Starting phenix.real_space_refine
on Tue Feb  3 20:30:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zk4_60176/02_2026/8zk4_60176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zk4_60176/02_2026/8zk4_60176.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zk4_60176/02_2026/8zk4_60176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zk4_60176/02_2026/8zk4_60176.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zk4_60176/02_2026/8zk4_60176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zk4_60176/02_2026/8zk4_60176.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4255      2.51       5
     N    1151      2.21       5
     O    1278      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6720
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1676
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200}
    Chain: "B"
      Number of atoms: 1676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1676
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200}
    Chain: "D"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1586
          Classifications: {'peptide': 203}
          Link IDs: {'CIS': 10, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 181}
    Chain: "G"
      Number of atoms: 1782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1782
          Classifications: {'peptide': 224}
          Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 210}
  Time building chain proxies: 1.45, per 1000 atoms: 0.22
  Number of scatterers: 6720
  At special positions: 0
  Unit cell: (111.961, 140.223, 95.656, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1278      8.00
     N    1151      7.00
     C    4255      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS A 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 219 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  51 " - pdb=" SG  CYS B 125 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 165 " - pdb=" SG  CYS B 219 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  97 " distance=2.05
    Simple disulfide: pdb=" SG  CYS G 154 " - pdb=" SG  CYS G 210 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 259.5 milliseconds
  

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 19 sheets defined
      1.9% alpha, 33.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 93
      removed outlier: 3.597A  pdb=" N   ARG A  93 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 88 through 92
      removed outlier: 4.126A  pdb=" N   ILE G  92 " --> pdb=" O   LYS G  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 200 through 205
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33
      removed outlier: 3.563A  pdb=" N   ALA A 109 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40
      removed outlier: 3.756A  pdb=" N   VAL A 141 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS A  79 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG A  82 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 157
      removed outlier: 4.448A  pdb=" N   GLY A 155 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL A 203 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   ARG A 168 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   THR A 205 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   ILE A 166 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 157
      removed outlier: 4.448A  pdb=" N   GLY A 155 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 186
      removed outlier: 4.482A  pdb=" N   TRP A 178 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 33
      removed outlier: 4.086A  pdb=" N   ALA B 109 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 83
      removed outlier: 3.732A  pdb=" N   ARG B  82 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LYS B  79 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 156
      removed outlier: 3.915A  pdb=" N   ILE B 166 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ARG B 162 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL B 207 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   CYS B 165 " --> pdb=" O   THR B 205 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   THR B 205 " --> pdb=" O   CYS B 165 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA B 206 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LYS B 190 " --> pdb=" O   ALA B 206 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 179
    Processing sheet with id=AB1, first strand: chain 'D' and resid 47 through 51
      removed outlier: 5.362A  pdb=" N   PHE D  48 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ARG D  39 " --> pdb=" O   PHE D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 64 through 69
    Processing sheet with id=AB3, first strand: chain 'D' and resid 151 through 155
    Processing sheet with id=AB4, first strand: chain 'D' and resid 166 through 169
    Processing sheet with id=AB5, first strand: chain 'G' and resid 12 through 13
      removed outlier: 3.732A  pdb=" N   LYS G  13 " --> pdb=" O   ILE G 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'G' and resid 19 through 24
    Processing sheet with id=AB7, first strand: chain 'G' and resid 46 through 53
      removed outlier: 5.811A  pdb=" N   PHE G  48 " --> pdb=" O   ARG G  39 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ARG G  39 " --> pdb=" O   PHE G  48 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   SER G  34 " --> pdb=" O   TRP G 100 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   TRP G 100 " --> pdb=" O   SER G  34 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 46 through 53
      removed outlier: 5.811A  pdb=" N   PHE G  48 " --> pdb=" O   ARG G  39 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ARG G  39 " --> pdb=" O   PHE G  48 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   SER G  34 " --> pdb=" O   TRP G 100 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   TRP G 100 " --> pdb=" O   SER G  34 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 152 through 157
      removed outlier: 4.100A  pdb=" N   MET G 185 " --> pdb=" O   MET G 192 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'G' and resid 168 through 169

    197 hydrogen bonds defined for protein.
    459 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2193
        1.34 -     1.46: 1551
        1.46 -     1.58: 3064
        1.58 -     1.70: 0
        1.70 -     1.82: 56
  Bond restraints: 6864
  Sorted by residual:
  bond pdb=" N   PRO G  75 "
       pdb=" CD  PRO G  75 "
    ideal  model  delta    sigma   weight residual
    1.473  1.533 -0.060 1.40e-02 5.10e+03 1.84e+01
  bond pdb=" C   ILE G  74 "
       pdb=" N   PRO G  75 "
    ideal  model  delta    sigma   weight residual
    1.333  1.390 -0.057 1.44e-02 4.82e+03 1.57e+01
  bond pdb=" CA  PRO A 187 "
       pdb=" C   PRO A 187 "
    ideal  model  delta    sigma   weight residual
    1.520  1.537 -0.016 1.09e-02 8.42e+03 2.16e+00
  bond pdb=" CA  PRO B 195 "
       pdb=" C   PRO B 195 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 1.42e-02 4.96e+03 1.13e+00
  bond pdb=" CB  PRO G 161 "
       pdb=" CG  PRO G 161 "
    ideal  model  delta    sigma   weight residual
    1.492  1.444  0.048 5.00e-02 4.00e+02 9.25e-01
  ... (remaining 6859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 9209
        2.63 -     5.26: 66
        5.26 -     7.88: 9
        7.88 -    10.51: 5
       10.51 -    13.14: 1
  Bond angle restraints: 9290
  Sorted by residual:
  angle pdb=" C   MET D  25 "
        pdb=" N   LYS D  26 "
        pdb=" CA  LYS D  26 "
      ideal   model   delta    sigma   weight residual
     121.70  130.85   -9.15 1.80e+00 3.09e-01 2.58e+01
  angle pdb=" C   ARG D  85 "
        pdb=" N   ASP D  86 "
        pdb=" CA  ASP D  86 "
      ideal   model   delta    sigma   weight residual
     121.70  130.82   -9.12 1.80e+00 3.09e-01 2.57e+01
  angle pdb=" C   MET D  99 "
        pdb=" N   GLY D 100 "
        pdb=" CA  GLY D 100 "
      ideal   model   delta    sigma   weight residual
     121.70  130.48   -8.78 1.80e+00 3.09e-01 2.38e+01
  angle pdb=" C   ASN G 217 "
        pdb=" N   LYS G 218 "
        pdb=" CA  LYS G 218 "
      ideal   model   delta    sigma   weight residual
     121.70  130.19   -8.49 1.80e+00 3.09e-01 2.22e+01
  angle pdb=" C   ILE G  74 "
        pdb=" N   PRO G  75 "
        pdb=" CA  PRO G  75 "
      ideal   model   delta    sigma   weight residual
     119.47  114.06    5.41 1.16e+00 7.43e-01 2.17e+01
  ... (remaining 9285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 3778
       17.93 -    35.85: 336
       35.85 -    53.78: 46
       53.78 -    71.70: 8
       71.70 -    89.63: 5
  Dihedral angle restraints: 4173
    sinusoidal: 1716
      harmonic: 2457
  Sorted by residual:
  dihedral pdb=" CB  CYS B  51 "
           pdb=" SG  CYS B  51 "
           pdb=" SG  CYS B 125 "
           pdb=" CB  CYS B 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.69  -53.69     1      1.00e+01 1.00e-02 3.91e+01
  dihedral pdb=" CA  THR G 190 "
           pdb=" C   THR G 190 "
           pdb=" N   TYR G 191 "
           pdb=" CA  TYR G 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.17  -24.83     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  THR G 187 "
           pdb=" C   THR G 187 "
           pdb=" N   ASN G 188 "
           pdb=" CA  ASN G 188 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.88   21.12     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 4170 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 571
       0.031 -    0.061: 294
       0.061 -    0.092: 81
       0.092 -    0.123: 70
       0.123 -    0.154: 18
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CA  PRO B 195 "
            pdb=" N   PRO B 195 "
            pdb=" C   PRO B 195 "
            pdb=" CB  PRO B 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.87   -0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  ILE B 115 "
            pdb=" N   ILE B 115 "
            pdb=" C   ILE B 115 "
            pdb=" CB  ILE B 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.62e-01
  chirality pdb=" CA  ILE D  70 "
            pdb=" N   ILE D  70 "
            pdb=" C   ILE D  70 "
            pdb=" CB  ILE D  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.39e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 194 "   -0.064 5.00e-02 4.00e+02   9.86e-02 1.55e+01
        pdb=" N   PRO B 195 "    0.171 5.00e-02 4.00e+02
        pdb=" CA  PRO B 195 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 195 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE G 160 "    0.047 5.00e-02 4.00e+02   7.14e-02 8.16e+00
        pdb=" N   PRO G 161 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO G 161 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO G 161 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 118 "   -0.030 5.00e-02 4.00e+02   4.53e-02 3.28e+00
        pdb=" N   PRO D 119 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO D 119 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 119 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1191 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 59
        2.52 -     3.11: 5089
        3.11 -     3.71: 9198
        3.71 -     4.30: 12535
        4.30 -     4.90: 21992
  Nonbonded interactions: 48873
  Sorted by model distance:
  nonbonded pdb=" O   TYR D 103 "
            pdb=" OH  TYR G  36 "
     model   vdw
     1.921 3.040
  nonbonded pdb=" OE1 GLU G  40 "
            pdb=" OH  TYR G  96 "
     model   vdw
     1.990 3.040
  nonbonded pdb=" OH  TYR D  38 "
            pdb=" O   LYS G 111 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" OH  TYR G 152 "
            pdb=" O   SER G 203 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" N   GLU G   5 "
            pdb=" OE1 GLU G   5 "
     model   vdw
     2.168 3.120
  ... (remaining 48868 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.590
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6551
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6871  Z= 0.163
  Angle     :  0.675  13.139   9304  Z= 0.369
  Chirality :  0.047   0.154   1034
  Planarity :  0.006   0.099   1194
  Dihedral  : 13.755  89.628   2576
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.35 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.60 (0.26), residues: 845
  helix: -5.78 (0.29), residues: 6
  sheet: -1.92 (0.26), residues: 352
  loop : -2.79 (0.24), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  51 
 TYR   0.014   0.001   TYR B 126 
 PHE   0.023   0.001   PHE G  48 
 TRP   0.006   0.001   TRP D  37 
 HIS   0.007   0.001   HIS G 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6864)
  covalent geometry    : angle       0.67486 ( 9290)
  SS BOND              : bond        0.00861 (    7)
  SS BOND              : angle       0.82261 (   14)
  hydrogen bonds       : bond        0.11363 (  180)
  hydrogen bonds       : angle       7.38533 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B  158 ASP cc_start: 0.7658 (t70) cc_final: 0.7243 (t70)
REVERT: D   35 ILE cc_start: 0.7080 (mm) cc_final: 0.6868 (mm)
REVERT: G  121 ILE cc_start: 0.8540 (mt) cc_final: 0.8167 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0710
  time to fit residues: 10.9771
Evaluate side-chains
  100 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.4184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.216421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.176258 restraints weight = 89935.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.179148 restraints weight = 56519.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.178855 restraints weight = 46632.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.177959 restraints weight = 48409.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.178414 restraints weight = 45380.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.1084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6871  Z= 0.193
  Angle     :  0.718   7.745   9304  Z= 0.384
  Chirality :  0.050   0.160   1034
  Planarity :  0.005   0.058   1194
  Dihedral  :  5.593  23.941    927
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.07 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.36 (0.26), residues: 845
  helix: -5.75 (0.28), residues: 6
  sheet: -1.78 (0.27), residues: 350
  loop : -2.60 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  84 
 TYR   0.015   0.002   TYR G 191 
 PHE   0.012   0.002   PHE A  30 
 TRP   0.008   0.001   TRP D  37 
 HIS   0.009   0.002   HIS G 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6864)
  covalent geometry    : angle       0.71796 ( 9290)
  SS BOND              : bond        0.00861 (    7)
  SS BOND              : angle       0.98133 (   14)
  hydrogen bonds       : bond        0.04293 (  180)
  hydrogen bonds       : angle       7.03255 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.7398 (p0) cc_final: 0.6862 (p0)
REVERT: B   37 ASP cc_start: 0.7149 (p0) cc_final: 0.6359 (m-30)
REVERT: B  128 GLN cc_start: 0.7771 (tt0) cc_final: 0.6920 (tt0)
REVERT: B  158 ASP cc_start: 0.7733 (t70) cc_final: 0.7354 (t70)
REVERT: B  215 ARG cc_start: 0.8928 (mmp-170) cc_final: 0.8531 (mmp-170)
REVERT: D   25 MET cc_start: 0.3450 (mpp) cc_final: 0.3146 (mpp)
REVERT: D   35 ILE cc_start: 0.7122 (mm) cc_final: 0.6909 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 115
  average time/residue: 0.0765
  time to fit residues: 11.7017
Evaluate side-chains
  100 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
D 134 ASN
G 103 GLN
G 208 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.228352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.190033 restraints weight = 90320.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.193992 restraints weight = 53537.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.192363 restraints weight = 43957.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.192595 restraints weight = 45222.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.192624 restraints weight = 41342.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6871  Z= 0.142
  Angle     :  0.645   7.219   9304  Z= 0.345
  Chirality :  0.049   0.159   1034
  Planarity :  0.005   0.049   1194
  Dihedral  :  5.195  21.585    927
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.27), residues: 845
  helix: -5.75 (0.28), residues: 6
  sheet: -1.65 (0.27), residues: 355
  loop : -2.44 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  84 
 TYR   0.015   0.001   TYR G 191 
 PHE   0.017   0.001   PHE A  98 
 TRP   0.009   0.001   TRP D  37 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6864)
  covalent geometry    : angle       0.64458 ( 9290)
  SS BOND              : bond        0.00710 (    7)
  SS BOND              : angle       0.83813 (   14)
  hydrogen bonds       : bond        0.03598 (  180)
  hydrogen bonds       : angle       6.77446 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   37 ASP cc_start: 0.7379 (p0) cc_final: 0.6912 (p0)
REVERT: B   37 ASP cc_start: 0.7014 (p0) cc_final: 0.6338 (m-30)
REVERT: B  158 ASP cc_start: 0.7706 (t70) cc_final: 0.7242 (t70)
REVERT: B  201 PHE cc_start: 0.7949 (m-10) cc_final: 0.7667 (m-10)
REVERT: B  215 ARG cc_start: 0.8766 (mmp-170) cc_final: 0.8388 (mmp-170)
REVERT: D    9 GLN cc_start: 0.7023 (mp10) cc_final: 0.6626 (mp10)
REVERT: D   25 MET cc_start: 0.3240 (mpp) cc_final: 0.2774 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0555
  time to fit residues: 8.7393
Evaluate side-chains
  100 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
A 139 HIS
** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.221715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.182026 restraints weight = 89489.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.185743 restraints weight = 55178.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.184352 restraints weight = 46031.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.184372 restraints weight = 49233.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.184312 restraints weight = 45778.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6871  Z= 0.215
  Angle     :  0.717   7.557   9304  Z= 0.381
  Chirality :  0.050   0.187   1034
  Planarity :  0.005   0.055   1194
  Dihedral  :  5.594  24.036    927
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.22 (0.27), residues: 845
  helix: -5.76 (0.29), residues: 6
  sheet: -1.73 (0.26), residues: 369
  loop : -2.45 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  51 
 TYR   0.013   0.002   TYR A 126 
 PHE   0.019   0.002   PHE A  98 
 TRP   0.008   0.002   TRP B 170 
 HIS   0.004   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 6864)
  covalent geometry    : angle       0.71650 ( 9290)
  SS BOND              : bond        0.00811 (    7)
  SS BOND              : angle       1.09165 (   14)
  hydrogen bonds       : bond        0.04495 (  180)
  hydrogen bonds       : angle       7.06141 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.7484 (p0) cc_final: 0.6965 (p0)
REVERT: B   37 ASP cc_start: 0.7166 (p0) cc_final: 0.6413 (m-30)
REVERT: B  128 GLN cc_start: 0.7628 (tt0) cc_final: 0.6936 (tt0)
REVERT: B  158 ASP cc_start: 0.7659 (t70) cc_final: 0.7154 (t70)
REVERT: D   25 MET cc_start: 0.3331 (mpp) cc_final: 0.2932 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0725
  time to fit residues: 11.0343
Evaluate side-chains
  96 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 61 optimal weight:    0.1980
   chunk 56 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
A 156 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.226188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.187540 restraints weight = 88831.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.192449 restraints weight = 53980.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.190503 restraints weight = 44353.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.189831 restraints weight = 46322.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.190085 restraints weight = 44693.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6871  Z= 0.157
  Angle     :  0.659   7.260   9304  Z= 0.352
  Chirality :  0.048   0.169   1034
  Planarity :  0.005   0.049   1194
  Dihedral  :  5.301  22.160    927
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.99 (0.27), residues: 845
  helix: -5.76 (0.29), residues: 6
  sheet: -1.61 (0.27), residues: 364
  loop : -2.27 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  51 
 TYR   0.014   0.001   TYR G 191 
 PHE   0.017   0.002   PHE B 127 
 TRP   0.014   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6864)
  covalent geometry    : angle       0.65857 ( 9290)
  SS BOND              : bond        0.00725 (    7)
  SS BOND              : angle       1.03727 (   14)
  hydrogen bonds       : bond        0.03899 (  180)
  hydrogen bonds       : angle       6.90332 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.7450 (p0) cc_final: 0.6991 (p0)
REVERT: B   37 ASP cc_start: 0.6960 (p0) cc_final: 0.6269 (m-30)
REVERT: B  158 ASP cc_start: 0.7725 (t70) cc_final: 0.7299 (t70)
REVERT: B  201 PHE cc_start: 0.8085 (m-10) cc_final: 0.7841 (m-10)
REVERT: D   25 MET cc_start: 0.3239 (mpp) cc_final: 0.2933 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0658
  time to fit residues: 10.3221
Evaluate side-chains
  101 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0060
   chunk 72 optimal weight:    0.0370
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4274

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

Flipped N/Q/H residues before XYZ refinement:
A 139 HIS
** D  36 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 = 0.4414 r_free = 0.4414 target = 0.232444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.194162 restraints weight = 89968.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.197616 restraints weight = 53805.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.196251 restraints weight = 44117.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.196729 restraints weight = 47476.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.196839 restraints weight = 43282.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6871  Z= 0.115
  Angle     :  0.613   7.284   9304  Z= 0.326
  Chirality :  0.047   0.159   1034
  Planarity :  0.004   0.048   1194
  Dihedral  :  4.852  19.076    927
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.27), residues: 845
  helix: -5.74 (0.29), residues: 6
  sheet: -1.31 (0.27), residues: 346
  loop : -2.19 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 154 
 TYR   0.015   0.001   TYR G 191 
 PHE   0.018   0.001   PHE B 127 
 TRP   0.014   0.001   TRP D  37 
 HIS   0.003   0.001   HIS G 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6864)
  covalent geometry    : angle       0.61264 ( 9290)
  SS BOND              : bond        0.00546 (    7)
  SS BOND              : angle       0.85029 (   14)
  hydrogen bonds       : bond        0.03147 (  180)
  hydrogen bonds       : angle       6.45500 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.7295 (p0) cc_final: 0.6699 (p0)
REVERT: B   37 ASP cc_start: 0.6746 (p0) cc_final: 0.6207 (m-30)
REVERT: B  158 ASP cc_start: 0.7571 (t70) cc_final: 0.7289 (t70)
REVERT: D   25 MET cc_start: 0.2839 (mpp) cc_final: 0.2516 (mpp)
REVERT: G   54 TYR cc_start: 0.4523 (p90) cc_final: 0.4314 (p90)
REVERT: G   59 ARG cc_start: 0.7970 (ttt-90) cc_final: 0.7765 (ttt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0690
  time to fit residues: 11.3122
Evaluate side-chains
  101 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 57 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0570
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0970
   chunk 70 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
D 134 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.233961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.195231 restraints weight = 91053.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.201838 restraints weight = 53235.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.198261 restraints weight = 42202.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.198158 restraints weight = 44562.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.198457 restraints weight = 43110.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6871  Z= 0.116
  Angle     :  0.610   7.322   9304  Z= 0.324
  Chirality :  0.047   0.157   1034
  Planarity :  0.004   0.047   1194
  Dihedral  :  4.661  18.044    927
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.65 (0.27), residues: 845
  helix: -5.72 (0.29), residues: 6
  sheet: -1.20 (0.28), residues: 332
  loop : -2.16 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  51 
 TYR   0.024   0.001   TYR B 171 
 PHE   0.008   0.001   PHE G 159 
 TRP   0.013   0.001   TRP D  37 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6864)
  covalent geometry    : angle       0.60975 ( 9290)
  SS BOND              : bond        0.00645 (    7)
  SS BOND              : angle       0.89876 (   14)
  hydrogen bonds       : bond        0.03149 (  180)
  hydrogen bonds       : angle       6.32021 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.7362 (p0) cc_final: 0.6867 (p0)
REVERT: B   37 ASP cc_start: 0.6708 (p0) cc_final: 0.6239 (m-30)
REVERT: B  128 GLN cc_start: 0.7438 (tt0) cc_final: 0.7057 (tt0)
REVERT: B  158 ASP cc_start: 0.7406 (t70) cc_final: 0.7176 (t70)
REVERT: B  198 ASP cc_start: 0.6633 (t0) cc_final: 0.6401 (t0)
REVERT: D   25 MET cc_start: 0.2769 (mpp) cc_final: 0.2503 (mpp)
REVERT: G   39 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.8035 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0631
  time to fit residues: 10.3936
Evaluate side-chains
  105 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0670
   chunk 56 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.1922

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
A 139 HIS
B  88 GLN
D 134 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.229767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.187799 restraints weight = 91882.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.192569 restraints weight = 55046.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.191323 restraints weight = 41858.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.190952 restraints weight = 41642.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.191032 restraints weight = 41137.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6871  Z= 0.167
  Angle     :  0.669   7.219   9304  Z= 0.356
  Chirality :  0.049   0.176   1034
  Planarity :  0.005   0.047   1194
  Dihedral  :  5.027  19.539    927
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.27), residues: 845
  helix: -5.69 (0.31), residues: 6
  sheet: -1.31 (0.27), residues: 348
  loop : -2.15 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  51 
 TYR   0.014   0.001   TYR G 191 
 PHE   0.020   0.002   PHE B 127 
 TRP   0.009   0.001   TRP B  66 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6864)
  covalent geometry    : angle       0.66834 ( 9290)
  SS BOND              : bond        0.00646 (    7)
  SS BOND              : angle       0.96513 (   14)
  hydrogen bonds       : bond        0.03950 (  180)
  hydrogen bonds       : angle       6.57065 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 ASP cc_start: 0.6986 (p0) cc_final: 0.6507 (m-30)
REVERT: B  158 ASP cc_start: 0.7436 (t70) cc_final: 0.7167 (t70)
REVERT: D   25 MET cc_start: 0.2773 (mpp) cc_final: 0.2463 (mpp)
REVERT: G   59 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7903 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0678
  time to fit residues: 10.5381
Evaluate side-chains
  100 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    0.1980
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
** D 134 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 = 0.4358 r_free = 0.4358 target = 0.226835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.187070 restraints weight = 90424.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.189698 restraints weight = 56175.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.189496 restraints weight = 47484.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.189193 restraints weight = 47837.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.189432 restraints weight = 43045.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6871  Z= 0.166
  Angle     :  0.676   7.218   9304  Z= 0.360
  Chirality :  0.049   0.169   1034
  Planarity :  0.005   0.048   1194
  Dihedral  :  5.115  20.623    927
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.71 (0.27), residues: 845
  helix: -5.63 (0.35), residues: 6
  sheet: -1.32 (0.27), residues: 353
  loop : -2.16 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  51 
 TYR   0.021   0.001   TYR B 126 
 PHE   0.013   0.002   PHE B 201 
 TRP   0.009   0.001   TRP D  37 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6864)
  covalent geometry    : angle       0.67557 ( 9290)
  SS BOND              : bond        0.00727 (    7)
  SS BOND              : angle       0.93245 (   14)
  hydrogen bonds       : bond        0.03912 (  180)
  hydrogen bonds       : angle       6.57681 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.166 
Fit side-chains
REVERT: B   37 ASP cc_start: 0.6861 (p0) cc_final: 0.6343 (m-30)
REVERT: B  158 ASP cc_start: 0.7465 (t70) cc_final: 0.7222 (t70)
REVERT: B  215 ARG cc_start: 0.8752 (mmp-170) cc_final: 0.7867 (mmp-170)
REVERT: D   25 MET cc_start: 0.3044 (mpp) cc_final: 0.2740 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0671
  time to fit residues: 10.3696
Evaluate side-chains
  95 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 139 HIS
B  88 GLN
** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.230126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.187916 restraints weight = 91238.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.192538 restraints weight = 54634.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.192086 restraints weight = 44191.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.191220 restraints weight = 42726.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.191323 restraints weight = 43366.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6871  Z= 0.152
  Angle     :  0.666   7.278   9304  Z= 0.353
  Chirality :  0.049   0.176   1034
  Planarity :  0.005   0.063   1194
  Dihedral  :  5.041  18.675    927
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.27), residues: 845
  helix: -5.59 (0.37), residues: 6
  sheet: -1.27 (0.27), residues: 355
  loop : -2.12 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  51 
 TYR   0.012   0.001   TYR G 191 
 PHE   0.016   0.002   PHE B 201 
 TRP   0.011   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6864)
  covalent geometry    : angle       0.66505 ( 9290)
  SS BOND              : bond        0.00717 (    7)
  SS BOND              : angle       0.94287 (   14)
  hydrogen bonds       : bond        0.03691 (  180)
  hydrogen bonds       : angle       6.52667 (  459)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  234 ILE cc_start: 0.9562 (tp) cc_final: 0.9349 (tp)
REVERT: B   37 ASP cc_start: 0.6824 (p0) cc_final: 0.6331 (m-30)
REVERT: B  158 ASP cc_start: 0.7597 (t70) cc_final: 0.7308 (t70)
REVERT: B  215 ARG cc_start: 0.8732 (mmp-170) cc_final: 0.7840 (mmp-170)
REVERT: D   25 MET cc_start: 0.2982 (mpp) cc_final: 0.2719 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0697
  time to fit residues: 10.1349
Evaluate side-chains
  93 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0070
   chunk 35 optimal weight:    2.9990
   chunk 57 optimal weight:   20.0000
   chunk 63 optimal weight:    0.2980
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0030
   overall best weight:    0.4612

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
D 134 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.225819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.186138 restraints weight = 92048.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.189467 restraints weight = 56153.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.188302 restraints weight = 46605.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.188081 restraints weight = 48535.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.188246 restraints weight = 44034.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6871  Z= 0.115
  Angle     :  0.611   7.355   9304  Z= 0.326
  Chirality :  0.047   0.154   1034
  Planarity :  0.005   0.061   1194
  Dihedral  :  4.625  19.436    927
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.62 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.27), residues: 845
  helix: -5.54 (0.39), residues: 6
  sheet: -1.13 (0.27), residues: 349
  loop : -1.96 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  51 
 TYR   0.016   0.001   TYR B 126 
 PHE   0.007   0.001   PHE A  98 
 TRP   0.016   0.001   TRP G 196 
 HIS   0.003   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6864)
  covalent geometry    : angle       0.61015 ( 9290)
  SS BOND              : bond        0.00521 (    7)
  SS BOND              : angle       0.82284 (   14)
  hydrogen bonds       : bond        0.03099 (  180)
  hydrogen bonds       : angle       6.21217 (  459)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1008.11 seconds
wall clock time: 18 minutes 8.43 seconds (1088.43 seconds total)