03_2025/8crb_16807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8crb_16807/03_2025/8crb_16807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8crb_16807/03_2025/8crb_16807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8crb_16807/03_2025/8crb_16807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8crb_16807/03_2025/8crb_16807.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    2743      2.51       5
     N     738      2.21       5
     O     885      1.98       5
     H    4286      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8665
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 3320
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214}
    Chain: "B"
      Number of atoms: 3187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 3187
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 198}
    Chain: "C"
      Number of atoms: 2158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2158
          Classifications: {'peptide': 139}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 4.38, per 1000 atoms: 0.51
  Number of scatterers: 8665
  At special positions: 0
  Unit cell: (73.1, 81.6, 113.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     O     885      8.00
     N     738      7.00
     C    2743      6.00
     H    4286      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.93
  Conformation dependent library (CDL) restraints added in 748.2 milliseconds
  

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1064

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 11 sheets defined
      21.8% alpha, 29.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 76
      No H-bonds generated for 'chain 'A' and resid 74 through 76'
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.666A  pdb=" N   ASP A  90 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 146
      removed outlier: 4.321A  pdb=" N   SER A 146 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 80 through 84
    Processing helix  chain 'B' and resid 125 through 130
    Processing helix  chain 'B' and resid 185 through 192
    Processing helix  chain 'B' and resid 211 through 215
    Processing helix  chain 'C' and resid 129 through 158
      removed outlier: 3.584A  pdb=" N   ALA C 154 " --> pdb=" O   SER C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 177
    Processing helix  chain 'C' and resid 189 through 198
    Processing helix  chain 'C' and resid 206 through 212
    Processing helix  chain 'C' and resid 236 through 264
      Proline residue:  C 250  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.546A  pdb=" N   THR A 121 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.546A  pdb=" N   THR A 121 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR A 116 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 137
      removed outlier: 3.518A  pdb=" N   SER A 134 " --> pdb=" O   LYS A 157 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   TYR A 190 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 168
    Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.715A  pdb=" N   ASP B  86 " --> pdb=" O   GLN B  39 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN B  39 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23
    Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 122
      removed outlier: 6.162A  pdb=" N   TYR B 176 " --> pdb=" O   ASP B 142 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 122
      removed outlier: 6.162A  pdb=" N   TYR B 176 " --> pdb=" O   ASP B 142 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 157 through 158
    Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163

    198 hydrogen bonds defined for protein.
    501 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: 2.75

  Time building geometry restraints manager: 2.42 seconds

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

  Histogram of bond lengths:
        0.93 -     1.11: 4275
        1.11 -     1.29: 732
        1.29 -     1.46: 1380
        1.46 -     1.64: 2361
        1.64 -     1.81: 15
  Bond restraints: 8763
  Sorted by residual:
  bond pdb=" N   SER A  49 "
       pdb=" H   SER A  49 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   ASN A  74 "
       pdb=" H   ASN A  74 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   GLY B  69 "
       pdb=" H   GLY B  69 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   ASN B 174 "
       pdb=" H   ASN B 174 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" CD1 PHE A 160 "
       pdb=" HD1 PHE A 160 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 8758 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.08: 13930
        3.08 -     6.15: 1519
        6.15 -     9.23: 352
        9.23 -    12.31: 8
       12.31 -    15.39: 5
  Bond angle restraints: 15814
  Sorted by residual:
  angle pdb=" N   PRO B   7 "
        pdb=" CA  PRO B   7 "
        pdb=" C   PRO B   7 "
      ideal   model   delta    sigma   weight residual
     110.70  121.25  -10.55 1.22e+00 6.72e-01 7.48e+01
  angle pdb=" C   LYS B  46 "
        pdb=" N   VAL B  47 "
        pdb=" CA  VAL B  47 "
      ideal   model   delta    sigma   weight residual
     120.50  128.86   -8.36 1.34e+00 5.57e-01 3.89e+01
  angle pdb=" CA  PHE A 114 "
        pdb=" CB  PHE A 114 "
        pdb=" CG  PHE A 114 "
      ideal   model   delta    sigma   weight residual
     113.80  119.77   -5.97 1.00e+00 1.00e+00 3.57e+01
  angle pdb=" CA  PHE A  27 "
        pdb=" CB  PHE A  27 "
        pdb=" CG  PHE A  27 "
      ideal   model   delta    sigma   weight residual
     113.80  119.39   -5.59 1.00e+00 1.00e+00 3.13e+01
  angle pdb=" C   GLY B 102 "
        pdb=" N   PRO B 103 "
        pdb=" CA  PRO B 103 "
      ideal   model   delta    sigma   weight residual
     119.87  125.68   -5.81 1.04e+00 9.25e-01 3.12e+01
  ... (remaining 15809 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 3783
       17.77 -    35.55: 282
       35.55 -    53.32: 102
       53.32 -    71.10: 30
       71.10 -    88.87: 8
  Dihedral angle restraints: 4205
    sinusoidal: 2281
      harmonic: 1924
  Sorted by residual:
  dihedral pdb=" CA  PRO B   7 "
           pdb=" C   PRO B   7 "
           pdb=" N   PRO B   8 "
           pdb=" CA  PRO B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.74  -29.26     0      5.00e+00 4.00e-02 3.42e+01
  dihedral pdb=" CA  SER B   2 "
           pdb=" C   SER B   2 "
           pdb=" N   VAL B   3 "
           pdb=" CA  VAL B   3 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.96  -29.04     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  ASN C 234 "
           pdb=" C   ASN C 234 "
           pdb=" N   ASN C 235 "
           pdb=" CA  ASN C 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.13  -28.87     0      5.00e+00 4.00e-02 3.33e+01
  ... (remaining 4202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 384
       0.083 -    0.165: 226
       0.165 -    0.248: 59
       0.248 -    0.330: 11
       0.330 -    0.412: 2
  Chirality restraints: 682
  Sorted by residual:
  chirality pdb=" CA  ASN B 174 "
            pdb=" N   ASN B 174 "
            pdb=" C   ASN B 174 "
            pdb=" CB  ASN B 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.25e+00
  chirality pdb=" CA  TYR A 108 "
            pdb=" N   TYR A 108 "
            pdb=" C   TYR A 108 "
            pdb=" CB  TYR A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.07e+00
  chirality pdb=" CA  ASN A 218 "
            pdb=" N   ASN A 218 "
            pdb=" C   ASN A 218 "
            pdb=" CB  ASN A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.44e+00
  ... (remaining 679 not shown)

  Planarity restraints: 1332
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  37 "    0.307 2.00e-02 2.50e+03   1.40e-01 5.87e+02
        pdb=" CG  TYR B  37 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  37 "   -0.086 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  37 "   -0.094 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  37 "   -0.082 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  37 "   -0.074 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  37 "    0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR B  37 "    0.306 2.00e-02 2.50e+03
        pdb=" HD1 TYR B  37 "   -0.047 2.00e-02 2.50e+03
        pdb=" HD2 TYR B  37 "   -0.073 2.00e-02 2.50e+03
        pdb=" HE1 TYR B  37 "   -0.077 2.00e-02 2.50e+03
        pdb=" HE2 TYR B  37 "   -0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 117 "    0.179 2.00e-02 2.50e+03   1.18e-01 5.53e+02
        pdb=" CG  TRP A 117 "    0.094 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 117 "    0.055 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 117 "   -0.058 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 117 "   -0.092 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 117 "   -0.078 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 117 "   -0.133 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 117 "   -0.037 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 117 "   -0.028 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 117 "    0.078 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 117 "    0.101 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 117 "   -0.153 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 117 "   -0.188 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 117 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 117 "    0.005 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 117 "    0.254 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  36 "   -0.175 2.00e-02 2.50e+03   7.09e-02 2.01e+02
        pdb=" CG  TRP A  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  36 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  36 "    0.050 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  36 "    0.069 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  36 "    0.026 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  36 "    0.069 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  36 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  36 "    0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  36 "   -0.037 2.00e-02 2.50e+03
        pdb=" HD1 TRP A  36 "   -0.047 2.00e-02 2.50e+03
        pdb=" HE1 TRP A  36 "    0.106 2.00e-02 2.50e+03
        pdb=" HE3 TRP A  36 "    0.079 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A  36 "   -0.076 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A  36 "    0.021 2.00e-02 2.50e+03
        pdb=" HH2 TRP A  36 "   -0.090 2.00e-02 2.50e+03
  ... (remaining 1329 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 639
        2.19 -     2.79: 15350
        2.79 -     3.39: 23731
        3.39 -     4.00: 29777
        4.00 -     4.60: 43550
  Nonbonded interactions: 113047
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  73 "
            pdb=" HG  SER A  75 "
     model   vdw
     1.584 2.450
  nonbonded pdb=" H   ASP A  73 "
            pdb=" HG  LEU A  79 "
     model   vdw
     1.586 2.270
  nonbonded pdb=" OD2 ASP C 199 "
            pdb=" HG  SER C 214 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" OD1 ASP C 173 "
            pdb=" HG1 THR C 175 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" HG  SER A  54 "
            pdb=" OD2 ASP C 246 "
     model   vdw
     1.625 2.450
  ... (remaining 113042 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:             0.330
  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:             0.150
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.230
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6407
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      :  0.013   0.043   4477  Z= 0.858
  Angle     :  1.985  10.554   6092  Z= 1.299
  Chirality :  0.105   0.412    682
  Planarity :  0.016   0.162    789
  Dihedral  : 14.753  88.871   1621
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  1.91 %
    Allowed  : 10.07 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  5.33 %
    Favored  : 93.44 %
  Cbeta Deviations :  0.38 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.30), residues: 576
  helix: -1.56 (0.40), residues: 109
  sheet: -1.03 (0.52), residues: 98
  loop : -2.13 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.144   0.030   TRP A 117 
 HIS   0.013   0.007   HIS A 214 
 PHE   0.079   0.017   PHE A 114 
 TYR   0.279   0.029   TYR B  37 
 ARG   0.004   0.001   ARG B  62 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 PHE cc_start: 0.0319 (p90) cc_final: -0.0730 (p90)
REVERT: A   67 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7382 (mpp80)
REVERT: A  117 TRP cc_start: 0.7366 (m100) cc_final: 0.7067 (m100)
REVERT: A  225 VAL cc_start: 0.7751 (t) cc_final: 0.7332 (t)
REVERT: B   67 LYS cc_start: 0.7176 (pttt) cc_final: 0.6547 (ptpp)
REVERT: B  159 VAL cc_start: 0.6504 (m) cc_final: 0.6280 (t)
REVERT: B  180 SER cc_start: 0.8146 (p) cc_final: 0.7789 (t)
REVERT: C  139 THR cc_start: 0.8712 (m) cc_final: 0.8502 (p)
REVERT: C  143 LYS cc_start: 0.8901 (tttt) cc_final: 0.8693 (tttt)
REVERT: C  153 ASN cc_start: 0.8141 (m-40) cc_final: 0.7856 (m-40)
  outliers start: 6
  outliers final: 3
  residues processed: 150
  average time/residue: 0.4660
  time to fit residues: 82.3031
Evaluate side-chains
  105 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
B 174 ASN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.127306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.105556 restraints weight = 47379.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.110317 restraints weight = 28186.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.113744 restraints weight = 18661.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6493
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4477  Z= 0.332
  Angle     :  0.880   7.567   6092  Z= 0.489
  Chirality :  0.047   0.181    682
  Planarity :  0.007   0.078    789
  Dihedral  :  8.621  36.704    630
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  : 11.46 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.31), residues: 576
  helix: -0.32 (0.46), residues: 107
  sheet: -1.40 (0.39), residues: 150
  loop : -2.56 (0.30), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  47 
 HIS   0.003   0.002   HIS B 201 
 PHE   0.021   0.003   PHE A  29 
 TYR   0.035   0.003   TYR B  37 
 ARG   0.005   0.001   ARG B  51 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.7668 (m100) cc_final: 0.7277 (m100)
REVERT: A   67 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7884 (mpt180)
REVERT: A  122 ARG cc_start: 0.6965 (ttm170) cc_final: 0.6433 (ttp-170)
REVERT: A  124 THR cc_start: 0.7903 (m) cc_final: 0.6909 (m)
REVERT: B   67 LYS cc_start: 0.7557 (pttt) cc_final: 0.6700 (ptpp)
REVERT: B   84 GLU cc_start: 0.8235 (tp30) cc_final: 0.7633 (tm-30)
REVERT: C  139 THR cc_start: 0.9216 (m) cc_final: 0.9005 (p)
REVERT: C  141 GLU cc_start: 0.9654 (mt-10) cc_final: 0.9355 (mt-10)
REVERT: C  199 ASP cc_start: 0.8103 (m-30) cc_final: 0.7797 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.3843
  time to fit residues: 56.8277
Evaluate side-chains
  94 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0670
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    3.0126

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

Flipped N/Q/H residues before XYZ refinement:
B 174 ASN
C 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.129467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.107648 restraints weight = 48722.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.112528 restraints weight = 29187.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.115943 restraints weight = 19386.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6474
moved from start:          0.4785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4477  Z= 0.232
  Angle     :  0.738   7.694   6092  Z= 0.409
  Chirality :  0.045   0.179    682
  Planarity :  0.007   0.075    789
  Dihedral  :  7.423  31.677    630
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 11.98 %
    Favored  : 87.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.32), residues: 576
  helix:  0.35 (0.47), residues: 101
  sheet: -1.41 (0.41), residues: 145
  loop : -2.71 (0.30), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  47 
 HIS   0.004   0.002   HIS A 178 
 PHE   0.013   0.002   PHE A 114 
 TYR   0.019   0.002   TYR B  37 
 ARG   0.003   0.000   ARG A 110 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7975 (mpt180)
REVERT: A  115 GLU cc_start: 0.6693 (tm-30) cc_final: 0.6060 (tm-30)
REVERT: A  122 ARG cc_start: 0.6749 (ttm170) cc_final: 0.6240 (ttp-170)
REVERT: A  124 THR cc_start: 0.8021 (m) cc_final: 0.6879 (m)
REVERT: A  154 CYS cc_start: 0.8125 (p) cc_final: 0.7546 (m)
REVERT: A  155 LEU cc_start: 0.8338 (tt) cc_final: 0.8052 (tt)
REVERT: A  224 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7638 (tpt-90)
REVERT: B   67 LYS cc_start: 0.7411 (pttt) cc_final: 0.6475 (ptpp)
REVERT: B   84 GLU cc_start: 0.8128 (tp30) cc_final: 0.7739 (tm-30)
REVERT: B  174 ASN cc_start: 0.8329 (m-40) cc_final: 0.8006 (t0)
REVERT: C  139 THR cc_start: 0.9183 (m) cc_final: 0.8975 (p)
REVERT: C  199 ASP cc_start: 0.8017 (m-30) cc_final: 0.7750 (p0)
REVERT: C  217 GLN cc_start: 0.7305 (mt0) cc_final: 0.6752 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.4006
  time to fit residues: 55.8926
Evaluate side-chains
  96 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    0.4980
   chunk 47 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 50 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** 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 = 0.4155 r_free = 0.4155 target = 0.128486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.105855 restraints weight = 47616.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.110693 restraints weight = 28368.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.114147 restraints weight = 18964.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6499
moved from start:          0.5334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4477  Z= 0.252
  Angle     :  0.722   6.868   6092  Z= 0.396
  Chirality :  0.044   0.166    682
  Planarity :  0.007   0.075    789
  Dihedral  :  7.279  32.753    630
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.15 %
    Favored  : 87.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.32), residues: 576
  helix:  0.11 (0.46), residues: 107
  sheet: -1.63 (0.40), residues: 153
  loop : -2.81 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  47 
 HIS   0.006   0.002   HIS A 178 
 PHE   0.033   0.002   PHE A  68 
 TYR   0.028   0.002   TYR A  60 
 ARG   0.005   0.001   ARG A  19 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.6705 (ttm170) cc_final: 0.6149 (ttp-170)
REVERT: A  124 THR cc_start: 0.8049 (m) cc_final: 0.6928 (m)
REVERT: A  154 CYS cc_start: 0.8114 (p) cc_final: 0.7690 (m)
REVERT: A  155 LEU cc_start: 0.8215 (tt) cc_final: 0.8003 (tt)
REVERT: A  224 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7680 (tpt-90)
REVERT: B   67 LYS cc_start: 0.7442 (pttt) cc_final: 0.6447 (ptpp)
REVERT: B   84 GLU cc_start: 0.8159 (tp30) cc_final: 0.7842 (tm-30)
REVERT: B  112 GLN cc_start: 0.9071 (tt0) cc_final: 0.8330 (tm-30)
REVERT: B  174 ASN cc_start: 0.8353 (m-40) cc_final: 0.8125 (t0)
REVERT: C  139 THR cc_start: 0.9210 (m) cc_final: 0.9005 (p)
REVERT: C  217 GLN cc_start: 0.7345 (mt0) cc_final: 0.6805 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.4134
  time to fit residues: 54.2664
Evaluate side-chains
  97 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 33 optimal weight:    0.0270
   chunk 28 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 6 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 48 optimal weight:    0.4980
   chunk 53 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 38 optimal weight:    0.5980
   overall best weight:    3.2242

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.128513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.105895 restraints weight = 46575.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.110593 restraints weight = 28081.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.113938 restraints weight = 18919.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4477  Z= 0.235
  Angle     :  0.688   6.220   6092  Z= 0.375
  Chirality :  0.044   0.162    682
  Planarity :  0.007   0.075    789
  Dihedral  :  6.986  32.682    630
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.85 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.32), residues: 576
  helix:  0.26 (0.46), residues: 107
  sheet: -1.85 (0.39), residues: 158
  loop : -2.78 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  47 
 HIS   0.005   0.002   HIS A 178 
 PHE   0.029   0.002   PHE A  68 
 TYR   0.018   0.002   TYR A  60 
 ARG   0.005   0.001   ARG A  19 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.7739 (m100) cc_final: 0.7432 (m100)
REVERT: A   69 THR cc_start: 0.8210 (t) cc_final: 0.7988 (t)
REVERT: A  122 ARG cc_start: 0.6651 (ttm170) cc_final: 0.6263 (ttp-170)
REVERT: A  124 THR cc_start: 0.8152 (m) cc_final: 0.7011 (m)
REVERT: A  154 CYS cc_start: 0.8212 (p) cc_final: 0.7825 (m)
REVERT: B   67 LYS cc_start: 0.7331 (pttt) cc_final: 0.6393 (ptpp)
REVERT: C  217 GLN cc_start: 0.7371 (mt0) cc_final: 0.6891 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.4267
  time to fit residues: 57.4671
Evaluate side-chains
  92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0040
   chunk 13 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   overall best weight:    2.9798

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.129072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.106308 restraints weight = 46362.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.111103 restraints weight = 27800.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.114443 restraints weight = 18798.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6477
moved from start:          0.5998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4477  Z= 0.221
  Angle     :  0.656   5.373   6092  Z= 0.357
  Chirality :  0.043   0.159    682
  Planarity :  0.007   0.074    789
  Dihedral  :  6.702  24.567    630
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 11.98 %
    Favored  : 87.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.32), residues: 576
  helix:  0.57 (0.47), residues: 101
  sheet: -1.79 (0.41), residues: 149
  loop : -2.65 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  92 
 HIS   0.005   0.002   HIS A 178 
 PHE   0.020   0.002   PHE A  68 
 TYR   0.018   0.002   TYR A  60 
 ARG   0.002   0.000   ARG A  38 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.7674 (m100) cc_final: 0.7327 (m100)
REVERT: A   65 LYS cc_start: 0.6613 (tmmt) cc_final: 0.6238 (tttm)
REVERT: A  122 ARG cc_start: 0.6623 (ttm170) cc_final: 0.6409 (ttp-170)
REVERT: A  124 THR cc_start: 0.8146 (m) cc_final: 0.6919 (m)
REVERT: A  191 SER cc_start: 0.8696 (p) cc_final: 0.8483 (p)
REVERT: B   67 LYS cc_start: 0.7268 (pttt) cc_final: 0.6294 (ptpp)
REVERT: B   84 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: B  137 VAL cc_start: 0.7595 (t) cc_final: 0.7328 (t)
REVERT: C  217 GLN cc_start: 0.7385 (mt0) cc_final: 0.6890 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.4104
  time to fit residues: 55.8308
Evaluate side-chains
  94 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 ASN
** B  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.126062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.103519 restraints weight = 47242.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.108181 restraints weight = 28526.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.111397 restraints weight = 19243.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
moved from start:          0.6198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4477  Z= 0.324
  Angle     :  0.736   5.415   6092  Z= 0.405
  Chirality :  0.045   0.162    682
  Planarity :  0.007   0.072    789
  Dihedral  :  7.120  25.065    630
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 15.80 %
    Favored  : 84.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.32), residues: 576
  helix:  0.40 (0.48), residues: 101
  sheet: -1.74 (0.41), residues: 147
  loop : -2.89 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  92 
 HIS   0.007   0.002   HIS A 178 
 PHE   0.019   0.003   PHE A  29 
 TYR   0.023   0.002   TYR A  59 
 ARG   0.003   0.001   ARG A  19 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.6796 (ttm170) cc_final: 0.6519 (ttp-170)
REVERT: A  124 THR cc_start: 0.8143 (m) cc_final: 0.7109 (m)
REVERT: B   67 LYS cc_start: 0.7252 (pttt) cc_final: 0.6223 (ptpp)
REVERT: C  141 GLU cc_start: 0.9569 (mt-10) cc_final: 0.9282 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.4147
  time to fit residues: 49.7316
Evaluate side-chains
  89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 48 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0870
   chunk 41 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   overall best weight:    3.1164

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 ASN
B  28 ASN
B 174 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.128102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.105167 restraints weight = 47260.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.109981 restraints weight = 28360.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.113353 restraints weight = 19147.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6521
moved from start:          0.6350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4477  Z= 0.222
  Angle     :  0.654   5.521   6092  Z= 0.357
  Chirality :  0.043   0.158    682
  Planarity :  0.007   0.075    789
  Dihedral  :  6.590  24.759    630
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 13.37 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.33), residues: 576
  helix:  0.47 (0.47), residues: 103
  sheet: -1.69 (0.42), residues: 142
  loop : -2.76 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  92 
 HIS   0.004   0.001   HIS A 178 
 PHE   0.016   0.002   PHE A  29 
 TYR   0.016   0.002   TYR A  60 
 ARG   0.004   0.000   ARG C 163 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.7689 (m100) cc_final: 0.7381 (m100)
REVERT: A  115 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6393 (tm-30)
REVERT: A  122 ARG cc_start: 0.6657 (ttm170) cc_final: 0.6450 (ttp-170)
REVERT: A  124 THR cc_start: 0.8166 (m) cc_final: 0.6981 (m)
REVERT: B   67 LYS cc_start: 0.7242 (pttt) cc_final: 0.6179 (ptpp)
REVERT: B  112 GLN cc_start: 0.9106 (tt0) cc_final: 0.8695 (tm-30)
REVERT: C  141 GLU cc_start: 0.9622 (mt-10) cc_final: 0.8993 (mt-10)
REVERT: C  217 GLN cc_start: 0.7500 (mt0) cc_final: 0.6734 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.4349
  time to fit residues: 54.3031
Evaluate side-chains
  89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.130462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.108003 restraints weight = 46715.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.112919 restraints weight = 27677.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.116283 restraints weight = 18524.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6435
moved from start:          0.6632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4477  Z= 0.174
  Angle     :  0.614   5.650   6092  Z= 0.333
  Chirality :  0.043   0.152    682
  Planarity :  0.006   0.075    789
  Dihedral  :  6.058  23.609    630
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 12.50 %
    Favored  : 87.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.33), residues: 576
  helix:  0.70 (0.49), residues: 103
  sheet: -1.49 (0.42), residues: 140
  loop : -2.62 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  92 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.022   0.002   PHE A  68 
 TYR   0.014   0.001   TYR B  37 
 ARG   0.002   0.000   ARG A  38 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.7672 (m100) cc_final: 0.7459 (m100)
REVERT: A  115 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6400 (tm-30)
REVERT: A  122 ARG cc_start: 0.6438 (ttm170) cc_final: 0.5983 (ttp-170)
REVERT: A  124 THR cc_start: 0.8167 (m) cc_final: 0.6768 (m)
REVERT: B   67 LYS cc_start: 0.7107 (pttt) cc_final: 0.6102 (ptpp)
REVERT: C  141 GLU cc_start: 0.9588 (mt-10) cc_final: 0.9051 (mt-10)
REVERT: C  163 ARG cc_start: 0.7302 (mtp180) cc_final: 0.6948 (mtp85)
REVERT: C  217 GLN cc_start: 0.7398 (mt0) cc_final: 0.6618 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.4404
  time to fit residues: 57.0254
Evaluate side-chains
  92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** 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 = 0.4168 r_free = 0.4168 target = 0.128979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.105537 restraints weight = 45903.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.110545 restraints weight = 27090.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.114041 restraints weight = 18143.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6478
moved from start:          0.6781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4477  Z= 0.193
  Angle     :  0.616   5.752   6092  Z= 0.333
  Chirality :  0.043   0.150    682
  Planarity :  0.006   0.074    789
  Dihedral  :  5.989  23.095    630
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 12.85 %
    Favored  : 86.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.33), residues: 576
  helix:  0.82 (0.49), residues: 103
  sheet: -1.61 (0.41), residues: 147
  loop : -2.59 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 117 
 HIS   0.003   0.002   HIS A 214 
 PHE   0.029   0.002   PHE A  68 
 TYR   0.023   0.002   TYR B  35 
 ARG   0.002   0.000   ARG A 122 

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

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

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1152 Ramachandran restraints generated.
    576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 TRP cc_start: 0.7684 (m100) cc_final: 0.7453 (m100)
REVERT: A  115 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6299 (tm-30)
REVERT: A  124 THR cc_start: 0.8153 (m) cc_final: 0.6715 (m)
REVERT: C  141 GLU cc_start: 0.9598 (mt-10) cc_final: 0.9008 (mt-10)
REVERT: C  163 ARG cc_start: 0.7445 (mtp180) cc_final: 0.7070 (mtp85)
REVERT: C  217 GLN cc_start: 0.7417 (mt0) cc_final: 0.6638 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.4261
  time to fit residues: 53.5427
Evaluate side-chains
  89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 8 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 43 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** 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 = 0.4168 r_free = 0.4168 target = 0.128818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.105116 restraints weight = 45677.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.110251 restraints weight = 26746.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.113813 restraints weight = 17790.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6478
moved from start:          0.6914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4477  Z= 0.192
  Angle     :  0.619   5.617   6092  Z= 0.335
  Chirality :  0.043   0.150    682
  Planarity :  0.006   0.070    789
  Dihedral  :  5.898  22.867    630
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 12.15 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.33), residues: 576
  helix:  0.78 (0.49), residues: 103
  sheet: -1.59 (0.41), residues: 147
  loop : -2.63 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 117 
 HIS   0.006   0.002   HIS A 178 
 PHE   0.024   0.002   PHE A  68 
 TYR   0.016   0.002   TYR B  35 
 ARG   0.003   0.000   ARG A 122 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3231.23 seconds
wall clock time: 55 minutes 59.98 seconds (3359.98 seconds total)