Starting phenix.real_space_refine
on Wed Feb 12 22:28:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8crb_16807/02_2025/8crb_16807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8crb_16807/02_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_16807/02_2025/8crb_16807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8crb_16807/02_2025/8crb_16807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8crb_16807/02_2025/8crb_16807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8crb_16807/02_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-5592/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: 4.36, per 1000 atoms: 0.50
  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: 2.15
  Conformation dependent library (CDL) restraints added in 795.7 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: 0.81
  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: 2.93

  Time building geometry restraints manager: 2.59 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:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.160
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     21.930
  Find NCS groups from input model:        0.080
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.800
-------------------------------------------------------------------------------
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  : 0.954 
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: 0.4969
  time to fit residues: 88.1007
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  : 0.762 
-------------------------------------------------------------------------------
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 = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.105524 restraints weight = 47379.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.110217 restraints weight = 28305.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.113670 restraints weight = 18813.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6494
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  : 0.694 
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: 0.7660 (m100) cc_final: 0.7272 (m100)
REVERT: A   67 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7885 (mpt180)
REVERT: A  122 ARG cc_start: 0.6967 (ttm170) cc_final: 0.6433 (ttp-170)
REVERT: A  124 THR cc_start: 0.7901 (m) cc_final: 0.6910 (m)
REVERT: B   67 LYS cc_start: 0.7563 (pttt) cc_final: 0.6699 (ptpp)
REVERT: B   84 GLU cc_start: 0.8240 (tp30) cc_final: 0.7635 (tm-30)
REVERT: C  139 THR cc_start: 0.9213 (m) cc_final: 0.9000 (p)
REVERT: C  141 GLU cc_start: 0.9650 (mt-10) cc_final: 0.9352 (mt-10)
REVERT: C  199 ASP cc_start: 0.8101 (m-30) cc_final: 0.7795 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.4015
  time to fit residues: 59.3645
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  : 0.712 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.4150 r_free = 0.4150 target = 0.127644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.105836 restraints weight = 46963.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.110560 restraints weight = 28109.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.113817 restraints weight = 18741.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6494
moved from start:          0.4736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4477  Z= 0.254
  Angle     :  0.758   7.582   6092  Z= 0.420
  Chirality :  0.045   0.180    682
  Planarity :  0.007   0.077    789
  Dihedral  :  7.662  32.264    630
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.50 %
    Favored  : 87.33 %
  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: -2.75 (0.31), residues: 576
  helix: -0.01 (0.46), residues: 107
  sheet: -1.47 (0.41), residues: 145
  loop : -2.74 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  47 
 HIS   0.004   0.002   HIS A 178 
 PHE   0.014   0.002   PHE A 180 
 TYR   0.019   0.002   TYR B  37 
 ARG   0.002   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
  112 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.773 
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   43 LYS cc_start: 0.6178 (mmtt) cc_final: 0.4971 (mttt)
REVERT: A   67 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7987 (mpt180)
REVERT: A  115 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6055 (tm-30)
REVERT: A  122 ARG cc_start: 0.6758 (ttm170) cc_final: 0.6242 (ttp-170)
REVERT: A  124 THR cc_start: 0.8028 (m) cc_final: 0.6937 (m)
REVERT: A  224 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7623 (tpt-90)
REVERT: B   67 LYS cc_start: 0.7444 (pttt) cc_final: 0.6542 (ptpp)
REVERT: B   84 GLU cc_start: 0.8135 (tp30) cc_final: 0.7738 (tm-30)
REVERT: B  174 ASN cc_start: 0.8359 (m-40) cc_final: 0.7989 (t0)
REVERT: C  139 THR cc_start: 0.9193 (m) cc_final: 0.8985 (p)
REVERT: C  217 GLN cc_start: 0.7285 (mt0) cc_final: 0.6719 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.4256
  time to fit residues: 57.3769
Evaluate side-chains
  95 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 47 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
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 = 0.4159 r_free = 0.4159 target = 0.128538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.106057 restraints weight = 47698.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.111000 restraints weight = 28313.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.114506 restraints weight = 18750.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6499
moved from start:          0.5266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4477  Z= 0.255
  Angle     :  0.732   7.045   6092  Z= 0.401
  Chirality :  0.044   0.168    682
  Planarity :  0.007   0.074    789
  Dihedral  :  7.423  32.999    630
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.33 %
    Favored  : 87.50 %
  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 : 0.18 %

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: -2.89 (0.32), residues: 576
  helix:  0.05 (0.46), residues: 107
  sheet: -1.75 (0.39), residues: 158
  loop : -2.82 (0.31), residues: 311

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   0.032   0.002   PHE A  68 
 TYR   0.027   0.002   TYR A  60 
 ARG   0.004   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
  106 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.709 
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: A  122 ARG cc_start: 0.6705 (ttm170) cc_final: 0.6161 (ttp-170)
REVERT: A  124 THR cc_start: 0.8029 (m) cc_final: 0.6933 (m)
REVERT: A  154 CYS cc_start: 0.8065 (p) cc_final: 0.7720 (m)
REVERT: A  155 LEU cc_start: 0.8240 (tt) cc_final: 0.8035 (tt)
REVERT: A  224 ARG cc_start: 0.7953 (mtp85) cc_final: 0.7685 (tpt-90)
REVERT: B   67 LYS cc_start: 0.7382 (pttt) cc_final: 0.6367 (ptpp)
REVERT: B   84 GLU cc_start: 0.8121 (tp30) cc_final: 0.7807 (tm-30)
REVERT: C  139 THR cc_start: 0.9192 (m) cc_final: 0.8989 (p)
REVERT: C  217 GLN cc_start: 0.7261 (mt0) cc_final: 0.6724 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.4449
  time to fit residues: 56.7246
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  : 0.868 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    2.5562

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

Flipped N/Q/H residues before XYZ refinement:
C 160 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.128940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.106251 restraints weight = 46331.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.110951 restraints weight = 27909.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.114174 restraints weight = 18816.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6477
moved from start:          0.5583

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= 0.209
  Angle     :  0.675   6.502   6092  Z= 0.367
  Chirality :  0.044   0.162    682
  Planarity :  0.007   0.074    789
  Dihedral  :  6.939  32.844    630
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.85 %
    Favored  : 86.98 %
  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 : 0.18 %

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:  0.27 (0.47), residues: 107
  sheet: -1.85 (0.39), residues: 158
  loop : -2.74 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  47 
 HIS   0.004   0.002   HIS A 178 
 PHE   0.015   0.002   PHE A  29 
 TYR   0.015   0.002   TYR A  60 
 ARG   0.006   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
  113 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.711 
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: A   36 TRP cc_start: 0.7732 (m100) cc_final: 0.7439 (m100)
REVERT: A   69 THR cc_start: 0.8157 (t) cc_final: 0.7941 (t)
REVERT: A  122 ARG cc_start: 0.6599 (ttm170) cc_final: 0.6169 (ttp-170)
REVERT: A  124 THR cc_start: 0.8120 (m) cc_final: 0.6943 (m)
REVERT: A  154 CYS cc_start: 0.8076 (p) cc_final: 0.7851 (m)
REVERT: A  191 SER cc_start: 0.8723 (p) cc_final: 0.8523 (p)
REVERT: B   67 LYS cc_start: 0.7322 (pttt) cc_final: 0.6350 (ptpp)
REVERT: B  136 LEU cc_start: 0.8488 (mt) cc_final: 0.8204 (mt)
REVERT: C  139 THR cc_start: 0.9185 (m) cc_final: 0.8976 (p)
REVERT: C  141 GLU cc_start: 0.9637 (mt-10) cc_final: 0.9008 (mt-10)
REVERT: C  217 GLN cc_start: 0.7357 (mt0) cc_final: 0.6572 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.4389
  time to fit residues: 59.9629
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  : 0.708 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 55 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 49 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    3.1188

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.128566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.105703 restraints weight = 46715.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.110526 restraints weight = 27737.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.113954 restraints weight = 18659.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6474
moved from start:          0.5936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4477  Z= 0.230
  Angle     :  0.664   5.336   6092  Z= 0.362
  Chirality :  0.043   0.158    682
  Planarity :  0.007   0.073    789
  Dihedral  :  6.696  24.367    630
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.67 %
    Favored  : 87.15 %
  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 : 0.00 %

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: -2.66 (0.33), residues: 576
  helix:  0.56 (0.48), residues: 101
  sheet: -1.74 (0.40), residues: 153
  loop : -2.65 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B  92 
 HIS   0.005   0.002   HIS A 178 
 PHE   0.017   0.002   PHE B 101 
 TYR   0.020   0.002   TYR A  60 
 ARG   0.003   0.000   ARG C 163 

*********************** 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
  110 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.712 
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: 0.7738 (m100) cc_final: 0.7382 (m100)
REVERT: A  122 ARG cc_start: 0.6664 (ttm170) cc_final: 0.6430 (ttp-170)
REVERT: A  124 THR cc_start: 0.8144 (m) cc_final: 0.6912 (m)
REVERT: A  154 CYS cc_start: 0.8100 (p) cc_final: 0.7847 (m)
REVERT: A  191 SER cc_start: 0.8691 (p) cc_final: 0.8486 (p)
REVERT: B   67 LYS cc_start: 0.7314 (pttt) cc_final: 0.6317 (ptpp)
REVERT: B   84 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: B  137 VAL cc_start: 0.7529 (t) cc_final: 0.7291 (t)
REVERT: C  139 THR cc_start: 0.9184 (m) cc_final: 0.8982 (p)
REVERT: C  217 GLN cc_start: 0.7413 (mt0) cc_final: 0.6921 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.4086
  time to fit residues: 54.5398
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  : 0.681 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 47 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.125928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.103736 restraints weight = 46593.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.108346 restraints weight = 28076.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.111647 restraints weight = 18969.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6555
moved from start:          0.6177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4477  Z= 0.314
  Angle     :  0.719   5.366   6092  Z= 0.396
  Chirality :  0.044   0.160    682
  Planarity :  0.007   0.074    789
  Dihedral  :  6.987  25.001    630
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 14.41 %
    Favored  : 85.42 %
  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: -2.90 (0.32), residues: 576
  helix:  0.34 (0.48), residues: 102
  sheet: -1.71 (0.42), residues: 142
  loop : -2.90 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  92 
 HIS   0.005   0.002   HIS A 178 
 PHE   0.020   0.002   PHE A  29 
 TYR   0.015   0.002   TYR B  37 
 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
  97 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.698 
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: A   36 TRP cc_start: 0.7692 (m100) cc_final: 0.7332 (m100)
REVERT: A   65 LYS cc_start: 0.6577 (tmmt) cc_final: 0.5986 (tttm)
REVERT: A   67 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7840 (mpt180)
REVERT: A  122 ARG cc_start: 0.6778 (ttm170) cc_final: 0.6484 (ttp-170)
REVERT: A  124 THR cc_start: 0.8116 (m) cc_final: 0.7033 (m)
REVERT: A  154 CYS cc_start: 0.8110 (p) cc_final: 0.7735 (m)
REVERT: B   67 LYS cc_start: 0.7276 (pttt) cc_final: 0.6247 (ptpp)
REVERT: C  139 THR cc_start: 0.9173 (m) cc_final: 0.8968 (p)
REVERT: C  141 GLU cc_start: 0.9605 (mt-10) cc_final: 0.9333 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.4147
  time to fit residues: 49.0233
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  : 0.633 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0020
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.9992

-------------------------------------------------------------------------------
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**
B 174 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.129805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.106604 restraints weight = 45349.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.111605 restraints weight = 26604.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.115042 restraints weight = 17740.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6419
moved from start:          0.6365

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= 0.171
  Angle     :  0.612   5.489   6092  Z= 0.331
  Chirality :  0.043   0.153    682
  Planarity :  0.006   0.075    789
  Dihedral  :  6.132  24.130    630
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 12.33 %
    Favored  : 87.33 %
  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: -2.57 (0.33), residues: 576
  helix:  0.71 (0.49), residues: 102
  sheet: -1.65 (0.42), residues: 142
  loop : -2.64 (0.31), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  47 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.010   0.001   PHE A 180 
 TYR   0.012   0.001   TYR B  37 
 ARG   0.003   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
  114 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.813 
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: 0.7703 (m100) cc_final: 0.7442 (m100)
REVERT: A   65 LYS cc_start: 0.6769 (tmmt) cc_final: 0.6536 (tttm)
REVERT: A  115 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6483 (tm-30)
REVERT: A  122 ARG cc_start: 0.6544 (ttm170) cc_final: 0.6265 (ttp-170)
REVERT: A  124 THR cc_start: 0.8148 (m) cc_final: 0.6842 (m)
REVERT: B   67 LYS cc_start: 0.7271 (pttt) cc_final: 0.6205 (ptpp)
REVERT: C  139 THR cc_start: 0.9169 (m) cc_final: 0.8952 (p)
REVERT: C  141 GLU cc_start: 0.9634 (mt-10) cc_final: 0.9074 (mt-10)
REVERT: C  217 GLN cc_start: 0.7444 (mt0) cc_final: 0.6639 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.4441
  time to fit residues: 60.8298
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  : 0.673 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.130701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.107256 restraints weight = 45154.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.112407 restraints weight = 26454.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.115978 restraints weight = 17608.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6399
moved from start:          0.6637

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= 0.164
  Angle     :  0.596   5.451   6092  Z= 0.320
  Chirality :  0.043   0.149    682
  Planarity :  0.006   0.074    789
  Dihedral  :  5.785  23.261    630
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 12.33 %
    Favored  : 87.33 %
  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: -2.40 (0.34), residues: 576
  helix:  0.77 (0.50), residues: 104
  sheet: -1.43 (0.42), residues: 140
  loop : -2.58 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  47 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.009   0.001   PHE A  29 
 TYR   0.025   0.001   TYR B  35 
 ARG   0.002   0.000   ARG A  19 

*********************** 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
  107 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.722 
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: A   36 TRP cc_start: 0.7697 (m100) cc_final: 0.7452 (m100)
REVERT: A  115 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6090 (tm-30)
REVERT: A  124 THR cc_start: 0.8195 (m) cc_final: 0.6713 (m)
REVERT: B   67 LYS cc_start: 0.7149 (pttt) cc_final: 0.6015 (ptpp)
REVERT: C  139 THR cc_start: 0.9153 (m) cc_final: 0.8941 (p)
REVERT: C  141 GLU cc_start: 0.9591 (mt-10) cc_final: 0.9051 (mt-10)
REVERT: C  163 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6922 (mtp85)
REVERT: C  217 GLN cc_start: 0.7376 (mt0) cc_final: 0.6585 (mt0)
REVERT: C  236 PRO cc_start: 0.8729 (Cg_endo) cc_final: 0.8439 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.4583
  time to fit residues: 59.1146
Evaluate side-chains
  95 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 = 0.4175 r_free = 0.4175 target = 0.129501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.106930 restraints weight = 45584.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.111767 restraints weight = 27023.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.115160 restraints weight = 18103.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.6805

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= 0.180
  Angle     :  0.600   5.484   6092  Z= 0.324
  Chirality :  0.042   0.163    682
  Planarity :  0.006   0.071    789
  Dihedral  :  5.756  22.450    630
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 12.15 %
    Favored  : 87.50 %
  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: -2.37 (0.34), residues: 576
  helix:  0.82 (0.50), residues: 104
  sheet: -1.50 (0.41), residues: 145
  loop : -2.53 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 117 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.016   0.002   PHE A  29 
 TYR   0.010   0.001   TYR B  99 
 ARG   0.004   0.000   ARG A 224 

********************** 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
  105 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.748 
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   20 LEU cc_start: 0.8238 (mt) cc_final: 0.8018 (mt)
REVERT: A   36 TRP cc_start: 0.7643 (m100) cc_final: 0.7335 (m100)
REVERT: A  115 GLU cc_start: 0.6383 (tm-30) cc_final: 0.6103 (tm-30)
REVERT: B   67 LYS cc_start: 0.7027 (pttt) cc_final: 0.5931 (ptpp)
REVERT: C  163 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7010 (mtp85)
REVERT: C  217 GLN cc_start: 0.7356 (mt0) cc_final: 0.6889 (mt0)
REVERT: C  236 PRO cc_start: 0.8668 (Cg_endo) cc_final: 0.8395 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.3911
  time to fit residues: 50.8305
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  : 0.679 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 211 ASN
** B  28 ASN ** 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 = 0.4148 r_free = 0.4148 target = 0.127558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.105050 restraints weight = 46636.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.109891 restraints weight = 27576.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.113263 restraints weight = 18489.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6504
moved from start:          0.6944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4477  Z= 0.232
  Angle     :  0.643   5.325   6092  Z= 0.350
  Chirality :  0.043   0.169    682
  Planarity :  0.007   0.066    789
  Dihedral  :  5.991  22.594    630
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 13.72 %
    Favored  : 85.94 %
  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: -2.50 (0.34), residues: 576
  helix:  0.73 (0.50), residues: 104
  sheet: -1.55 (0.42), residues: 144
  loop : -2.64 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 117 
 HIS   0.006   0.002   HIS A 178 
 PHE   0.020   0.002   PHE A  29 
 TYR   0.015   0.002   TYR B  35 
 ARG   0.002   0.000   ARG B  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3208.59 seconds
wall clock time: 57 minutes 27.80 seconds (3447.80 seconds total)