Starting phenix.real_space_refine
on Tue Feb  3 17:50:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vxw_65443/02_2026/9vxw_65443_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vxw_65443/02_2026/9vxw_65443.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vxw_65443/02_2026/9vxw_65443.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vxw_65443/02_2026/9vxw_65443.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vxw_65443/02_2026/9vxw_65443_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vxw_65443/02_2026/9vxw_65443_neut.cif"
  }
  resolution = 2.3
  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=   0.001 sd=   0.069
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      60      5.16       5
     C    3921      2.51       5
     N     969      2.21       5
     O     987      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  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: 5937
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1969
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 243}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'D10': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.34, per 1000 atoms: 0.23
  Number of scatterers: 5937
  At special positions: 0
  Unit cell: (83.74, 85.32, 57.67, 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      60     16.00
     O     987      8.00
     N     969      7.00
     C    3921      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 155 " - pdb=" SG  CYS A 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 155 " - pdb=" SG  CYS B 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 155 " - pdb=" SG  CYS C 227 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.30
  Conformation dependent library (CDL) restraints added in 333.7 milliseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1446

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      86.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
    Processing helix  chain 'A' and resid 41 through 71
    Processing helix  chain 'A' and resid 74 through 93
      removed outlier: 3.836A  pdb=" N   THR A  78 " --> pdb=" O   HIS A  74 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A  79 " --> pdb=" O   PRO A  75 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR A  80 " --> pdb=" O   THR A  76 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A  81 " --> pdb=" O   TRP A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 109
    Processing helix  chain 'A' and resid 113 through 138
      removed outlier: 3.677A  pdb=" N   VAL A 119 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 154
      removed outlier: 4.008A  pdb=" N   PHE A 153 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 184
    Processing helix  chain 'A' and resid 188 through 208
      removed outlier: 3.553A  pdb=" N   HIS A 194 " --> pdb=" O   LYS A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 224
    Processing helix  chain 'A' and resid 224 through 231
    Processing helix  chain 'A' and resid 231 through 240
    Processing helix  chain 'A' and resid 240 through 256
      removed outlier: 3.546A  pdb=" N   SER A 244 " --> pdb=" O   TRP A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 262
    Processing helix  chain 'B' and resid 9 through 39
    Processing helix  chain 'B' and resid 41 through 71
    Processing helix  chain 'B' and resid 74 through 93
      removed outlier: 3.836A  pdb=" N   THR B  78 " --> pdb=" O   HIS B  74 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR B  80 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU B  81 " --> pdb=" O   TRP B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 109
    Processing helix  chain 'B' and resid 113 through 138
      removed outlier: 3.677A  pdb=" N   VAL B 119 " --> pdb=" O   GLU B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 154
      removed outlier: 4.008A  pdb=" N   PHE B 153 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 184
    Processing helix  chain 'B' and resid 188 through 208
      removed outlier: 3.553A  pdb=" N   HIS B 194 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
    Processing helix  chain 'B' and resid 224 through 231
    Processing helix  chain 'B' and resid 231 through 240
    Processing helix  chain 'B' and resid 240 through 256
      removed outlier: 3.546A  pdb=" N   SER B 244 " --> pdb=" O   TRP B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 262
    Processing helix  chain 'C' and resid 9 through 39
    Processing helix  chain 'C' and resid 41 through 71
    Processing helix  chain 'C' and resid 74 through 93
      removed outlier: 3.836A  pdb=" N   THR C  78 " --> pdb=" O   HIS C  74 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU C  79 " --> pdb=" O   PRO C  75 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR C  80 " --> pdb=" O   THR C  76 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU C  81 " --> pdb=" O   TRP C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 109
    Processing helix  chain 'C' and resid 113 through 138
      removed outlier: 3.677A  pdb=" N   VAL C 119 " --> pdb=" O   GLU C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 154
      removed outlier: 4.008A  pdb=" N   PHE C 153 " --> pdb=" O   GLU C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 184
    Processing helix  chain 'C' and resid 188 through 208
      removed outlier: 3.553A  pdb=" N   HIS C 194 " --> pdb=" O   LYS C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 224
    Processing helix  chain 'C' and resid 224 through 231
    Processing helix  chain 'C' and resid 231 through 240
    Processing helix  chain 'C' and resid 240 through 256
      removed outlier: 3.547A  pdb=" N   SER C 244 " --> pdb=" O   TRP C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 262

    483 hydrogen bonds defined for protein.
    1431 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: 0.99

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1806
        1.34 -     1.46: 1351
        1.46 -     1.58: 2846
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 6093
  Sorted by residual:
  bond pdb=" CG1 ILE B 251 "
       pdb=" CD1 ILE B 251 "
    ideal  model  delta    sigma   weight residual
    1.513  1.485  0.028 3.90e-02 6.57e+02 5.14e-01
  bond pdb=" CG1 ILE C 251 "
       pdb=" CD1 ILE C 251 "
    ideal  model  delta    sigma   weight residual
    1.513  1.485  0.028 3.90e-02 6.57e+02 5.06e-01
  bond pdb=" CG1 ILE A 251 "
       pdb=" CD1 ILE A 251 "
    ideal  model  delta    sigma   weight residual
    1.513  1.485  0.028 3.90e-02 6.57e+02 5.01e-01
  bond pdb=" CA  PHE C 215 "
       pdb=" CB  PHE C 215 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.70e-02 3.46e+03 4.87e-01
  bond pdb=" CA  PHE B 215 "
       pdb=" CB  PHE B 215 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.70e-02 3.46e+03 4.70e-01
  ... (remaining 6088 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 7947
        1.02 -     2.04: 249
        2.04 -     3.06: 66
        3.06 -     4.08: 15
        4.08 -     5.10: 12
  Bond angle restraints: 8289
  Sorted by residual:
  angle pdb=" CA  TYR B 146 "
        pdb=" CB  TYR B 146 "
        pdb=" CG  TYR B 146 "
      ideal   model   delta    sigma   weight residual
     113.90  117.12   -3.22 1.80e+00 3.09e-01 3.21e+00
  angle pdb=" CA  TYR C 146 "
        pdb=" CB  TYR C 146 "
        pdb=" CG  TYR C 146 "
      ideal   model   delta    sigma   weight residual
     113.90  117.11   -3.21 1.80e+00 3.09e-01 3.17e+00
  angle pdb=" CA  TYR A 146 "
        pdb=" CB  TYR A 146 "
        pdb=" CG  TYR A 146 "
      ideal   model   delta    sigma   weight residual
     113.90  117.09   -3.19 1.80e+00 3.09e-01 3.15e+00
  angle pdb=" C   SER A 152 "
        pdb=" N   PHE A 153 "
        pdb=" CA  PHE A 153 "
      ideal   model   delta    sigma   weight residual
     122.46  124.80   -2.34 1.41e+00 5.03e-01 2.75e+00
  angle pdb=" C   SER C 152 "
        pdb=" N   PHE C 153 "
        pdb=" CA  PHE C 153 "
      ideal   model   delta    sigma   weight residual
     122.46  124.78   -2.32 1.41e+00 5.03e-01 2.72e+00
  ... (remaining 8284 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 3024
       17.17 -    34.34: 345
       34.34 -    51.51: 150
       51.51 -    68.67: 30
       68.67 -    85.84: 3
  Dihedral angle restraints: 3552
    sinusoidal: 1332
      harmonic: 2220
  Sorted by residual:
  dihedral pdb=" CG  ARG C 192 "
           pdb=" CD  ARG C 192 "
           pdb=" NE  ARG C 192 "
           pdb=" CZ  ARG C 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.23   43.77     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG B 192 "
           pdb=" CD  ARG B 192 "
           pdb=" NE  ARG B 192 "
           pdb=" CZ  ARG B 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.24   43.76     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG A 192 "
           pdb=" CD  ARG A 192 "
           pdb=" NE  ARG A 192 "
           pdb=" CZ  ARG A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.26   43.74     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 3549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 491
       0.022 -    0.044: 284
       0.044 -    0.067: 123
       0.067 -    0.089: 49
       0.089 -    0.111: 49
  Chirality restraints: 996
  Sorted by residual:
  chirality pdb=" CA  PHE C 232 "
            pdb=" N   PHE C 232 "
            pdb=" C   PHE C 232 "
            pdb=" CB  PHE C 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.09e-01
  chirality pdb=" CA  PHE B 232 "
            pdb=" N   PHE B 232 "
            pdb=" C   PHE B 232 "
            pdb=" CB  PHE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.08e-01
  chirality pdb=" CA  PHE A 232 "
            pdb=" N   PHE A 232 "
            pdb=" C   PHE A 232 "
            pdb=" CB  PHE A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.03e-01
  ... (remaining 993 not shown)

  Planarity restraints: 1005
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 216 "    0.019 5.00e-02 4.00e+02   2.81e-02 1.27e+00
        pdb=" N   PRO C 217 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO C 217 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 217 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 216 "    0.018 5.00e-02 4.00e+02   2.80e-02 1.26e+00
        pdb=" N   PRO A 217 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 216 "   -0.018 5.00e-02 4.00e+02   2.80e-02 1.26e+00
        pdb=" N   PRO B 217 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO B 217 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 217 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1002 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.89: 2223
        2.89 -     3.39: 6107
        3.39 -     3.89: 10676
        3.89 -     4.40: 12144
        4.40 -     4.90: 20391
  Nonbonded interactions: 51541
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  17 "
            pdb=" OH  TYR A 146 "
     model   vdw
     2.382 3.040
  nonbonded pdb=" OG  SER C  17 "
            pdb=" OH  TYR C 146 "
     model   vdw
     2.382 3.040
  nonbonded pdb=" OG  SER B  17 "
            pdb=" OH  TYR B 146 "
     model   vdw
     2.382 3.040
  nonbonded pdb=" O   VAL C  82 "
            pdb=" OG  SER C  86 "
     model   vdw
     2.400 3.040
  nonbonded pdb=" O   VAL B  82 "
            pdb=" OG  SER B  86 "
     model   vdw
     2.400 3.040
  ... (remaining 51536 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.020
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
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   0.028   6096  Z= 0.121
  Angle     :  0.495   5.100   8295  Z= 0.255
  Chirality :  0.039   0.111    996
  Planarity :  0.004   0.028   1005
  Dihedral  : 17.678  85.842   2097
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 17.44 %
    Favored  : 76.54 %
  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 are not related in a simple way.
  whole:  1.81 (0.31), residues: 756
  helix:  1.81 (0.22), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.08 (0.45), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  36 
 TYR   0.014   0.002   TYR A 146 
 PHE   0.013   0.002   PHE B  85 
 TRP   0.008   0.001   TRP C 260 
 HIS   0.002   0.001   HIS B 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6093)
  covalent geometry    : angle       0.49524 ( 8289)
  SS BOND              : bond        0.00018 (    3)
  SS BOND              : angle       0.03496 (    6)
  hydrogen bonds       : bond        0.20609 (  483)
  hydrogen bonds       : angle       7.16030 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 105
  time to evaluate  : 0.211 
Fit side-chains
  outliers start: 39
  outliers final: 21
  residues processed: 135
  average time/residue: 0.5665
  time to fit residues: 79.4231
Evaluate side-chains
  121 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain B residue   15 CYS
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
A  70 GLN
A  71 HIS
A 234 GLN
B  38 GLN
C  38 GLN
C  70 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.173604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.135847 restraints weight = 5741.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.46
r_work: 0.3409 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6096  Z= 0.126
  Angle     :  0.489   4.776   8295  Z= 0.262
  Chirality :  0.038   0.118    996
  Planarity :  0.004   0.031   1005
  Dihedral  :  7.822  58.421    848
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 14.97 %
    Favored  : 79.94 %
  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 are not related in a simple way.
  whole:  2.97 (0.31), residues: 756
  helix:  2.98 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop : -1.94 (0.45), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 132 
 TYR   0.012   0.002   TYR A 146 
 PHE   0.010   0.002   PHE B  85 
 TRP   0.010   0.001   TRP A 260 
 HIS   0.003   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6093)
  covalent geometry    : angle       0.48925 ( 8289)
  SS BOND              : bond        0.00032 (    3)
  SS BOND              : angle       0.32759 (    6)
  hydrogen bonds       : bond        0.04165 (  483)
  hydrogen bonds       : angle       4.68201 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (tp)
REVERT: A  186 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.7031 (mm-30)
REVERT: B   38 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6859 (pp30)
REVERT: B  186 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6885 (mp0)
REVERT: C  186 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6978 (tp30)
  outliers start: 33
  outliers final: 9
  residues processed: 138
  average time/residue: 0.5230
  time to fit residues: 74.9940
Evaluate side-chains
  127 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   15 CYS
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:   20.0000
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 234 GLN
C  38 GLN
C  70 GLN
C 234 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.174496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.136585 restraints weight = 5728.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.47
r_work: 0.3424 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6096  Z= 0.116
  Angle     :  0.471   4.773   8295  Z= 0.251
  Chirality :  0.038   0.115    996
  Planarity :  0.004   0.035   1005
  Dihedral  :  6.620  59.197    829
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 15.12 %
    Favored  : 79.94 %
  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 are not related in a simple way.
  whole:  3.03 (0.31), residues: 756
  helix:  3.00 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.92 (0.45), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 132 
 TYR   0.010   0.002   TYR B 146 
 PHE   0.012   0.002   PHE C  85 
 TRP   0.008   0.001   TRP A 260 
 HIS   0.003   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6093)
  covalent geometry    : angle       0.47098 ( 8289)
  SS BOND              : bond        0.00314 (    3)
  SS BOND              : angle       0.43263 (    6)
  hydrogen bonds       : bond        0.03888 (  483)
  hydrogen bonds       : angle       4.46169 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 112
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8035 (tp)
REVERT: B   20 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7991 (tp)
REVERT: C   20 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8021 (tp)
  outliers start: 32
  outliers final: 11
  residues processed: 131
  average time/residue: 0.5056
  time to fit residues: 68.6836
Evaluate side-chains
  118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain B residue   15 CYS
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 38 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 234 GLN
B  38 GLN
B 234 GLN
C  70 GLN
C 234 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.176037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.138063 restraints weight = 5766.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.48
r_work: 0.3466 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6096  Z= 0.117
  Angle     :  0.471   4.797   8295  Z= 0.249
  Chirality :  0.038   0.119    996
  Planarity :  0.004   0.036   1005
  Dihedral  :  6.420  58.019    827
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 15.12 %
    Favored  : 79.01 %
  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 are not related in a simple way.
  whole:  3.13 (0.31), residues: 756
  helix:  3.08 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.92 (0.45), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 132 
 TYR   0.010   0.002   TYR B 146 
 PHE   0.012   0.002   PHE C  85 
 TRP   0.008   0.001   TRP B 260 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6093)
  covalent geometry    : angle       0.47106 ( 8289)
  SS BOND              : bond        0.00104 (    3)
  SS BOND              : angle       0.52115 (    6)
  hydrogen bonds       : bond        0.03762 (  483)
  hydrogen bonds       : angle       4.38860 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8123 (tp)
REVERT: B   20 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8036 (tp)
REVERT: B  132 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7591 (tpp-160)
REVERT: C   20 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8139 (tp)
REVERT: C  186 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7022 (tp30)
  outliers start: 38
  outliers final: 12
  residues processed: 127
  average time/residue: 0.4942
  time to fit residues: 65.1531
Evaluate side-chains
  119 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain B residue   15 CYS
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  165 LYS
Chi-restraints excluded: chain C residue  186 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0770
   chunk 72 optimal weight:    0.9990
   overall best weight:    1.6146

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
B  38 GLN
B 234 GLN
C  38 GLN
C  70 GLN
C 234 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.173615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.134285 restraints weight = 5820.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.54
r_work: 0.3404 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6096  Z= 0.132
  Angle     :  0.495   4.855   8295  Z= 0.262
  Chirality :  0.039   0.120    996
  Planarity :  0.004   0.037   1005
  Dihedral  :  6.120  58.648    825
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 15.59 %
    Favored  : 79.17 %
  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 are not related in a simple way.
  whole:  3.10 (0.31), residues: 756
  helix:  3.04 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.87 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 132 
 TYR   0.010   0.002   TYR B 146 
 PHE   0.014   0.002   PHE C 215 
 TRP   0.007   0.001   TRP A 260 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6093)
  covalent geometry    : angle       0.49525 ( 8289)
  SS BOND              : bond        0.00072 (    3)
  SS BOND              : angle       0.64351 (    6)
  hydrogen bonds       : bond        0.03969 (  483)
  hydrogen bonds       : angle       4.42100 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8044 (tp)
REVERT: A   69 GLU cc_start: 0.7744 (pt0) cc_final: 0.7521 (pt0)
REVERT: B   20 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8006 (tp)
REVERT: B   38 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6680 (pp30)
REVERT: B  132 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7601 (tpp-160)
REVERT: C   20 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8016 (tp)
  outliers start: 34
  outliers final: 15
  residues processed: 123
  average time/residue: 0.5552
  time to fit residues: 70.7498
Evaluate side-chains
  122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain B residue   15 CYS
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   38 GLN
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  165 LYS
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 44 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 67 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0170
   overall best weight:    1.0420

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
B 234 GLN
C  70 GLN
C 234 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.176300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.138162 restraints weight = 5750.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.49
r_work: 0.3466 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6096  Z= 0.118
  Angle     :  0.474   4.808   8295  Z= 0.250
  Chirality :  0.038   0.117    996
  Planarity :  0.004   0.036   1005
  Dihedral  :  5.883  57.421    825
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.05 %
    Favored  : 79.01 %
  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 are not related in a simple way.
  whole:  3.17 (0.31), residues: 756
  helix:  3.11 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.89 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 132 
 TYR   0.011   0.002   TYR B 146 
 PHE   0.011   0.002   PHE C  85 
 TRP   0.007   0.001   TRP B 260 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6093)
  covalent geometry    : angle       0.47433 ( 8289)
  SS BOND              : bond        0.00050 (    3)
  SS BOND              : angle       0.44504 (    6)
  hydrogen bonds       : bond        0.03708 (  483)
  hydrogen bonds       : angle       4.36133 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8114 (tp)
REVERT: B   20 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8039 (tp)
REVERT: B  132 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7603 (tpp-160)
REVERT: C   20 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8133 (tp)
  outliers start: 32
  outliers final: 16
  residues processed: 124
  average time/residue: 0.4911
  time to fit residues: 63.4495
Evaluate side-chains
  120 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 CYS
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain B residue   15 CYS
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   15 CYS
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  165 LYS
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 67 optimal weight:    7.9990
   chunk 12 optimal weight:    0.8980
   chunk 69 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
B  38 GLN
C  70 GLN
C 234 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.176294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137671 restraints weight = 5874.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 1.55
r_work: 0.3439 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6096  Z= 0.111
  Angle     :  0.460   4.805   8295  Z= 0.243
  Chirality :  0.038   0.113    996
  Planarity :  0.004   0.037   1005
  Dihedral  :  5.302  54.287    825
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.28 %
    Favored  : 78.70 %
  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 are not related in a simple way.
  whole:  3.26 (0.31), residues: 756
  helix:  3.17 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.87 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 132 
 TYR   0.010   0.001   TYR B 146 
 PHE   0.011   0.002   PHE C  85 
 TRP   0.007   0.001   TRP A 260 
 HIS   0.003   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 6093)
  covalent geometry    : angle       0.45959 ( 8289)
  SS BOND              : bond        0.00044 (    3)
  SS BOND              : angle       0.38186 (    6)
  hydrogen bonds       : bond        0.03500 (  483)
  hydrogen bonds       : angle       4.28462 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8062 (tp)
REVERT: B   20 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7973 (tp)
REVERT: B  132 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7542 (tpp-160)
REVERT: B  234 GLN cc_start: 0.8177 (tm130) cc_final: 0.7815 (tm-30)
REVERT: C   20 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8120 (tp)
REVERT: C   66 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7728 (mt)
  outliers start: 26
  outliers final: 12
  residues processed: 121
  average time/residue: 0.5497
  time to fit residues: 69.0513
Evaluate side-chains
  117 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  165 LYS
Chi-restraints excluded: chain C residue  241 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 63 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:   30.0000
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
B  38 GLN
C  70 GLN
** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.173064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.133354 restraints weight = 5679.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.54
r_work: 0.3385 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6096  Z= 0.153
  Angle     :  0.533   4.918   8295  Z= 0.280
  Chirality :  0.041   0.115    996
  Planarity :  0.004   0.038   1005
  Dihedral  :  5.481  59.066    822
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.13 %
    Favored  : 78.86 %
  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 are not related in a simple way.
  whole:  3.01 (0.31), residues: 756
  helix:  2.97 (0.21), residues: 585
  sheet:  None (None), residues: 0
  loop : -1.79 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 132 
 TYR   0.010   0.002   TYR C 146 
 PHE   0.016   0.002   PHE C 215 
 TRP   0.007   0.001   TRP B 260 
 HIS   0.004   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6093)
  covalent geometry    : angle       0.53331 ( 8289)
  SS BOND              : bond        0.00059 (    3)
  SS BOND              : angle       0.45468 (    6)
  hydrogen bonds       : bond        0.04160 (  483)
  hydrogen bonds       : angle       4.47809 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8051 (tp)
REVERT: A   69 GLU cc_start: 0.7743 (pt0) cc_final: 0.7525 (pt0)
REVERT: B   20 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7940 (tp)
REVERT: B  132 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7577 (tpp-160)
REVERT: C  185 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7273 (mp10)
  outliers start: 26
  outliers final: 14
  residues processed: 119
  average time/residue: 0.6147
  time to fit residues: 75.8799
Evaluate side-chains
  116 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  165 LYS
Chi-restraints excluded: chain C residue  185 GLN
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
B  38 GLN
C  70 GLN
C 234 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.175905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.137341 restraints weight = 5738.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 1.50
r_work: 0.3453 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6096  Z= 0.133
  Angle     :  0.509   4.860   8295  Z= 0.267
  Chirality :  0.040   0.155    996
  Planarity :  0.004   0.038   1005
  Dihedral  :  5.401  59.018    822
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.59 %
    Favored  : 78.55 %
  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 are not related in a simple way.
  whole:  3.07 (0.31), residues: 756
  helix:  3.02 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.87 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 132 
 TYR   0.010   0.002   TYR C 146 
 PHE   0.013   0.002   PHE C 215 
 TRP   0.012   0.001   TRP C 139 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6093)
  covalent geometry    : angle       0.50934 ( 8289)
  SS BOND              : bond        0.00040 (    3)
  SS BOND              : angle       0.32806 (    6)
  hydrogen bonds       : bond        0.03902 (  483)
  hydrogen bonds       : angle       4.41703 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8109 (tp)
REVERT: B   20 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7981 (tp)
REVERT: B  132 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7616 (tpp-160)
REVERT: C   20 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8147 (tp)
REVERT: C  185 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7302 (mp10)
  outliers start: 25
  outliers final: 14
  residues processed: 119
  average time/residue: 0.5492
  time to fit residues: 67.7755
Evaluate side-chains
  118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  165 LYS
Chi-restraints excluded: chain C residue  185 GLN
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 69 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0970
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C  70 GLN
C 234 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.176819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.138028 restraints weight = 5866.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 1.55
r_work: 0.3442 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6096  Z= 0.110
  Angle     :  0.466   4.823   8295  Z= 0.244
  Chirality :  0.038   0.119    996
  Planarity :  0.004   0.036   1005
  Dihedral  :  5.059  54.921    822
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.21 %
    Favored  : 78.55 %
  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 are not related in a simple way.
  whole:  3.23 (0.32), residues: 756
  helix:  3.14 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.87 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 132 
 TYR   0.010   0.001   TYR B 146 
 PHE   0.011   0.002   PHE C  85 
 TRP   0.012   0.001   TRP C 139 
 HIS   0.003   0.001   HIS A  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6093)
  covalent geometry    : angle       0.46622 ( 8289)
  SS BOND              : bond        0.00048 (    3)
  SS BOND              : angle       0.22112 (    6)
  hydrogen bonds       : bond        0.03431 (  483)
  hydrogen bonds       : angle       4.29694 ( 1431)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8048 (tp)
REVERT: B   20 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7989 (tp)
REVERT: B  132 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7562 (tpp-160)
REVERT: B  234 GLN cc_start: 0.8155 (tm130) cc_final: 0.7820 (tm-30)
REVERT: C   20 LEU cc_start: 0.8400 (mm) cc_final: 0.8156 (tp)
REVERT: C  185 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7318 (mp10)
  outliers start: 21
  outliers final: 14
  residues processed: 115
  average time/residue: 0.6196
  time to fit residues: 73.8794
Evaluate side-chains
  112 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   97 SER
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  185 GLN
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  261 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 45 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0000
   chunk 6 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.0788

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

Flipped N/Q/H residues before XYZ refinement:
C  70 GLN
C 234 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.175879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.136801 restraints weight = 5821.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 1.54
r_work: 0.3428 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6096  Z= 0.119
  Angle     :  0.483   4.818   8295  Z= 0.254
  Chirality :  0.039   0.124    996
  Planarity :  0.004   0.036   1005
  Dihedral  :  5.141  54.597    822
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.21 %
    Favored  : 78.40 %
  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 are not related in a simple way.
  whole:  3.17 (0.31), residues: 756
  helix:  3.09 (0.20), residues: 597
  sheet:  None (None), residues: 0
  loop : -2.14 (0.49), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 132 
 TYR   0.009   0.001   TYR C 146 
 PHE   0.011   0.002   PHE C  85 
 TRP   0.009   0.001   TRP C 139 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6093)
  covalent geometry    : angle       0.48296 ( 8289)
  SS BOND              : bond        0.00043 (    3)
  SS BOND              : angle       0.25348 (    6)
  hydrogen bonds       : bond        0.03593 (  483)
  hydrogen bonds       : angle       4.33851 ( 1431)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2382.65 seconds
wall clock time: 41 minutes 18.03 seconds (2478.03 seconds total)