Starting phenix.real_space_refine
on Tue Feb  3 16:03:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9og1_70449/02_2026/9og1_70449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9og1_70449/02_2026/9og1_70449.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9og1_70449/02_2026/9og1_70449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9og1_70449/02_2026/9og1_70449.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9og1_70449/02_2026/9og1_70449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9og1_70449/02_2026/9og1_70449.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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      24      5.16       5
     C    2940      2.51       5
     N     781      2.21       5
     O     861      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4606
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2851
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 7, 'TRANS': 338}
    Chain: "B"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 959
          Classifications: {'peptide': 122}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 796
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
  Time building chain proxies: 1.20, per 1000 atoms: 0.26
  Number of scatterers: 4606
  At special positions: 0
  Unit cell: (69.975, 70.908, 95.166, 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      24     16.00
     O     861      8.00
     N     781      7.00
     C    2940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  43 " - pdb=" SG  CYS A 342 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  26 " - pdb=" SG  CYS C  91 " 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: 0.35
  Conformation dependent library (CDL) restraints added in 291.8 milliseconds
  

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1068

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 6 sheets defined
      31.9% alpha, 19.2% 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 20 through 33
    Processing helix  chain 'A' and resid 45 through 63
      removed outlier: 4.329A  pdb=" N   TYR A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 81
      removed outlier: 3.506A  pdb=" N   TRP A  80 " --> pdb=" O   PRO A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 89 through 97
    Processing helix  chain 'A' and resid 101 through 108
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 4.071A  pdb=" N   ILE A 146 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 177
      removed outlier: 3.574A  pdb=" N   ILE A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 191
      removed outlier: 4.084A  pdb=" N   PHE A 191 " --> pdb=" O   TYR A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 203
    Processing helix  chain 'A' and resid 206 through 211
    Processing helix  chain 'A' and resid 215 through 228
    Processing helix  chain 'A' and resid 232 through 236
      removed outlier: 3.614A  pdb=" N   ALA A 236 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 262
      removed outlier: 3.529A  pdb=" N   LEU A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.713A  pdb=" N   ILE A 328 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   HIS A 329 " --> pdb=" O   GLN A 326 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   PHE A 330 " --> pdb=" O   HIS A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'B' and resid 83 through 87
      removed outlier: 4.169A  pdb=" N   THR B  87 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 86
      removed outlier: 4.183A  pdb=" N   PHE C  86 " --> pdb=" O   PRO C  83 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 249
      removed outlier: 3.784A  pdb=" N   THR A 268 " --> pdb=" O   THR A 241 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 319
      removed outlier: 5.947A  pdb=" N   ILE A 313 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ARG A 282 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA A 315 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ALA A 276 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
      removed outlier: 5.638A  pdb=" N   LEU A 278 " --> pdb=" O   PHE A 294 " (cutoff:3.500A)
      removed outlier: 7.516A  pdb=" N   PHE A 294 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   TYR A 280 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ALA A 292 " --> pdb=" O   TYR A 280 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG A 282 " --> pdb=" O   ASP A 290 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.507A  pdb=" N   ALA B  88 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   MET B  34 " --> pdb=" O   TRP B  50 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   TRP B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP B  50 " --> pdb=" O   ASN B  58 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 7 through 9
      removed outlier: 3.587A  pdb=" N   PHE C  74 " --> pdb=" O   CYS C  26 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 15
      removed outlier: 3.636A  pdb=" N   GLU C 108 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   TRP C  38 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)

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

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 734
        1.31 -     1.43: 1391
        1.43 -     1.56: 2555
        1.56 -     1.69: 1
        1.69 -     1.81: 39
  Bond restraints: 4720
  Sorted by residual:
  bond pdb=" CA  PCA B   1 "
       pdb=" CB  PCA B   1 "
    ideal  model  delta    sigma   weight residual
    1.530  1.408  0.122 2.00e-02 2.50e+03 3.71e+01
  bond pdb=" N   PCA B   1 "
       pdb=" CA  PCA B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.570 -0.112 1.90e-02 2.77e+03 3.50e+01
  bond pdb=" N   TYR A 113 "
       pdb=" CA  TYR A 113 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.26e-02 6.30e+03 8.87e+00
  bond pdb=" N   ILE B  75 "
       pdb=" CA  ILE B  75 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.29e-02 6.01e+03 8.75e+00
  bond pdb=" N   ARG A 286 "
       pdb=" CA  ARG A 286 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.16e-02 7.43e+03 8.56e+00
  ... (remaining 4715 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 6152
        1.40 -     2.80: 202
        2.80 -     4.21: 33
        4.21 -     5.61: 4
        5.61 -     7.01: 1
  Bond angle restraints: 6392
  Sorted by residual:
  angle pdb=" C   SER C  33 "
        pdb=" CA  SER C  33 "
        pdb=" CB  SER C  33 "
      ideal   model   delta    sigma   weight residual
     116.34  111.32    5.02 1.40e+00 5.10e-01 1.28e+01
  angle pdb=" N   ILE B  75 "
        pdb=" CA  ILE B  75 "
        pdb=" C   ILE B  75 "
      ideal   model   delta    sigma   weight residual
     112.17  108.84    3.33 9.50e-01 1.11e+00 1.23e+01
  angle pdb=" CA  ASN A 206 "
        pdb=" C   ASN A 206 "
        pdb=" O   ASN A 206 "
      ideal   model   delta    sigma   weight residual
     122.14  118.36    3.78 1.24e+00 6.50e-01 9.29e+00
  angle pdb=" CA  ARG A 205 "
        pdb=" C   ARG A 205 "
        pdb=" O   ARG A 205 "
      ideal   model   delta    sigma   weight residual
     121.88  117.96    3.92 1.30e+00 5.92e-01 9.10e+00
  angle pdb=" CA  THR B  77 "
        pdb=" CB  THR B  77 "
        pdb=" OG1 THR B  77 "
      ideal   model   delta    sigma   weight residual
     109.60  105.31    4.29 1.50e+00 4.44e-01 8.18e+00
  ... (remaining 6387 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.34: 2647
       16.34 -    32.67: 107
       32.67 -    49.01: 26
       49.01 -    65.34: 1
       65.34 -    81.68: 1
  Dihedral angle restraints: 2782
    sinusoidal: 1105
      harmonic: 1677
  Sorted by residual:
  dihedral pdb=" CB  GLU A  68 "
           pdb=" CG  GLU A  68 "
           pdb=" CD  GLU A  68 "
           pdb=" OE1 GLU A  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.68  -81.68     1      3.00e+01 1.11e-03 9.12e+00
  dihedral pdb=" N   VAL C  14 "
           pdb=" CA  VAL C  14 "
           pdb=" CB  VAL C  14 "
           pdb=" CG1 VAL C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -127.66  -52.34     3      1.50e+01 4.44e-03 9.11e+00
  dihedral pdb=" CA  LEU C  50 "
           pdb=" CB  LEU C  50 "
           pdb=" CG  LEU C  50 "
           pdb=" CD1 LEU C  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  103.48  -43.48     3      1.50e+01 4.44e-03 7.82e+00
  ... (remaining 2779 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 476
       0.039 -    0.077: 143
       0.077 -    0.116: 52
       0.116 -    0.154: 11
       0.154 -    0.193: 5
  Chirality restraints: 687
  Sorted by residual:
  chirality pdb=" CA  ILE B  75 "
            pdb=" N   ILE B  75 "
            pdb=" C   ILE B  75 "
            pdb=" CB  ILE B  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.28e-01
  chirality pdb=" CA  VAL A 198 "
            pdb=" N   VAL A 198 "
            pdb=" C   VAL A 198 "
            pdb=" CB  VAL A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.22e-01
  chirality pdb=" CA  VAL A 193 "
            pdb=" N   VAL A 193 "
            pdb=" C   VAL A 193 "
            pdb=" CB  VAL A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.66e-01
  ... (remaining 684 not shown)

  Planarity restraints: 811
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 286 "   -0.275 9.50e-02 1.11e+02   1.23e-01 9.34e+00
        pdb=" NE  ARG A 286 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 286 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 286 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 286 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  82 "    0.025 5.00e-02 4.00e+02   3.73e-02 2.23e+00
        pdb=" N   PRO C  83 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO C  83 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  83 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 204 "   -0.006 2.00e-02 2.50e+03   1.19e-02 1.41e+00
        pdb=" C   ASP A 204 "    0.021 2.00e-02 2.50e+03
        pdb=" O   ASP A 204 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ARG A 205 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 808 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 1525
        2.85 -     3.36: 3893
        3.36 -     3.87: 7663
        3.87 -     4.39: 8898
        4.39 -     4.90: 15549
  Nonbonded interactions: 37528
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 169 "
            pdb=" O   ILE A 183 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" O   ILE C   5 "
            pdb=" OG1 THR C 100 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" OD1 ASN A 320 "
            pdb=" OG  SER A 322 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   LYS A 151 "
            pdb=" ND2 ASN A 155 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" OG1 THR A  24 "
            pdb=" OH  TYR A  98 "
     model   vdw
     2.416 3.040
  ... (remaining 37523 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 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:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.350
  Find NCS groups from input model:        0.020
  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:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
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   0.122   4723  Z= 0.279
  Angle     :  0.572   7.010   6398  Z= 0.373
  Chirality :  0.046   0.193    687
  Planarity :  0.006   0.123    811
  Dihedral  :  9.345  81.676   1705
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  4.40 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.86 (0.35), residues: 567
  helix:  0.44 (0.41), residues: 130
  sheet: -1.18 (0.47), residues: 129
  loop : -0.65 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 230 
 TYR   0.015   0.001   TYR A 121 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.007   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 4720)
  covalent geometry    : angle       0.57211 ( 6392)
  SS BOND              : bond        0.00047 (    3)
  SS BOND              : angle       0.59431 (    6)
  hydrogen bonds       : bond        0.21893 (  178)
  hydrogen bonds       : angle       7.84609 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 133
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.8358 (tttt) cc_final: 0.8070 (tttm)
REVERT: A   82 THR cc_start: 0.8254 (m) cc_final: 0.7996 (p)
REVERT: A   88 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8360 (ttmm)
REVERT: A  104 ASN cc_start: 0.8254 (t0) cc_final: 0.8018 (t0)
REVERT: A  142 TYR cc_start: 0.7990 (m-80) cc_final: 0.7788 (m-80)
REVERT: A  187 MET cc_start: 0.8063 (ptp) cc_final: 0.7819 (ptp)
REVERT: A  255 GLU cc_start: 0.7163 (tt0) cc_final: 0.6864 (tt0)
REVERT: A  264 SER cc_start: 0.8623 (t) cc_final: 0.8380 (p)
REVERT: A  310 ASP cc_start: 0.7914 (t70) cc_final: 0.7600 (t0)
REVERT: A  311 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8359 (mtpp)
REVERT: A  318 LEU cc_start: 0.8498 (mt) cc_final: 0.8282 (mt)
REVERT: A  333 ARG cc_start: 0.7211 (ttt-90) cc_final: 0.6942 (ttt-90)
REVERT: B   48 MET cc_start: 0.7961 (mtp) cc_final: 0.7744 (mtp)
REVERT: B   90 TYR cc_start: 0.8488 (m-80) cc_final: 0.7686 (m-80)
REVERT: B  100 ASP cc_start: 0.7416 (t0) cc_final: 0.7215 (t0)
REVERT: C   55 SER cc_start: 0.7920 (m) cc_final: 0.7642 (t)
REVERT: C   96 SER cc_start: 0.8501 (t) cc_final: 0.8182 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 135
  average time/residue: 0.0930
  time to fit residues: 15.1236
Evaluate side-chains
  117 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain C residue   14 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0570
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.3980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 169 GLN
A 364 ASN
B  39 GLN
C  41 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.103070 restraints weight = 6659.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.95
r_work: 0.3146 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4723  Z= 0.147
  Angle     :  0.466   6.141   6398  Z= 0.250
  Chirality :  0.042   0.141    687
  Planarity :  0.003   0.029    811
  Dihedral  :  4.100  41.019    639
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.60 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.09 (0.37), residues: 567
  helix:  1.45 (0.46), residues: 130
  sheet: -0.79 (0.46), residues: 128
  loop : -0.31 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  83 
 TYR   0.021   0.002   TYR A 121 
 PHE   0.011   0.001   PHE A 221 
 TRP   0.009   0.001   TRP B  50 
 HIS   0.002   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4720)
  covalent geometry    : angle       0.46485 ( 6392)
  SS BOND              : bond        0.00681 (    3)
  SS BOND              : angle       0.95454 (    6)
  hydrogen bonds       : bond        0.04296 (  178)
  hydrogen bonds       : angle       5.08569 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 123
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.8449 (tttt) cc_final: 0.8140 (tttm)
REVERT: A   65 LYS cc_start: 0.8495 (mttt) cc_final: 0.8234 (mmtm)
REVERT: A   71 LYS cc_start: 0.8164 (tttt) cc_final: 0.7756 (ttpp)
REVERT: A   84 TYR cc_start: 0.8635 (t80) cc_final: 0.8345 (t80)
REVERT: A   88 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8356 (ttmt)
REVERT: A   95 MET cc_start: 0.8429 (tpp) cc_final: 0.8152 (tpp)
REVERT: A  187 MET cc_start: 0.7854 (ptp) cc_final: 0.7454 (ptp)
REVERT: A  193 VAL cc_start: 0.8781 (t) cc_final: 0.8544 (p)
REVERT: A  264 SER cc_start: 0.8700 (t) cc_final: 0.8310 (p)
REVERT: A  310 ASP cc_start: 0.8016 (t70) cc_final: 0.7686 (t0)
REVERT: A  311 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8326 (mtpp)
REVERT: A  318 LEU cc_start: 0.8432 (mt) cc_final: 0.8226 (mp)
REVERT: B   34 MET cc_start: 0.8150 (mmm) cc_final: 0.7817 (mmm)
REVERT: B   48 MET cc_start: 0.8018 (mtp) cc_final: 0.7773 (mtp)
REVERT: B   90 TYR cc_start: 0.8590 (m-80) cc_final: 0.7649 (m-80)
REVERT: C   55 SER cc_start: 0.8013 (m) cc_final: 0.7738 (t)
REVERT: C   96 SER cc_start: 0.8480 (t) cc_final: 0.8086 (p)
  outliers start: 9
  outliers final: 7
  residues processed: 125
  average time/residue: 0.0879
  time to fit residues: 13.5272
Evaluate side-chains
  119 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain C residue   14 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 169 GLN
A 309 ASN
A 314 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.110523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.098733 restraints weight = 6715.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.94
r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   4723  Z= 0.255
  Angle     :  0.527   6.343   6398  Z= 0.282
  Chirality :  0.044   0.137    687
  Planarity :  0.003   0.031    811
  Dihedral  :  4.357  39.115    639
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 11.60 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.32 (0.36), residues: 567
  helix:  0.97 (0.44), residues: 136
  sheet: -0.63 (0.46), residues: 128
  loop : -0.49 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  83 
 TYR   0.023   0.002   TYR A 121 
 PHE   0.018   0.002   PHE A 221 
 TRP   0.011   0.002   TRP B  50 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 4720)
  covalent geometry    : angle       0.52574 ( 6392)
  SS BOND              : bond        0.00553 (    3)
  SS BOND              : angle       1.15792 (    6)
  hydrogen bonds       : bond        0.04782 (  178)
  hydrogen bonds       : angle       4.98890 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.8523 (tttt) cc_final: 0.8183 (tttm)
REVERT: A   65 LYS cc_start: 0.8620 (mttt) cc_final: 0.8351 (mmtm)
REVERT: A   71 LYS cc_start: 0.8223 (tttt) cc_final: 0.7875 (ttpp)
REVERT: A   84 TYR cc_start: 0.8657 (t80) cc_final: 0.8313 (t80)
REVERT: A   95 MET cc_start: 0.8458 (tpp) cc_final: 0.8116 (tpp)
REVERT: A  187 MET cc_start: 0.7915 (ptp) cc_final: 0.7571 (ptp)
REVERT: A  264 SER cc_start: 0.8630 (t) cc_final: 0.8279 (p)
REVERT: A  310 ASP cc_start: 0.8050 (t70) cc_final: 0.7752 (t0)
REVERT: A  318 LEU cc_start: 0.8521 (mt) cc_final: 0.8154 (mm)
REVERT: C   13 SER cc_start: 0.8123 (p) cc_final: 0.7902 (p)
REVERT: C   55 SER cc_start: 0.8014 (m) cc_final: 0.7768 (t)
REVERT: C   96 SER cc_start: 0.8481 (t) cc_final: 0.8057 (p)
  outliers start: 13
  outliers final: 10
  residues processed: 115
  average time/residue: 0.0868
  time to fit residues: 12.2680
Evaluate side-chains
  120 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  178 ASN
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue  105 GLN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue   63 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 46 optimal weight:    0.3980
   chunk 29 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 169 GLN
A 210 HIS
A 314 HIS
A 329 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.113706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.102030 restraints weight = 6605.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.93
r_work: 0.3136 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   4723  Z= 0.172
  Angle     :  0.478   6.139   6398  Z= 0.253
  Chirality :  0.042   0.135    687
  Planarity :  0.003   0.030    811
  Dihedral  :  4.156  37.852    637
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.20 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.05 (0.37), residues: 567
  helix:  1.45 (0.44), residues: 129
  sheet: -0.57 (0.44), residues: 141
  loop : -0.34 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.023   0.001   TYR A 121 
 PHE   0.013   0.001   PHE A 221 
 TRP   0.012   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 4720)
  covalent geometry    : angle       0.47787 ( 6392)
  SS BOND              : bond        0.00356 (    3)
  SS BOND              : angle       0.75577 (    6)
  hydrogen bonds       : bond        0.04161 (  178)
  hydrogen bonds       : angle       4.75811 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A   65 LYS cc_start: 0.8612 (mttt) cc_final: 0.8347 (mmtm)
REVERT: A   71 LYS cc_start: 0.8189 (tttt) cc_final: 0.7846 (ttpp)
REVERT: A   84 TYR cc_start: 0.8617 (t80) cc_final: 0.8280 (t80)
REVERT: A   95 MET cc_start: 0.8469 (tpp) cc_final: 0.8010 (tpp)
REVERT: A  169 GLN cc_start: 0.8035 (mt0) cc_final: 0.7738 (mt0)
REVERT: A  187 MET cc_start: 0.7828 (ptp) cc_final: 0.7466 (ptp)
REVERT: A  264 SER cc_start: 0.8614 (t) cc_final: 0.8322 (p)
REVERT: A  293 GLU cc_start: 0.7549 (tt0) cc_final: 0.7342 (tt0)
REVERT: A  310 ASP cc_start: 0.8044 (t70) cc_final: 0.7765 (t0)
REVERT: A  318 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8170 (mm)
REVERT: C    7 MET cc_start: 0.8371 (mmm) cc_final: 0.7825 (mmm)
REVERT: C   13 SER cc_start: 0.8049 (p) cc_final: 0.7834 (p)
REVERT: C   55 SER cc_start: 0.7996 (m) cc_final: 0.7745 (t)
REVERT: C   96 SER cc_start: 0.8473 (t) cc_final: 0.8057 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 113
  average time/residue: 0.0799
  time to fit residues: 11.1712
Evaluate side-chains
  116 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  105 GLN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue   63 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.111115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.099633 restraints weight = 6765.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.93
r_work: 0.3126 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4723  Z= 0.240
  Angle     :  0.518   6.704   6398  Z= 0.275
  Chirality :  0.044   0.133    687
  Planarity :  0.003   0.031    811
  Dihedral  :  4.305  36.526    637
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.20 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.14 (0.36), residues: 567
  helix:  1.22 (0.44), residues: 131
  sheet: -0.51 (0.44), residues: 141
  loop : -0.39 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.023   0.002   TYR A 121 
 PHE   0.018   0.002   PHE A 221 
 TRP   0.013   0.002   TRP B  50 
 HIS   0.003   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 ( 4720)
  covalent geometry    : angle       0.51767 ( 6392)
  SS BOND              : bond        0.00471 (    3)
  SS BOND              : angle       0.90723 (    6)
  hydrogen bonds       : bond        0.04552 (  178)
  hydrogen bonds       : angle       4.83953 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   65 LYS cc_start: 0.8620 (mttt) cc_final: 0.8371 (mmtm)
REVERT: A   71 LYS cc_start: 0.8217 (tttt) cc_final: 0.7901 (ttpp)
REVERT: A   81 LEU cc_start: 0.8498 (mt) cc_final: 0.8295 (mp)
REVERT: A   84 TYR cc_start: 0.8642 (t80) cc_final: 0.8200 (t80)
REVERT: A  187 MET cc_start: 0.7828 (ptp) cc_final: 0.7482 (ptp)
REVERT: A  264 SER cc_start: 0.8599 (t) cc_final: 0.8285 (p)
REVERT: A  310 ASP cc_start: 0.8069 (t70) cc_final: 0.7792 (t0)
REVERT: A  318 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8202 (mm)
REVERT: A  327 HIS cc_start: 0.7200 (m170) cc_final: 0.6911 (m90)
REVERT: C   13 SER cc_start: 0.8084 (p) cc_final: 0.7862 (p)
REVERT: C   55 SER cc_start: 0.7993 (m) cc_final: 0.7746 (t)
REVERT: C   96 SER cc_start: 0.8465 (t) cc_final: 0.8047 (p)
  outliers start: 16
  outliers final: 11
  residues processed: 127
  average time/residue: 0.0943
  time to fit residues: 14.2370
Evaluate side-chains
  127 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  105 GLN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue   63 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 49 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 169 GLN
A 210 HIS
A 329 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.113076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.101386 restraints weight = 6825.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.99
r_work: 0.3125 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4723  Z= 0.209
  Angle     :  0.502   6.229   6398  Z= 0.267
  Chirality :  0.044   0.186    687
  Planarity :  0.003   0.030    811
  Dihedral  :  4.242  36.098    637
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.00 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.09 (0.36), residues: 567
  helix:  1.20 (0.44), residues: 130
  sheet: -0.32 (0.46), residues: 128
  loop : -0.42 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.030   0.002   TYR A 121 
 PHE   0.015   0.002   PHE A 221 
 TRP   0.014   0.001   TRP B  50 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 4720)
  covalent geometry    : angle       0.50173 ( 6392)
  SS BOND              : bond        0.00387 (    3)
  SS BOND              : angle       0.76090 (    6)
  hydrogen bonds       : bond        0.04351 (  178)
  hydrogen bonds       : angle       4.78373 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   65 LYS cc_start: 0.8617 (mttt) cc_final: 0.8358 (mmtm)
REVERT: A   71 LYS cc_start: 0.8239 (tttt) cc_final: 0.7908 (ttpp)
REVERT: A   81 LEU cc_start: 0.8498 (mt) cc_final: 0.8291 (mp)
REVERT: A   84 TYR cc_start: 0.8645 (t80) cc_final: 0.8216 (t80)
REVERT: A  115 ILE cc_start: 0.8366 (mp) cc_final: 0.8141 (mp)
REVERT: A  172 MET cc_start: 0.8305 (mtt) cc_final: 0.8093 (mtt)
REVERT: A  187 MET cc_start: 0.7846 (ptp) cc_final: 0.7474 (ptp)
REVERT: A  264 SER cc_start: 0.8599 (t) cc_final: 0.8245 (p)
REVERT: A  293 GLU cc_start: 0.7678 (tt0) cc_final: 0.7457 (tt0)
REVERT: A  310 ASP cc_start: 0.8083 (t70) cc_final: 0.7807 (t0)
REVERT: A  318 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8218 (mm)
REVERT: A  327 HIS cc_start: 0.7196 (m170) cc_final: 0.6921 (m90)
REVERT: C   13 SER cc_start: 0.8077 (p) cc_final: 0.7856 (p)
REVERT: C   55 SER cc_start: 0.7990 (m) cc_final: 0.7743 (t)
REVERT: C   96 SER cc_start: 0.8485 (t) cc_final: 0.8075 (p)
  outliers start: 11
  outliers final: 10
  residues processed: 118
  average time/residue: 0.0905
  time to fit residues: 13.1456
Evaluate side-chains
  122 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  105 GLN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue   63 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 23 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 169 GLN
A 314 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.113043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.101491 restraints weight = 6727.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.96
r_work: 0.3116 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4723  Z= 0.219
  Angle     :  0.513   6.305   6398  Z= 0.272
  Chirality :  0.044   0.171    687
  Planarity :  0.003   0.030    811
  Dihedral  :  4.270  35.472    637
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.00 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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: -0.09 (0.36), residues: 567
  helix:  1.23 (0.45), residues: 130
  sheet: -0.31 (0.45), residues: 128
  loop : -0.45 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.026   0.002   TYR A 121 
 PHE   0.016   0.002   PHE A 221 
 TRP   0.014   0.001   TRP B  50 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 4720)
  covalent geometry    : angle       0.51237 ( 6392)
  SS BOND              : bond        0.00411 (    3)
  SS BOND              : angle       0.77040 (    6)
  hydrogen bonds       : bond        0.04402 (  178)
  hydrogen bonds       : angle       4.78070 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   65 LYS cc_start: 0.8642 (mttt) cc_final: 0.8376 (mmtm)
REVERT: A   71 LYS cc_start: 0.8234 (tttt) cc_final: 0.7919 (ttpp)
REVERT: A  115 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: A  187 MET cc_start: 0.7842 (ptp) cc_final: 0.7490 (ptp)
REVERT: A  264 SER cc_start: 0.8581 (t) cc_final: 0.8242 (p)
REVERT: A  293 GLU cc_start: 0.7658 (tt0) cc_final: 0.7441 (tt0)
REVERT: A  310 ASP cc_start: 0.8089 (t70) cc_final: 0.7816 (t0)
REVERT: A  318 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8219 (mm)
REVERT: A  327 HIS cc_start: 0.7172 (m170) cc_final: 0.6913 (m90)
REVERT: C   13 SER cc_start: 0.8086 (p) cc_final: 0.7856 (p)
REVERT: C   55 SER cc_start: 0.7994 (m) cc_final: 0.7747 (t)
REVERT: C   96 SER cc_start: 0.8494 (t) cc_final: 0.8089 (p)
  outliers start: 13
  outliers final: 11
  residues processed: 116
  average time/residue: 0.0917
  time to fit residues: 13.1101
Evaluate side-chains
  123 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  105 GLN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue   63 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 169 GLN
A 309 ASN
** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.111712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.100178 restraints weight = 6802.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.95
r_work: 0.3137 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4723  Z= 0.178
  Angle     :  0.503   6.452   6398  Z= 0.264
  Chirality :  0.043   0.139    687
  Planarity :  0.003   0.030    811
  Dihedral  :  4.166  35.271    637
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.60 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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:  0.01 (0.36), residues: 567
  helix:  1.29 (0.45), residues: 130
  sheet: -0.21 (0.46), residues: 128
  loop : -0.40 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.026   0.001   TYR A 121 
 PHE   0.013   0.002   PHE A 221 
 TRP   0.014   0.001   TRP B  50 
 HIS   0.002   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 4720)
  covalent geometry    : angle       0.50333 ( 6392)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       0.65238 (    6)
  hydrogen bonds       : bond        0.04158 (  178)
  hydrogen bonds       : angle       4.68012 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A   65 LYS cc_start: 0.8604 (mttt) cc_final: 0.8356 (mmtm)
REVERT: A   71 LYS cc_start: 0.8198 (tttt) cc_final: 0.7892 (ttpp)
REVERT: A   84 TYR cc_start: 0.8624 (t80) cc_final: 0.8238 (t80)
REVERT: A  115 ILE cc_start: 0.8531 (mp) cc_final: 0.8290 (mp)
REVERT: A  121 TYR cc_start: 0.8189 (t80) cc_final: 0.7776 (t80)
REVERT: A  169 GLN cc_start: 0.7968 (mt0) cc_final: 0.7516 (mt0)
REVERT: A  187 MET cc_start: 0.7859 (ptp) cc_final: 0.7520 (ptp)
REVERT: A  264 SER cc_start: 0.8573 (t) cc_final: 0.8255 (p)
REVERT: A  310 ASP cc_start: 0.8055 (t70) cc_final: 0.7788 (t0)
REVERT: A  318 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8228 (mm)
REVERT: A  327 HIS cc_start: 0.7146 (m170) cc_final: 0.6901 (m90)
REVERT: C   55 SER cc_start: 0.7991 (m) cc_final: 0.7742 (t)
REVERT: C   96 SER cc_start: 0.8475 (t) cc_final: 0.8063 (p)
  outliers start: 14
  outliers final: 11
  residues processed: 119
  average time/residue: 0.0867
  time to fit residues: 12.7771
Evaluate side-chains
  122 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  105 GLN
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   52 ASN
Chi-restraints excluded: chain C residue   63 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
A 309 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.114678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.103211 restraints weight = 6695.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.96
r_work: 0.3137 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4723  Z= 0.131
  Angle     :  0.475   6.366   6398  Z= 0.253
  Chirality :  0.042   0.145    687
  Planarity :  0.003   0.029    811
  Dihedral  :  3.999  34.517    637
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.00 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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:  0.16 (0.37), residues: 567
  helix:  1.50 (0.45), residues: 129
  sheet: -0.24 (0.44), residues: 140
  loop : -0.26 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.022   0.001   TYR A 121 
 PHE   0.009   0.001   PHE A 221 
 TRP   0.014   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4720)
  covalent geometry    : angle       0.47482 ( 6392)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       0.63002 (    6)
  hydrogen bonds       : bond        0.03829 (  178)
  hydrogen bonds       : angle       4.54507 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A   65 LYS cc_start: 0.8637 (mttt) cc_final: 0.8362 (mmtm)
REVERT: A   71 LYS cc_start: 0.8172 (tttt) cc_final: 0.7873 (ttpp)
REVERT: A   81 LEU cc_start: 0.8488 (mt) cc_final: 0.8284 (mp)
REVERT: A  115 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (mp)
REVERT: A  121 TYR cc_start: 0.8186 (t80) cc_final: 0.7708 (t80)
REVERT: A  169 GLN cc_start: 0.7971 (mt0) cc_final: 0.7444 (mt0)
REVERT: A  187 MET cc_start: 0.7833 (ptp) cc_final: 0.7480 (ptp)
REVERT: A  264 SER cc_start: 0.8610 (t) cc_final: 0.8319 (p)
REVERT: A  293 GLU cc_start: 0.7631 (tt0) cc_final: 0.7424 (tt0)
REVERT: A  310 ASP cc_start: 0.8074 (t70) cc_final: 0.7799 (t0)
REVERT: A  318 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8261 (mm)
REVERT: A  327 HIS cc_start: 0.7139 (m170) cc_final: 0.6917 (m90)
REVERT: B   70 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8057 (p)
REVERT: C    7 MET cc_start: 0.8351 (mmm) cc_final: 0.7774 (mmm)
REVERT: C   55 SER cc_start: 0.8007 (m) cc_final: 0.7757 (t)
REVERT: C   96 SER cc_start: 0.8478 (t) cc_final: 0.8070 (p)
  outliers start: 12
  outliers final: 8
  residues processed: 116
  average time/residue: 0.0888
  time to fit residues: 12.7321
Evaluate side-chains
  116 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain C residue   14 VAL
Chi-restraints excluded: chain C residue   63 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 24 optimal weight:    0.0870
   chunk 54 optimal weight:    0.9990
   chunk 55 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 45 optimal weight:    0.1980
   chunk 50 optimal weight:    0.0980
   chunk 17 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9990
   chunk 18 optimal weight:    0.1980
   overall best weight:    0.1958

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

Flipped N/Q/H residues before XYZ refinement:
A 309 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.116383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.104842 restraints weight = 6702.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.97
r_work: 0.3179 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4723  Z= 0.095
  Angle     :  0.448   6.964   6398  Z= 0.240
  Chirality :  0.042   0.134    687
  Planarity :  0.003   0.026    811
  Dihedral  :  3.787  32.894    637
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.60 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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:  0.36 (0.37), residues: 567
  helix:  1.64 (0.45), residues: 126
  sheet: -0.12 (0.45), residues: 140
  loop : -0.10 (0.40), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.020   0.001   TYR A 121 
 PHE   0.010   0.001   PHE A 180 
 TRP   0.014   0.001   TRP B  50 
 HIS   0.002   0.000   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 4720)
  covalent geometry    : angle       0.44805 ( 6392)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       0.45273 (    6)
  hydrogen bonds       : bond        0.03462 (  178)
  hydrogen bonds       : angle       4.38412 (  456)

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   65 LYS cc_start: 0.8601 (mttt) cc_final: 0.8347 (mmtm)
REVERT: A   71 LYS cc_start: 0.8143 (tttt) cc_final: 0.7854 (ttpp)
REVERT: A   81 LEU cc_start: 0.8488 (mt) cc_final: 0.8275 (mp)
REVERT: A   84 TYR cc_start: 0.8592 (t80) cc_final: 0.8267 (t80)
REVERT: A   95 MET cc_start: 0.8499 (tpp) cc_final: 0.7945 (tpp)
REVERT: A  115 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8197 (mp)
REVERT: A  121 TYR cc_start: 0.8160 (t80) cc_final: 0.7804 (t80)
REVERT: A  187 MET cc_start: 0.7810 (ptp) cc_final: 0.7518 (ptp)
REVERT: A  264 SER cc_start: 0.8615 (t) cc_final: 0.8330 (p)
REVERT: A  293 GLU cc_start: 0.7586 (tt0) cc_final: 0.7371 (tt0)
REVERT: A  310 ASP cc_start: 0.8050 (t70) cc_final: 0.7780 (t0)
REVERT: B   70 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8064 (p)
REVERT: C    7 MET cc_start: 0.8306 (mmm) cc_final: 0.7742 (mmm)
REVERT: C   55 SER cc_start: 0.7989 (m) cc_final: 0.7738 (t)
REVERT: C   96 SER cc_start: 0.8473 (t) cc_final: 0.8082 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 116
  average time/residue: 0.0674
  time to fit residues: 9.9581
Evaluate side-chains
  118 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  114 MET
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain C residue   14 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 51 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0770
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 169 GLN
A 309 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.113538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.102425 restraints weight = 6753.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.84
r_work: 0.3136 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4723  Z= 0.165
  Angle     :  0.496   6.631   6398  Z= 0.265
  Chirality :  0.044   0.260    687
  Planarity :  0.003   0.026    811
  Dihedral  :  3.916  30.939    637
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.60 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    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:  0.36 (0.37), residues: 567
  helix:  1.53 (0.45), residues: 129
  sheet:  0.04 (0.46), residues: 128
  loop : -0.16 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.024   0.001   TYR A 121 
 PHE   0.016   0.002   PHE A 180 
 TRP   0.011   0.001   TRP B  50 
 HIS   0.012   0.001   HIS A 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4720)
  covalent geometry    : angle       0.49574 ( 6392)
  SS BOND              : bond        0.00325 (    3)
  SS BOND              : angle       0.69390 (    6)
  hydrogen bonds       : bond        0.03975 (  178)
  hydrogen bonds       : angle       4.49900 (  456)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1311.84 seconds
wall clock time: 23 minutes 12.63 seconds (1392.63 seconds total)