Starting phenix.real_space_refine
on Wed Sep 17 22:34:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zw1_14991/09_2025/7zw1_14991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zw1_14991/09_2025/7zw1_14991.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zw1_14991/09_2025/7zw1_14991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zw1_14991/09_2025/7zw1_14991.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zw1_14991/09_2025/7zw1_14991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zw1_14991/09_2025/7zw1_14991.map"
  }
  resolution = 3.7
  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=   0.007
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      35      5.16       5
     C    3796      2.51       5
     N    1018      2.21       5
     O    1075      1.98       5
     H    5883      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11807
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 5117
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 11, 'TRANS': 305}
    Chain: "B"
      Number of atoms: 4759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 4759
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 19, 'TRANS': 296}
    Chain: "C"
      Number of atoms: 1931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1931
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
  Time building chain proxies: 2.42, per 1000 atoms: 0.20
  Number of scatterers: 11807
  At special positions: 0
  Unit cell: (69.536, 120.048, 139.072, 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      35     16.00
     O    1075      8.00
     N    1018      7.00
     C    3796      6.00
     H    5883      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 166 " - pdb=" SG  CYS A 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 168 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 217 " - pdb=" SG  CYS B 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  98 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 465.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1378

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      61.4% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 48
      removed outlier: 3.694A  pdb=" N   ARG A  48 " --> pdb=" O   GLU A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 87
      removed outlier: 3.920A  pdb=" N   ASP A  87 " --> pdb=" O   TYR A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 93
      removed outlier: 4.398A  pdb=" N   ARG A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 96
      No H-bonds generated for 'chain 'A' and resid 94 through 96'
    Processing helix  chain 'A' and resid 97 through 122
      removed outlier: 3.699A  pdb=" N   PHE A 120 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 140
      removed outlier: 4.326A  pdb=" N   LEU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   GLU A 127 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ASN A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   THR A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 164
      removed outlier: 4.271A  pdb=" N   LYS A 153 " --> pdb=" O   ARG A 149 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 177
    Processing helix  chain 'A' and resid 189 through 199
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.621A  pdb=" N   HIS A 233 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 293
    Processing helix  chain 'A' and resid 311 through 321
    Processing helix  chain 'B' and resid 10 through 48
      removed outlier: 4.121A  pdb=" N   HIS B  48 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 53
    Processing helix  chain 'B' and resid 60 through 89
      removed outlier: 3.727A  pdb=" N   GLN B  64 " --> pdb=" O   PRO B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 97
      Proline residue:  B  94  - end of helix
    Processing helix  chain 'B' and resid 99 through 143
      Proline residue:  B 126  - end of helix
      removed outlier: 3.747A  pdb=" N   LEU B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ASP B 130 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   GLU B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 167
      removed outlier: 4.431A  pdb=" N   ARG B 157 " --> pdb=" O   CYS B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 180
    Processing helix  chain 'B' and resid 184 through 188
    Processing helix  chain 'B' and resid 192 through 202
    Processing helix  chain 'B' and resid 203 through 206
      removed outlier: 3.776A  pdb=" N   LEU B 206 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 203 through 206'
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 252 through 297
      removed outlier: 3.876A  pdb=" N   GLY B 295 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU B 296 " --> pdb=" O   ALA B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 322
    Processing helix  chain 'C' and resid 30 through 34
    Processing helix  chain 'C' and resid 64 through 67
    Processing helix  chain 'C' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 9
    Processing sheet with id=AA3, first strand: chain 'C' and resid 13 through 15
      removed outlier: 6.608A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 127 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA C  51 " --> pdb=" O   TRP C  38 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   CYS C  40 " --> pdb=" O   PHE C  49 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   PHE C  49 " --> pdb=" O   CYS C  40 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TRP C  61 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 15
      removed outlier: 6.608A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 127 " (cutoff:3.500A)

    378 hydrogen bonds defined for protein.
    1041 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: 2.52

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5874
        1.03 -     1.23: 9
        1.23 -     1.42: 2584
        1.42 -     1.62: 3436
        1.62 -     1.81: 47
  Bond restraints: 11950
  Sorted by residual:
  bond pdb=" CA  GLN B 246 "
       pdb=" CB  GLN B 246 "
    ideal  model  delta    sigma   weight residual
    1.526  1.537 -0.011 1.44e-02 4.82e+03 6.01e-01
  bond pdb=" CA  ASN B 247 "
       pdb=" CB  ASN B 247 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.69e-02 3.50e+03 4.99e-01
  bond pdb=" N   LEU B   9 "
       pdb=" CA  LEU B   9 "
    ideal  model  delta    sigma   weight residual
    1.463  1.454  0.008 1.22e-02 6.72e+03 4.83e-01
  bond pdb=" CA  TYR B 174 "
       pdb=" CB  TYR B 174 "
    ideal  model  delta    sigma   weight residual
    1.536  1.526  0.010 1.46e-02 4.69e+03 4.79e-01
  bond pdb=" CA  GLY B 170 "
       pdb=" C   GLY B 170 "
    ideal  model  delta    sigma   weight residual
    1.514  1.524 -0.009 1.41e-02 5.03e+03 4.27e-01
  ... (remaining 11945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 21420
        1.81 -     3.62: 135
        3.62 -     5.42: 17
        5.42 -     7.23: 1
        7.23 -     9.04: 1
  Bond angle restraints: 21574
  Sorted by residual:
  angle pdb=" CB  MET C  85 "
        pdb=" CG  MET C  85 "
        pdb=" SD  MET C  85 "
      ideal   model   delta    sigma   weight residual
     112.70  121.74   -9.04 3.00e+00 1.11e-01 9.08e+00
  angle pdb=" CA  TYR C 106 "
        pdb=" CB  TYR C 106 "
        pdb=" CG  TYR C 106 "
      ideal   model   delta    sigma   weight residual
     113.90  118.76   -4.86 1.80e+00 3.09e-01 7.30e+00
  angle pdb=" CA  VAL B 212 "
        pdb=" C   VAL B 212 "
        pdb=" N   PRO B 213 "
      ideal   model   delta    sigma   weight residual
     117.00  119.10   -2.10 9.50e-01 1.11e+00 4.88e+00
  angle pdb=" CA  MET C  85 "
        pdb=" CB  MET C  85 "
        pdb=" CG  MET C  85 "
      ideal   model   delta    sigma   weight residual
     114.10  118.39   -4.29 2.00e+00 2.50e-01 4.59e+00
  angle pdb=" CB  MET A 265 "
        pdb=" CG  MET A 265 "
        pdb=" SD  MET A 265 "
      ideal   model   delta    sigma   weight residual
     112.70  118.60   -5.90 3.00e+00 1.11e-01 3.87e+00
  ... (remaining 21569 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4910
       18.00 -    36.00: 456
       36.00 -    53.99: 220
       53.99 -    71.99: 43
       71.99 -    89.99: 7
  Dihedral angle restraints: 5636
    sinusoidal: 3043
      harmonic: 2593
  Sorted by residual:
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 222 "
           pdb=" CB  CYS A 222 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.92   48.08     1      1.00e+01 1.00e-02 3.19e+01
  dihedral pdb=" CB  CYS B 169 "
           pdb=" SG  CYS B 169 "
           pdb=" SG  CYS B 216 "
           pdb=" CB  CYS B 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.31  -45.31     1      1.00e+01 1.00e-02 2.85e+01
  dihedral pdb=" CB  CYS C  24 "
           pdb=" SG  CYS C  24 "
           pdb=" SG  CYS C  98 "
           pdb=" CB  CYS C  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.80   41.20     1      1.00e+01 1.00e-02 2.38e+01
  ... (remaining 5633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 694
       0.033 -    0.065: 136
       0.065 -    0.098: 57
       0.098 -    0.130: 17
       0.130 -    0.163: 3
  Chirality restraints: 907
  Sorted by residual:
  chirality pdb=" CA  MET C  85 "
            pdb=" N   MET C  85 "
            pdb=" C   MET C  85 "
            pdb=" CB  MET C  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.63e-01
  chirality pdb=" CA  VAL B 149 "
            pdb=" N   VAL B 149 "
            pdb=" C   VAL B 149 "
            pdb=" CB  VAL B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CA  VAL C  53 "
            pdb=" N   VAL C  53 "
            pdb=" C   VAL C  53 "
            pdb=" CB  VAL C  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.30e-01
  ... (remaining 904 not shown)

  Planarity restraints: 1774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 106 "    0.018 2.00e-02 2.50e+03   1.02e-02 3.11e+00
        pdb=" CG  TYR C 106 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 106 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 106 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 106 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 106 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 106 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR C 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 106 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 106 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  62 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.45e+00
        pdb=" N   PRO B  63 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B  63 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  63 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 253 "    0.005 2.00e-02 2.50e+03   1.04e-02 1.09e+00
        pdb=" C   CYS B 253 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   CYS B 253 "    0.007 2.00e-02 2.50e+03
        pdb=" N   HIS B 254 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1771 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 1330
        2.23 -     2.82: 25687
        2.82 -     3.41: 32081
        3.41 -     4.01: 40716
        4.01 -     4.60: 62067
  Nonbonded interactions: 161881
  Sorted by model distance:
  nonbonded pdb="HH21 ARG B 171 "
            pdb=" O   TYR C 106 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" OD1 ASP A   9 "
            pdb=" H   LYS A  12 "
     model   vdw
     1.643 2.450
  nonbonded pdb=" OD1 ASP A 237 "
            pdb=" H   THR A 240 "
     model   vdw
     1.655 2.450
  nonbonded pdb="HD22 ASN B 202 "
            pdb=" O   LEU B 206 "
     model   vdw
     1.659 2.450
  nonbonded pdb=" O   VAL B  81 "
            pdb=" HG  SER B  84 "
     model   vdw
     1.661 2.450
  ... (remaining 161876 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:             5.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.070
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.780
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
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      :  0.002   0.030   6074  Z= 0.109
  Angle     :  0.497   9.040   8253  Z= 0.259
  Chirality :  0.035   0.163    907
  Planarity :  0.003   0.039   1050
  Dihedral  : 17.278  89.990   2182
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 22.87 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  3.09 (0.32), residues: 754
  helix:  3.84 (0.25), residues: 378
  sheet:  0.70 (0.67), residues: 58
  loop :  0.06 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 171 
 TYR   0.029   0.001   TYR C 106 
 PHE   0.009   0.001   PHE B 239 
 TRP   0.013   0.001   TRP C  61 
 HIS   0.004   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 6067)
  covalent geometry    : angle       0.49713 ( 8239)
  SS BOND              : bond        0.00189 (    7)
  SS BOND              : angle       0.63152 (   14)
  hydrogen bonds       : bond        0.06890 (  374)
  hydrogen bonds       : angle       3.68718 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1890
  time to fit residues: 8.1413
Evaluate side-chains
  30 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.0270
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.4046

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.062325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.050459 restraints weight = 109908.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.052376 restraints weight = 46872.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.053539 restraints weight = 26502.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.054188 restraints weight = 18393.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.054597 restraints weight = 14939.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.0488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6074  Z= 0.174
  Angle     :  0.510   4.979   8253  Z= 0.267
  Chirality :  0.035   0.135    907
  Planarity :  0.004   0.047   1050
  Dihedral  :  3.748  19.881    828
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 22.87 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.85 (0.31), residues: 754
  helix:  3.66 (0.25), residues: 380
  sheet:  0.71 (0.67), residues: 58
  loop : -0.16 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 171 
 TYR   0.031   0.001   TYR C 106 
 PHE   0.016   0.001   PHE B 239 
 TRP   0.012   0.001   TRP C  61 
 HIS   0.004   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6067)
  covalent geometry    : angle       0.50956 ( 8239)
  SS BOND              : bond        0.00322 (    7)
  SS BOND              : angle       0.74239 (   14)
  hydrogen bonds       : bond        0.03647 (  374)
  hydrogen bonds       : angle       3.65725 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.329 
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: B  135 GLU cc_start: 0.8924 (tp30) cc_final: 0.8495 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 35
  average time/residue: 0.1595
  time to fit residues: 7.8454
Evaluate side-chains
  34 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.066654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.055134 restraints weight = 125177.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.057050 restraints weight = 52114.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.058209 restraints weight = 29767.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.058785 restraints weight = 21091.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.059103 restraints weight = 17628.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.0541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6074  Z= 0.099
  Angle     :  0.472   5.310   8253  Z= 0.241
  Chirality :  0.035   0.135    907
  Planarity :  0.004   0.050   1050
  Dihedral  :  3.652  20.274    828
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 21.92 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  3.00 (0.32), residues: 754
  helix:  3.78 (0.25), residues: 380
  sheet:  0.75 (0.67), residues: 58
  loop : -0.06 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 171 
 TYR   0.031   0.001   TYR C 106 
 PHE   0.010   0.001   PHE A 171 
 TRP   0.010   0.001   TRP C  61 
 HIS   0.002   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 6067)
  covalent geometry    : angle       0.47216 ( 8239)
  SS BOND              : bond        0.00185 (    7)
  SS BOND              : angle       0.56314 (   14)
  hydrogen bonds       : bond        0.03521 (  374)
  hydrogen bonds       : angle       3.48892 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.326 
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: B  135 GLU cc_start: 0.8878 (tp30) cc_final: 0.8421 (tp30)
REVERT: C  110 MET cc_start: 0.5351 (mmt) cc_final: 0.5096 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 39
  average time/residue: 0.1811
  time to fit residues: 9.6654
Evaluate side-chains
  35 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0670
   chunk 56 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 4 optimal weight:    0.3980
   chunk 71 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.8924

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 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 = 0.3695 r_free = 0.3695 target = 0.063044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.051455 restraints weight = 104394.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.053431 restraints weight = 42517.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.054660 restraints weight = 23375.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.055391 restraints weight = 15772.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.055846 restraints weight = 12365.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.0684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6074  Z= 0.101
  Angle     :  0.468   5.231   8253  Z= 0.239
  Chirality :  0.035   0.135    907
  Planarity :  0.004   0.053   1050
  Dihedral  :  3.602  20.918    828
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 22.24 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  3.03 (0.32), residues: 754
  helix:  3.81 (0.25), residues: 380
  sheet:  0.67 (0.67), residues: 58
  loop : -0.04 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 171 
 TYR   0.031   0.001   TYR C 106 
 PHE   0.010   0.001   PHE B 239 
 TRP   0.010   0.001   TRP C  61 
 HIS   0.003   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6067)
  covalent geometry    : angle       0.46782 ( 8239)
  SS BOND              : bond        0.00197 (    7)
  SS BOND              : angle       0.56155 (   14)
  hydrogen bonds       : bond        0.03408 (  374)
  hydrogen bonds       : angle       3.44981 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.386 
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: C  110 MET cc_start: 0.5573 (mmt) cc_final: 0.5304 (mmt)
  outliers start: 7
  outliers final: 4
  residues processed: 39
  average time/residue: 0.1749
  time to fit residues: 9.4171
Evaluate side-chains
  35 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 1 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.061888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.050353 restraints weight = 105719.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.052286 restraints weight = 43255.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.053474 restraints weight = 23836.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.054156 restraints weight = 16176.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.054600 restraints weight = 12828.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.0874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6074  Z= 0.171
  Angle     :  0.505   5.335   8253  Z= 0.264
  Chirality :  0.035   0.133    907
  Planarity :  0.004   0.057   1050
  Dihedral  :  3.723  20.466    828
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 23.66 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.86 (0.31), residues: 754
  helix:  3.69 (0.25), residues: 380
  sheet:  0.65 (0.67), residues: 58
  loop : -0.19 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 171 
 TYR   0.034   0.001   TYR C 106 
 PHE   0.015   0.001   PHE B 239 
 TRP   0.013   0.001   TRP C  61 
 HIS   0.004   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6067)
  covalent geometry    : angle       0.50437 ( 8239)
  SS BOND              : bond        0.00383 (    7)
  SS BOND              : angle       0.72087 (   14)
  hydrogen bonds       : bond        0.03514 (  374)
  hydrogen bonds       : angle       3.60015 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8917 (tp30) cc_final: 0.8626 (tp30)
REVERT: C  110 MET cc_start: 0.5707 (mmt) cc_final: 0.5313 (mmt)
  outliers start: 7
  outliers final: 5
  residues processed: 39
  average time/residue: 0.1742
  time to fit residues: 9.2823
Evaluate side-chains
  39 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.1522

-------------------------------------------------------------------------------
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 = 0.3683 r_free = 0.3683 target = 0.062791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.050938 restraints weight = 110186.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.052872 restraints weight = 46520.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.054022 restraints weight = 26295.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.054708 restraints weight = 18346.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.055117 restraints weight = 14752.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6074  Z= 0.108
  Angle     :  0.478   5.520   8253  Z= 0.244
  Chirality :  0.035   0.134    907
  Planarity :  0.004   0.056   1050
  Dihedral  :  3.663  20.655    828
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 23.82 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.98 (0.31), residues: 754
  helix:  3.79 (0.25), residues: 380
  sheet:  0.64 (0.67), residues: 58
  loop : -0.10 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 171 
 TYR   0.034   0.001   TYR C 106 
 PHE   0.009   0.001   PHE B 239 
 TRP   0.011   0.001   TRP C  61 
 HIS   0.002   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6067)
  covalent geometry    : angle       0.47740 ( 8239)
  SS BOND              : bond        0.00223 (    7)
  SS BOND              : angle       0.56950 (   14)
  hydrogen bonds       : bond        0.03460 (  374)
  hydrogen bonds       : angle       3.49481 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8893 (tp30) cc_final: 0.8594 (tp30)
REVERT: C  110 MET cc_start: 0.5753 (mmt) cc_final: 0.5413 (mmt)
  outliers start: 7
  outliers final: 5
  residues processed: 40
  average time/residue: 0.1683
  time to fit residues: 9.1320
Evaluate side-chains
  36 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0060
   chunk 10 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    1.3802

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.062503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.050933 restraints weight = 104825.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.052889 restraints weight = 42749.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.054036 restraints weight = 23522.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.054749 restraints weight = 16141.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.055180 restraints weight = 12733.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.0992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6074  Z= 0.117
  Angle     :  0.477   5.271   8253  Z= 0.246
  Chirality :  0.035   0.133    907
  Planarity :  0.004   0.056   1050
  Dihedral  :  3.652  21.095    828
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 23.97 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.99 (0.31), residues: 754
  helix:  3.81 (0.25), residues: 380
  sheet:  0.55 (0.66), residues: 58
  loop : -0.08 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 171 
 TYR   0.034   0.001   TYR C 106 
 PHE   0.015   0.001   PHE A 319 
 TRP   0.012   0.001   TRP C  61 
 HIS   0.003   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6067)
  covalent geometry    : angle       0.47732 ( 8239)
  SS BOND              : bond        0.00249 (    7)
  SS BOND              : angle       0.56746 (   14)
  hydrogen bonds       : bond        0.03419 (  374)
  hydrogen bonds       : angle       3.49428 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.330 
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: B  135 GLU cc_start: 0.8912 (tp30) cc_final: 0.8594 (tp30)
REVERT: C  110 MET cc_start: 0.5734 (mmt) cc_final: 0.5360 (mmt)
  outliers start: 9
  outliers final: 7
  residues processed: 39
  average time/residue: 0.1622
  time to fit residues: 8.7970
Evaluate side-chains
  38 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.062479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.050654 restraints weight = 109572.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.052526 restraints weight = 46255.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.053702 restraints weight = 26437.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.054384 restraints weight = 18219.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.054808 restraints weight = 14705.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6074  Z= 0.122
  Angle     :  0.480   5.277   8253  Z= 0.247
  Chirality :  0.035   0.133    907
  Planarity :  0.004   0.056   1050
  Dihedral  :  3.653  21.527    828
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 22.87 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  3.00 (0.31), residues: 754
  helix:  3.80 (0.25), residues: 380
  sheet:  0.55 (0.66), residues: 58
  loop : -0.06 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 171 
 TYR   0.034   0.001   TYR C 106 
 PHE   0.011   0.001   PHE B 239 
 TRP   0.012   0.001   TRP C  61 
 HIS   0.002   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6067)
  covalent geometry    : angle       0.48007 ( 8239)
  SS BOND              : bond        0.00263 (    7)
  SS BOND              : angle       0.56454 (   14)
  hydrogen bonds       : bond        0.03415 (  374)
  hydrogen bonds       : angle       3.49935 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 30
  time to evaluate  : 0.337 
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: A  118 CYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8731 (p)
REVERT: B  135 GLU cc_start: 0.8896 (tp30) cc_final: 0.8568 (tp30)
REVERT: C  110 MET cc_start: 0.5784 (mmt) cc_final: 0.5430 (mmt)
  outliers start: 11
  outliers final: 9
  residues processed: 40
  average time/residue: 0.1570
  time to fit residues: 8.7299
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  118 CYS
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3680 r_free = 0.3680 target = 0.062727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.050940 restraints weight = 108433.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.052872 restraints weight = 45806.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.054062 restraints weight = 25798.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.054618 restraints weight = 17798.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 75)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.055073 restraints weight = 14651.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6074  Z= 0.106
  Angle     :  0.476   6.522   8253  Z= 0.243
  Chirality :  0.035   0.136    907
  Planarity :  0.004   0.056   1050
  Dihedral  :  3.609  21.846    828
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 23.03 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  3.03 (0.31), residues: 754
  helix:  3.82 (0.25), residues: 380
  sheet:  0.57 (0.66), residues: 58
  loop : -0.04 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 171 
 TYR   0.034   0.001   TYR C 106 
 PHE   0.009   0.001   PHE B 239 
 TRP   0.011   0.001   TRP C  61 
 HIS   0.002   0.001   HIS B 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6067)
  covalent geometry    : angle       0.47583 ( 8239)
  SS BOND              : bond        0.00212 (    7)
  SS BOND              : angle       0.52300 (   14)
  hydrogen bonds       : bond        0.03390 (  374)
  hydrogen bonds       : angle       3.46653 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.346 
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: B  135 GLU cc_start: 0.8881 (tp30) cc_final: 0.8548 (tp30)
REVERT: C  110 MET cc_start: 0.5740 (mmt) cc_final: 0.5406 (mmt)
  outliers start: 10
  outliers final: 9
  residues processed: 41
  average time/residue: 0.1659
  time to fit residues: 9.6313
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0050
   chunk 70 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0000
   overall best weight:    0.4798

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.063154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.051942 restraints weight = 102234.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.053824 restraints weight = 42139.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.054934 restraints weight = 23214.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.055661 restraints weight = 15928.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.056045 restraints weight = 12494.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6074  Z= 0.090
  Angle     :  0.471   5.746   8253  Z= 0.239
  Chirality :  0.035   0.179    907
  Planarity :  0.004   0.055   1050
  Dihedral  :  3.529  22.595    828
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 23.50 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  3.16 (0.32), residues: 754
  helix:  3.88 (0.25), residues: 380
  sheet:  0.58 (0.65), residues: 58
  loop :  0.10 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 171 
 TYR   0.033   0.001   TYR C 106 
 PHE   0.006   0.001   PHE B 239 
 TRP   0.009   0.001   TRP C  61 
 HIS   0.002   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 6067)
  covalent geometry    : angle       0.47118 ( 8239)
  SS BOND              : bond        0.00141 (    7)
  SS BOND              : angle       0.45033 (   14)
  hydrogen bonds       : bond        0.03340 (  374)
  hydrogen bonds       : angle       3.39852 ( 1041)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.330 
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: A  118 CYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8744 (p)
REVERT: B  135 GLU cc_start: 0.8846 (tp30) cc_final: 0.8503 (tp30)
  outliers start: 8
  outliers final: 6
  residues processed: 39
  average time/residue: 0.1575
  time to fit residues: 8.6989
Evaluate side-chains
  37 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 CYS
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   chunk 38 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.065768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.054307 restraints weight = 124629.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.056152 restraints weight = 52348.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.057310 restraints weight = 30133.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.057866 restraints weight = 21423.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.058067 restraints weight = 17954.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6074  Z= 0.147
  Angle     :  0.491   6.376   8253  Z= 0.254
  Chirality :  0.035   0.133    907
  Planarity :  0.004   0.056   1050
  Dihedral  :  3.581  22.675    828
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 23.19 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 aren not related in a simple way.
  whole:  3.06 (0.32), residues: 754
  helix:  3.83 (0.25), residues: 379
  sheet:  0.59 (0.66), residues: 58
  loop :  0.01 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 171 
 TYR   0.033   0.001   TYR C 106 
 PHE   0.013   0.001   PHE B 239 
 TRP   0.011   0.001   TRP C  61 
 HIS   0.003   0.001   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6067)
  covalent geometry    : angle       0.49047 ( 8239)
  SS BOND              : bond        0.00308 (    7)
  SS BOND              : angle       0.62671 (   14)
  hydrogen bonds       : bond        0.03378 (  374)
  hydrogen bonds       : angle       3.52757 ( 1041)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2276.13 seconds
wall clock time: 39 minutes 27.62 seconds (2367.62 seconds total)