Starting phenix.real_space_refine
on Fri Aug 22 18:26:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uzc_42839/08_2025/8uzc_42839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uzc_42839/08_2025/8uzc_42839.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uzc_42839/08_2025/8uzc_42839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uzc_42839/08_2025/8uzc_42839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uzc_42839/08_2025/8uzc_42839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uzc_42839/08_2025/8uzc_42839.cif"
  }
  resolution = 3.8
  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=  -0.002 sd=   0.055
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      15      5.16       5
     C    2182      2.51       5
     N     610      2.21       5
     O     657      1.98       5
     H    3367      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6831
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 1834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1834
          Classifications: {'peptide': 123}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "L"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 1613
          Classifications: {'peptide': 104}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 96}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 3384
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 13, 'TRANS': 202}
          Chain breaks: 2
  Time building chain proxies: 1.06, per 1000 atoms: 0.16
  Number of scatterers: 6831
  At special positions: 0
  Unit cell: (68.739, 79.154, 89.569, 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      15     16.00
     O     657      8.00
     N     610      7.00
     C    2182      6.00
     H    3367      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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: 0.46
  Conformation dependent library (CDL) restraints added in 248.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  808

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 10 sheets defined
      9.9% alpha, 25.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.721A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.535A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 72
    Processing helix  chain 'A' and resid 73 through 80
      removed outlier: 5.355A  pdb=" N   GLY A  78 " --> pdb=" O   GLN A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 156 through 160
      removed outlier: 3.518A  pdb=" N   THR A 160 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.618A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA H  23 " --> pdb=" O   VAL H   5 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 5.826A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA4, first strand: chain 'L' and resid 19 through 22
    Processing sheet with id=AA5, first strand: chain 'L' and resid 48 through 50
      removed outlier: 6.528A  pdb=" N   ASN L  53 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 88
      removed outlier: 5.641A  pdb=" N   PHE A  87 " --> pdb=" O   MET A 268 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122
      removed outlier: 3.555A  pdb=" N   LYS A 121 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   TYR A 257 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   GLY A 256 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   ILE A 179 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 122
      removed outlier: 3.555A  pdb=" N   LYS A 121 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   TYR A 257 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   GLY A 256 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   ILE A 179 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141
      removed outlier: 3.611A  pdb=" N   SER A 146 " --> pdb=" O   SER A 136 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   ALA A 138 " --> pdb=" O   SER A 144 " (cutoff:3.500A)
      removed outlier: 8.733A  pdb=" N   SER A 144 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 167 through 169

    83 hydrogen bonds defined for protein.
    189 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: 1.11

  Time building geometry restraints manager: 0.67 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: 3361
        1.03 -     1.23: 33
        1.23 -     1.43: 1515
        1.43 -     1.62: 1982
        1.62 -     1.82: 20
  Bond restraints: 6911
  Sorted by residual:
  bond pdb=" CA  PHE H  52A"
       pdb=" C   PHE H  52A"
    ideal  model  delta    sigma   weight residual
    1.523  1.465  0.058 1.34e-02 5.57e+03 1.86e+01
  bond pdb=" CA  ASP H  53 "
       pdb=" C   ASP H  53 "
    ideal  model  delta    sigma   weight residual
    1.524  1.465  0.059 1.40e-02 5.10e+03 1.79e+01
  bond pdb=" CA  SER H  55 "
       pdb=" C   SER H  55 "
    ideal  model  delta    sigma   weight residual
    1.523  1.472  0.051 1.28e-02 6.10e+03 1.61e+01
  bond pdb=" N   GLN H   1 "
       pdb=" H3  GLN H   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" N   GLU L   1 "
       pdb=" H3  GLU L   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.24e+01
  ... (remaining 6906 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 12115
        1.64 -     3.28: 246
        3.28 -     4.92: 32
        4.92 -     6.57: 2
        6.57 -     8.21: 3
  Bond angle restraints: 12398
  Sorted by residual:
  angle pdb=" N   SER H  55 "
        pdb=" CA  SER H  55 "
        pdb=" C   SER H  55 "
      ideal   model   delta    sigma   weight residual
     112.94  107.37    5.57 1.41e+00 5.03e-01 1.56e+01
  angle pdb=" O   SER H  52 "
        pdb=" C   SER H  52 "
        pdb=" N   PHE H  52A"
      ideal   model   delta    sigma   weight residual
     122.03  125.58   -3.55 1.08e+00 8.57e-01 1.08e+01
  angle pdb=" N   ARG A 220 "
        pdb=" CA  ARG A 220 "
        pdb=" C   ARG A 220 "
      ideal   model   delta    sigma   weight residual
     108.07  110.92   -2.85 8.90e-01 1.26e+00 1.03e+01
  angle pdb=" N   TYR H 100A"
        pdb=" CA  TYR H 100A"
        pdb=" C   TYR H 100A"
      ideal   model   delta    sigma   weight residual
     114.75  110.72    4.03 1.26e+00 6.30e-01 1.02e+01
  angle pdb=" N   GLY H  10 "
        pdb=" CA  GLY H  10 "
        pdb=" C   GLY H  10 "
      ideal   model   delta    sigma   weight residual
     110.20  114.40   -4.20 1.32e+00 5.74e-01 1.01e+01
  ... (remaining 12393 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 2861
       17.94 -    35.89: 337
       35.89 -    53.83: 70
       53.83 -    71.78: 17
       71.78 -    89.72: 7
  Dihedral angle restraints: 3292
    sinusoidal: 1777
      harmonic: 1515
  Sorted by residual:
  dihedral pdb=" CA  TRP A 153 "
           pdb=" C   TRP A 153 "
           pdb=" N   LEU A 154 "
           pdb=" CA  LEU A 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.93  -20.07     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  92 "
           pdb=" CB  CYS H  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.69   32.31     1      1.00e+01 1.00e-02 1.49e+01
  dihedral pdb=" CA  CYS A  64 "
           pdb=" C   CYS A  64 "
           pdb=" N   THR A  65 "
           pdb=" CA  THR A  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.10   18.90     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 3289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 302
       0.030 -    0.061: 148
       0.061 -    0.091: 29
       0.091 -    0.122: 33
       0.122 -    0.152: 6
  Chirality restraints: 518
  Sorted by residual:
  chirality pdb=" CA  ILE L  48 "
            pdb=" N   ILE L  48 "
            pdb=" C   ILE L  48 "
            pdb=" CB  ILE L  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.78e-01
  chirality pdb=" CA  ILE H  51 "
            pdb=" N   ILE H  51 "
            pdb=" C   ILE H  51 "
            pdb=" CB  ILE H  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.20e-01
  chirality pdb=" CA  ILE A 214 "
            pdb=" N   ILE A 214 "
            pdb=" C   ILE A 214 "
            pdb=" CB  ILE A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.97e-01
  ... (remaining 515 not shown)

  Planarity restraints: 1032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H  52 "    0.013 2.00e-02 2.50e+03   2.83e-02 7.99e+00
        pdb=" C   SER H  52 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   SER H  52 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE H  52A"    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 229 "    0.241 9.50e-02 1.11e+02   8.05e-02 7.13e+00
        pdb=" NE  ARG A 229 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 229 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 229 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 229 "    0.007 2.00e-02 2.50e+03
        pdb="HH11 ARG A 229 "   -0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG A 229 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A 229 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A 229 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER H  55 "   -0.014 2.00e-02 2.50e+03   2.56e-02 6.56e+00
        pdb=" N   LYS H  56 "    0.044 2.00e-02 2.50e+03
        pdb=" CA  LYS H  56 "   -0.011 2.00e-02 2.50e+03
        pdb=" H   LYS H  56 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1029 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 151
        2.09 -     2.72: 11512
        2.72 -     3.34: 19075
        3.34 -     3.97: 24056
        3.97 -     4.60: 37864
  Nonbonded interactions: 92658
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU L  81 "
            pdb=" H   GLU L  81 "
     model   vdw
     1.462 2.450
  nonbonded pdb=" OE1 GLN H 105 "
            pdb=" H   GLN H 105 "
     model   vdw
     1.586 2.450
  nonbonded pdb=" OD1 ASP H  61 "
            pdb="HH22 ARG H  64 "
     model   vdw
     1.608 2.450
  nonbonded pdb="HE21 GLN H  39 "
            pdb=" O   LYS H  43 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" H   TYR H 100F"
            pdb=" OH  TYR L  36 "
     model   vdw
     1.647 2.450
  ... (remaining 92653 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  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:             0.030
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.060
  Find NCS groups from input model:        0.010
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
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      :  0.004   0.059   3546  Z= 0.233
  Angle     :  0.713   7.085   4807  Z= 0.412
  Chirality :  0.044   0.152    518
  Planarity :  0.006   0.107    618
  Dihedral  : 16.347  89.722   1287
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.74 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.95 %
    Favored  : 75.60 %
  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: -2.81 (0.39), residues: 431
  helix:  0.22 (1.15), residues: 21
  sheet: -2.36 (0.43), residues: 122
  loop : -1.86 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  90 
 TYR   0.015   0.002   TYR L  92 
 PHE   0.011   0.001   PHE L  98 
 TRP   0.009   0.001   TRP H 103 
 HIS   0.002   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 3544)
  covalent geometry    : angle       0.71271 ( 4803)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       0.60409 (    4)
  hydrogen bonds       : bond        0.30237 (   81)
  hydrogen bonds       : angle      10.67771 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  71 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    4 MET cc_start: 0.7179 (mmt) cc_final: 0.6415 (mmm)
REVERT: L   85 VAL cc_start: 0.6119 (t) cc_final: 0.5909 (t)
REVERT: A   58 ILE cc_start: 0.8002 (mm) cc_final: 0.7719 (pt)
REVERT: A  154 LEU cc_start: 0.7755 (tp) cc_final: 0.7487 (mm)
  outliers start: 13
  outliers final: 12
  residues processed: 65
  average time/residue: 0.1421
  time to fit residues: 11.1299
Evaluate side-chains
  67 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue   94 TRP
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  246 ASN
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** 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 = 0.4229 r_free = 0.4229 target = 0.165869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.150254 restraints weight = 15514.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.154473 restraints weight = 8633.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.157365 restraints weight = 5530.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.159221 restraints weight = 3856.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.160670 restraints weight = 2885.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.0896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3546  Z= 0.148
  Angle     :  0.622   5.426   4807  Z= 0.328
  Chirality :  0.045   0.176    518
  Planarity :  0.006   0.091    618
  Dihedral  :  8.061  59.626    509
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.44 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.42 %
    Favored  : 76.13 %
  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 (0.38), residues: 431
  helix:  0.64 (1.15), residues: 21
  sheet: -2.23 (0.43), residues: 130
  loop : -2.00 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 150 
 TYR   0.013   0.002   TYR L  92 
 PHE   0.010   0.002   PHE L  98 
 TRP   0.008   0.001   TRP H 103 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3544)
  covalent geometry    : angle       0.62170 ( 4803)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       0.89498 (    4)
  hydrogen bonds       : bond        0.04557 (   81)
  hydrogen bonds       : angle       7.60114 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  70 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   62 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7750 (t)
REVERT: L    4 MET cc_start: 0.7226 (mmt) cc_final: 0.6403 (mmm)
REVERT: A   58 ILE cc_start: 0.8064 (mm) cc_final: 0.7772 (pt)
REVERT: A  154 LEU cc_start: 0.7757 (tp) cc_final: 0.7550 (mm)
  outliers start: 13
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0973
  time to fit residues: 8.1262
Evaluate side-chains
  61 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   95 GLU
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  228 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.166396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.151108 restraints weight = 15714.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.155129 restraints weight = 9046.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.157867 restraints weight = 5957.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.159744 restraints weight = 4230.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.160854 restraints weight = 3187.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3546  Z= 0.140
  Angle     :  0.595   4.929   4807  Z= 0.312
  Chirality :  0.045   0.174    518
  Planarity :  0.006   0.074    618
  Dihedral  :  7.041  56.474    501
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.21 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 20.69 %
    Favored  : 75.07 %
  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: -2.88 (0.39), residues: 431
  helix:  0.89 (1.19), residues: 21
  sheet: -2.32 (0.43), residues: 135
  loop : -1.98 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 150 
 TYR   0.013   0.002   TYR A 233 
 PHE   0.011   0.001   PHE L  98 
 TRP   0.012   0.001   TRP L  94 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3544)
  covalent geometry    : angle       0.59471 ( 4803)
  SS BOND              : bond        0.00271 (    2)
  SS BOND              : angle       0.89098 (    4)
  hydrogen bonds       : bond        0.03701 (   81)
  hydrogen bonds       : angle       7.01055 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  72 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.157 
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: H   62 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7769 (t)
REVERT: A   58 ILE cc_start: 0.8051 (mm) cc_final: 0.7818 (pt)
REVERT: A  244 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6195 (tt)
  outliers start: 16
  outliers final: 10
  residues processed: 66
  average time/residue: 0.1371
  time to fit residues: 10.8854
Evaluate side-chains
  66 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   95 GLU
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0770
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0000
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5344

-------------------------------------------------------------------------------
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 = 0.4230 r_free = 0.4230 target = 0.166540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.150922 restraints weight = 15641.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.155270 restraints weight = 8556.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.158156 restraints weight = 5400.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.159890 restraints weight = 3739.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.161354 restraints weight = 2826.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6803
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3546  Z= 0.107
  Angle     :  0.552   4.930   4807  Z= 0.290
  Chirality :  0.045   0.171    518
  Planarity :  0.005   0.058    618
  Dihedral  :  6.609  54.724    499
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.89 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.55 %
    Favored  : 74.54 %
  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 aren not related in a simple way.
  whole: -2.74 (0.39), residues: 431
  helix:  1.34 (1.19), residues: 21
  sheet: -2.27 (0.43), residues: 135
  loop : -1.89 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 229 
 TYR   0.011   0.001   TYR L  49 
 PHE   0.007   0.001   PHE L  98 
 TRP   0.009   0.001   TRP L  94 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3544)
  covalent geometry    : angle       0.55212 ( 4803)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       0.79667 (    4)
  hydrogen bonds       : bond        0.02986 (   81)
  hydrogen bonds       : angle       6.52133 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.175 
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: H   62 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7809 (t)
REVERT: A   58 ILE cc_start: 0.7989 (mm) cc_final: 0.7750 (pt)
REVERT: A  244 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6146 (tt)
  outliers start: 11
  outliers final: 8
  residues processed: 63
  average time/residue: 0.1367
  time to fit residues: 10.5126
Evaluate side-chains
  64 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   95 GLU
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.164712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.148935 restraints weight = 15663.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.153193 restraints weight = 8649.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.156063 restraints weight = 5527.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.157810 restraints weight = 3859.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.159287 restraints weight = 2930.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3546  Z= 0.127
  Angle     :  0.558   4.959   4807  Z= 0.293
  Chirality :  0.045   0.172    518
  Planarity :  0.005   0.054    618
  Dihedral  :  6.574  53.775    499
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 21.22 %
    Favored  : 74.54 %
  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 aren not related in a simple way.
  whole: -2.82 (0.39), residues: 431
  helix:  1.25 (1.17), residues: 21
  sheet: -2.16 (0.42), residues: 134
  loop : -2.04 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 150 
 TYR   0.012   0.001   TYR A 233 
 PHE   0.010   0.001   PHE L  98 
 TRP   0.011   0.001   TRP L  94 
 HIS   0.002   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3544)
  covalent geometry    : angle       0.55814 ( 4803)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       0.85888 (    4)
  hydrogen bonds       : bond        0.02909 (   81)
  hydrogen bonds       : angle       6.32927 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  71 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.204 
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: H   62 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7860 (t)
REVERT: A   58 ILE cc_start: 0.7987 (mm) cc_final: 0.7728 (pt)
REVERT: A  244 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6194 (tt)
  outliers start: 16
  outliers final: 12
  residues processed: 66
  average time/residue: 0.1494
  time to fit residues: 11.8523
Evaluate side-chains
  67 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   95 GLU
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   94 TRP
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.4185 r_free = 0.4185 target = 0.162463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.146517 restraints weight = 15946.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.150613 restraints weight = 9178.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.153362 restraints weight = 6027.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.155034 restraints weight = 4339.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.156496 restraints weight = 3381.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3546  Z= 0.169
  Angle     :  0.597   5.066   4807  Z= 0.318
  Chirality :  0.045   0.175    518
  Planarity :  0.006   0.061    618
  Dihedral  :  6.794  53.568    499
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.15 %
    Favored  : 85.85 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 20.42 %
    Favored  : 74.54 %
  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 aren not related in a simple way.
  whole: -3.07 (0.38), residues: 431
  helix:  0.76 (1.17), residues: 21
  sheet: -2.32 (0.42), residues: 134
  loop : -2.19 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  19 
 TYR   0.018   0.002   TYR A 233 
 PHE   0.015   0.001   PHE L  98 
 TRP   0.011   0.002   TRP L  94 
 HIS   0.003   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3544)
  covalent geometry    : angle       0.59636 ( 4803)
  SS BOND              : bond        0.00272 (    2)
  SS BOND              : angle       0.96239 (    4)
  hydrogen bonds       : bond        0.03185 (   81)
  hydrogen bonds       : angle       6.37384 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  74 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.174 
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: H   62 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7861 (t)
REVERT: A  244 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6313 (tt)
  outliers start: 19
  outliers final: 15
  residues processed: 66
  average time/residue: 0.1416
  time to fit residues: 11.1584
Evaluate side-chains
  68 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   94 TRP
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  156 HIS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.164356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.148285 restraints weight = 15378.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.152282 restraints weight = 8940.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.155006 restraints weight = 5942.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.156711 restraints weight = 4311.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.158125 restraints weight = 3364.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3546  Z= 0.134
  Angle     :  0.576   5.240   4807  Z= 0.305
  Chirality :  0.045   0.171    518
  Planarity :  0.009   0.180    618
  Dihedral  :  6.754  54.191    499
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.83 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 22.02 %
    Favored  : 74.01 %
  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 aren not related in a simple way.
  whole: -3.04 (0.38), residues: 431
  helix:  1.05 (1.17), residues: 21
  sheet: -2.54 (0.41), residues: 131
  loop : -2.06 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  19 
 TYR   0.012   0.001   TYR H  91 
 PHE   0.010   0.001   PHE L  98 
 TRP   0.012   0.001   TRP L  94 
 HIS   0.002   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3544)
  covalent geometry    : angle       0.57565 ( 4803)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       0.90663 (    4)
  hydrogen bonds       : bond        0.02915 (   81)
  hydrogen bonds       : angle       6.19467 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  66 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   62 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7854 (t)
REVERT: A   58 ILE cc_start: 0.8057 (mm) cc_final: 0.7798 (mm)
REVERT: A  244 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6301 (tt)
  outliers start: 15
  outliers final: 12
  residues processed: 61
  average time/residue: 0.1218
  time to fit residues: 9.2759
Evaluate side-chains
  64 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 TRP
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.164857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.148029 restraints weight = 15630.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.152206 restraints weight = 8805.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.154794 restraints weight = 5786.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.156956 restraints weight = 4248.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.158278 restraints weight = 3212.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3546  Z= 0.127
  Angle     :  0.562   4.977   4807  Z= 0.296
  Chirality :  0.045   0.170    518
  Planarity :  0.008   0.158    618
  Dihedral  :  6.372  53.676    497
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.83 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 23.08 %
    Favored  : 73.21 %
  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 (0.38), residues: 431
  helix: -0.17 (1.05), residues: 27
  sheet: -2.46 (0.42), residues: 131
  loop : -2.06 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 229 
 TYR   0.012   0.001   TYR H  91 
 PHE   0.010   0.001   PHE L  98 
 TRP   0.011   0.001   TRP L  94 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3544)
  covalent geometry    : angle       0.56195 ( 4803)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       0.87228 (    4)
  hydrogen bonds       : bond        0.02888 (   81)
  hydrogen bonds       : angle       6.09936 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  65 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   62 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7882 (t)
REVERT: A   58 ILE cc_start: 0.8043 (mm) cc_final: 0.7780 (mm)
REVERT: A  244 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6319 (tt)
  outliers start: 14
  outliers final: 12
  residues processed: 60
  average time/residue: 0.1058
  time to fit residues: 7.9625
Evaluate side-chains
  64 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   94 TRP
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  156 HIS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.165358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.148615 restraints weight = 15594.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.152826 restraints weight = 8708.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.155768 restraints weight = 5689.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.157614 restraints weight = 4034.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.159069 restraints weight = 3098.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3546  Z= 0.117
  Angle     :  0.551   4.894   4807  Z= 0.289
  Chirality :  0.044   0.169    518
  Planarity :  0.007   0.153    618
  Dihedral  :  6.247  51.747    497
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.81 %
    Favored  : 73.47 %
  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 (0.38), residues: 431
  helix: -0.04 (1.06), residues: 27
  sheet: -2.38 (0.43), residues: 131
  loop : -2.02 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 229 
 TYR   0.012   0.001   TYR H  91 
 PHE   0.010   0.001   PHE L  98 
 TRP   0.010   0.001   TRP L  94 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3544)
  covalent geometry    : angle       0.55046 ( 4803)
  SS BOND              : bond        0.00341 (    2)
  SS BOND              : angle       0.88846 (    4)
  hydrogen bonds       : bond        0.02789 (   81)
  hydrogen bonds       : angle       5.98670 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  66 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   62 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7875 (t)
REVERT: A   58 ILE cc_start: 0.8074 (mm) cc_final: 0.7820 (mm)
REVERT: A  244 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6324 (tt)
  outliers start: 14
  outliers final: 12
  residues processed: 61
  average time/residue: 0.1222
  time to fit residues: 9.2288
Evaluate side-chains
  66 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   94 TRP
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  156 HIS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.163673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.147095 restraints weight = 15433.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.151317 restraints weight = 8445.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.154229 restraints weight = 5408.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.156054 restraints weight = 3809.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.157481 restraints weight = 2917.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3546  Z= 0.122
  Angle     :  0.552   4.918   4807  Z= 0.290
  Chirality :  0.044   0.171    518
  Planarity :  0.008   0.151    618
  Dihedral  :  6.214  50.482    497
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.83 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.81 %
    Favored  : 73.47 %
  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: -3.01 (0.38), residues: 431
  helix: -0.02 (1.06), residues: 27
  sheet: -2.39 (0.42), residues: 131
  loop : -2.05 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  19 
 TYR   0.012   0.001   TYR H  91 
 PHE   0.009   0.001   PHE L  98 
 TRP   0.010   0.001   TRP L  94 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3544)
  covalent geometry    : angle       0.55172 ( 4803)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       0.86384 (    4)
  hydrogen bonds       : bond        0.02763 (   81)
  hydrogen bonds       : angle       5.93220 (  189)

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

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

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  862 Ramachandran restraints generated.
    431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   55 is missing expected H atoms. Skipping.
Residue LYS   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  63 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 ARG cc_start: 0.6737 (ttt90) cc_final: 0.6377 (ttt90)
REVERT: H   62 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7903 (t)
REVERT: A  244 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6372 (tt)
  outliers start: 14
  outliers final: 11
  residues processed: 58
  average time/residue: 0.1235
  time to fit residues: 9.0345
Evaluate side-chains
  62 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue  100 ILE
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   94 TRP
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  156 HIS
Chi-restraints excluded: chain A residue  178 TYR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.164091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.147227 restraints weight = 15455.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.151543 restraints weight = 8307.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.154565 restraints weight = 5268.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.156514 restraints weight = 3691.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.157969 restraints weight = 2774.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3546  Z= 0.115
  Angle     :  0.545   4.912   4807  Z= 0.286
  Chirality :  0.044   0.171    518
  Planarity :  0.008   0.146    618
  Dihedral  :  5.849  50.768    495
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.08 %
    Favored  : 73.47 %
  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: -2.94 (0.38), residues: 431
  helix:  0.09 (1.06), residues: 27
  sheet: -2.32 (0.42), residues: 131
  loop : -2.03 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  19 
 TYR   0.012   0.001   TYR H  91 
 PHE   0.008   0.001   PHE L  98 
 TRP   0.010   0.001   TRP L  94 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3544)
  covalent geometry    : angle       0.54441 ( 4803)
  SS BOND              : bond        0.00342 (    2)
  SS BOND              : angle       0.85576 (    4)
  hydrogen bonds       : bond        0.02717 (   81)
  hydrogen bonds       : angle       5.86749 (  189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1463.07 seconds
wall clock time: 25 minutes 44.33 seconds (1544.33 seconds total)