Starting phenix.real_space_refine
on Tue Jan 13 11:54:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i8a_35245/01_2026/8i8a_35245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i8a_35245/01_2026/8i8a_35245.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i8a_35245/01_2026/8i8a_35245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i8a_35245/01_2026/8i8a_35245.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i8a_35245/01_2026/8i8a_35245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i8a_35245/01_2026/8i8a_35245.cif"
  }
  resolution = 3.21
  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=   0.034
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      28      5.16       5
     C    3130      2.51       5
     N     880      2.21       5
     O     940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4978
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2489
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 13, 'TRANS': 293}
    Chain: "B"
      Number of atoms: 2489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2489
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 13, 'TRANS': 293}
  Time building chain proxies: 1.33, per 1000 atoms: 0.27
  Number of scatterers: 4978
  At special positions: 0
  Unit cell: (128.25, 59.4, 78.3, 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      28     16.00
     O     940      8.00
     N     880      7.00
     C    3130      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 229 " - pdb=" SG  CYS B 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  36 " - pdb=" SG  CYS B  49 " 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: 0.36
  Conformation dependent library (CDL) restraints added in 337.1 milliseconds
  

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1176

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 6 sheets defined
      33.7% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 23
      removed outlier: 3.627A  pdb=" N   SER A  22 " --> pdb=" O   ILE A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 49 through 57
    Processing helix  chain 'A' and resid 88 through 91
      removed outlier: 3.980A  pdb=" N   LYS A  91 " --> pdb=" O   ARG A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 88 through 91'
    Processing helix  chain 'A' and resid 111 through 122
    Processing helix  chain 'A' and resid 124 through 137
      removed outlier: 4.123A  pdb=" N   TYR A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 164
      removed outlier: 3.920A  pdb=" N   ASN A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   GLN A 146 " --> pdb=" O   THR A 142 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   ARG A 147 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   THR A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 198
      removed outlier: 3.815A  pdb=" N   GLN A 195 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 212
    Processing helix  chain 'A' and resid 278 through 285
    Processing helix  chain 'B' and resid 18 through 23
    Processing helix  chain 'B' and resid 37 through 42
    Processing helix  chain 'B' and resid 49 through 57
    Processing helix  chain 'B' and resid 88 through 91
      removed outlier: 3.892A  pdb=" N   LYS B  91 " --> pdb=" O   ARG B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 88 through 91'
    Processing helix  chain 'B' and resid 111 through 122
    Processing helix  chain 'B' and resid 124 through 137
      removed outlier: 4.200A  pdb=" N   TYR B 137 " --> pdb=" O   ASP B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 164
      removed outlier: 3.852A  pdb=" N   ASN B 144 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   GLN B 146 " --> pdb=" O   THR B 142 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   ARG B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   THR B 162 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 198
      removed outlier: 3.786A  pdb=" N   GLN B 195 " --> pdb=" O   GLY B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 212
      removed outlier: 3.553A  pdb=" N   VAL B 212 " --> pdb=" O   ILE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 284
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 66
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 95
      removed outlier: 6.445A  pdb=" N   LEU A 239 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 179
      removed outlier: 6.864A  pdb=" N   TYR A 216 " --> pdb=" O   GLN A 302 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   ILE A 304 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLN A 218 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 66
    Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 95
      removed outlier: 6.388A  pdb=" N   LEU B 239 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 176 through 179
      removed outlier: 6.717A  pdb=" N   TYR B 216 " --> pdb=" O   GLN B 302 " (cutoff:3.500A)
      removed outlier: 8.364A  pdb=" N   ILE B 304 " --> pdb=" O   TYR B 216 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   GLN B 218 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)

    153 hydrogen bonds defined for protein.
    393 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: 0.71

  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:
        1.22 -     1.34: 1693
        1.34 -     1.46: 1008
        1.46 -     1.58: 2339
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 5080
  Sorted by residual:
  bond pdb=" CA  ASN B 106 "
       pdb=" CB  ASN B 106 "
    ideal  model  delta    sigma   weight residual
    1.530  1.546 -0.016 1.69e-02 3.50e+03 8.59e-01
  bond pdb=" CG  MET A 259 "
       pdb=" SD  MET A 259 "
    ideal  model  delta    sigma   weight residual
    1.803  1.782  0.021 2.50e-02 1.60e+03 7.32e-01
  bond pdb=" CA  ASN A 106 "
       pdb=" CB  ASN A 106 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 6.80e-01
  bond pdb=" CG1 ILE B  78 "
       pdb=" CD1 ILE B  78 "
    ideal  model  delta    sigma   weight residual
    1.513  1.482  0.031 3.90e-02 6.57e+02 6.33e-01
  bond pdb=" CG1 ILE B  23 "
       pdb=" CD1 ILE B  23 "
    ideal  model  delta    sigma   weight residual
    1.513  1.483  0.030 3.90e-02 6.57e+02 5.96e-01
  ... (remaining 5075 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 6674
        1.55 -     3.10: 177
        3.10 -     4.66: 24
        4.66 -     6.21: 4
        6.21 -     7.76: 3
  Bond angle restraints: 6882
  Sorted by residual:
  angle pdb=" C   SER B 261 "
        pdb=" N   GLN B 262 "
        pdb=" CA  GLN B 262 "
      ideal   model   delta    sigma   weight residual
     121.80  129.56   -7.76 2.44e+00 1.68e-01 1.01e+01
  angle pdb=" N   GLN B 262 "
        pdb=" CA  GLN B 262 "
        pdb=" C   GLN B 262 "
      ideal   model   delta    sigma   weight residual
     109.81  116.16   -6.35 2.21e+00 2.05e-01 8.24e+00
  angle pdb=" N   GLN A 262 "
        pdb=" CA  GLN A 262 "
        pdb=" C   GLN A 262 "
      ideal   model   delta    sigma   weight residual
     109.81  116.00   -6.19 2.21e+00 2.05e-01 7.85e+00
  angle pdb=" C   PRO A 263 "
        pdb=" N   ASN A 264 "
        pdb=" CA  ASN A 264 "
      ideal   model   delta    sigma   weight residual
     121.87  127.95   -6.08 2.24e+00 1.99e-01 7.37e+00
  angle pdb=" C   SER A 261 "
        pdb=" N   GLN A 262 "
        pdb=" CA  GLN A 262 "
      ideal   model   delta    sigma   weight residual
     121.80  128.11   -6.31 2.44e+00 1.68e-01 6.68e+00
  ... (remaining 6877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 2787
       17.94 -    35.88: 269
       35.88 -    53.82: 23
       53.82 -    71.76: 0
       71.76 -    89.70: 10
  Dihedral angle restraints: 3089
    sinusoidal: 1275
      harmonic: 1814
  Sorted by residual:
  dihedral pdb=" CB  CYS B  36 "
           pdb=" SG  CYS B  36 "
           pdb=" SG  CYS B  49 "
           pdb=" CB  CYS B  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -42.90  -43.10     1      1.00e+01 1.00e-02 2.59e+01
  dihedral pdb=" CA  PHE A  26 "
           pdb=" C   PHE A  26 "
           pdb=" N   ASP A  27 "
           pdb=" CA  ASP A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.40   18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  HIS A  81 "
           pdb=" C   HIS A  81 "
           pdb=" N   LEU A  82 "
           pdb=" CA  LEU A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.52   18.48     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 3086 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 387
       0.027 -    0.054: 214
       0.054 -    0.081: 86
       0.081 -    0.109: 45
       0.109 -    0.136: 24
  Chirality restraints: 756
  Sorted by residual:
  chirality pdb=" CG  LEU A 297 "
            pdb=" CB  LEU A 297 "
            pdb=" CD1 LEU A 297 "
            pdb=" CD2 LEU A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CB  ILE B  23 "
            pdb=" CA  ILE B  23 "
            pdb=" CG1 ILE B  23 "
            pdb=" CG2 ILE B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CA  ILE A 303 "
            pdb=" N   ILE A 303 "
            pdb=" C   ILE A 303 "
            pdb=" CB  ILE A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  ... (remaining 753 not shown)

  Planarity restraints: 914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 316 "   -0.024 5.00e-02 4.00e+02   3.69e-02 2.17e+00
        pdb=" N   PRO B 317 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 317 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 317 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 316 "    0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO A 317 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 262 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 263 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 263 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 263 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 911 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 379
        2.74 -     3.28: 5321
        3.28 -     3.82: 7776
        3.82 -     4.36: 9150
        4.36 -     4.90: 15702
  Nonbonded interactions: 38328
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  37 "
            pdb=" OD1 ASP A  39 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLN A  73 "
            pdb=" OG1 THR B 278 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OH  TYR A 250 "
            pdb=" O   PHE B  67 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   PRO A  96 "
            pdb=" OH  TYR A 122 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   PHE A  67 "
            pdb=" OH  TYR B 250 "
     model   vdw
     2.273 3.040
  ... (remaining 38323 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             19.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.780
  Find NCS groups from input model:        0.070
  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:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5083  Z= 0.127
  Angle     :  0.606   7.759   6888  Z= 0.323
  Chirality :  0.045   0.136    756
  Planarity :  0.004   0.037    914
  Dihedral  : 13.677  89.699   1904
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.30 %
    Favored  : 87.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.34), residues: 610
  helix:  0.29 (0.41), residues: 170
  sheet: -2.87 (0.83), residues: 40
  loop : -2.28 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 254 
 TYR   0.015   0.001   TYR B 216 
 PHE   0.017   0.002   PHE B  26 
 TRP   0.009   0.002   TRP A  46 
 HIS   0.002   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5080)
  covalent geometry    : angle       0.60470 ( 6882)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       1.33630 (    6)
  hydrogen bonds       : bond        0.22104 (  153)
  hydrogen bonds       : angle       8.07306 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.8283 (tp) cc_final: 0.8027 (tp)
REVERT: B  311 LEU cc_start: 0.7358 (mm) cc_final: 0.7158 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1099
  time to fit residues: 16.4679
Evaluate side-chains
  66 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.0040
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0050
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.3980
   overall best weight:    0.3606

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 ASN
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.102027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.084628 restraints weight = 13019.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 3.78
r_work: 0.3374 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5083  Z= 0.150
  Angle     :  0.657   6.490   6888  Z= 0.352
  Chirality :  0.046   0.144    756
  Planarity :  0.004   0.030    914
  Dihedral  :  4.658  17.458    686
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.49 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.34), residues: 610
  helix:  0.41 (0.41), residues: 174
  sheet: -2.87 (0.74), residues: 44
  loop : -2.16 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 147 
 TYR   0.016   0.002   TYR A 294 
 PHE   0.018   0.002   PHE B  74 
 TRP   0.010   0.002   TRP A  46 
 HIS   0.004   0.001   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5080)
  covalent geometry    : angle       0.65627 ( 6882)
  SS BOND              : bond        0.00580 (    3)
  SS BOND              : angle       0.97764 (    6)
  hydrogen bonds       : bond        0.04207 (  153)
  hydrogen bonds       : angle       6.03586 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7839 (mmm) cc_final: 0.7480 (mpp)
REVERT: A   70 ASP cc_start: 0.7314 (t0) cc_final: 0.6842 (t0)
REVERT: A  147 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7616 (ttp80)
REVERT: A  315 PHE cc_start: 0.6509 (m-80) cc_final: 0.6308 (m-80)
REVERT: B  267 GLN cc_start: 0.7793 (tp40) cc_final: 0.7506 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1261
  time to fit residues: 11.6816
Evaluate side-chains
  66 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0070
   chunk 38 optimal weight:    0.4980
   chunk 9 optimal weight:    0.0970
   chunk 31 optimal weight:    0.0570
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.1514

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.103734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.086430 restraints weight = 13135.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 3.79
r_work: 0.3399 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5083  Z= 0.116
  Angle     :  0.604   7.284   6888  Z= 0.314
  Chirality :  0.044   0.137    756
  Planarity :  0.003   0.028    914
  Dihedral  :  4.335  19.056    686
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 12.59 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.34), residues: 610
  helix:  0.55 (0.42), residues: 174
  sheet: -2.94 (0.70), residues: 44
  loop : -2.05 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 147 
 TYR   0.013   0.001   TYR A 301 
 PHE   0.021   0.001   PHE B  67 
 TRP   0.007   0.001   TRP A  46 
 HIS   0.004   0.001   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5080)
  covalent geometry    : angle       0.60306 ( 6882)
  SS BOND              : bond        0.00974 (    3)
  SS BOND              : angle       1.05941 (    6)
  hydrogen bonds       : bond        0.03483 (  153)
  hydrogen bonds       : angle       5.64414 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7879 (mmm) cc_final: 0.7576 (mpp)
REVERT: A   70 ASP cc_start: 0.7360 (t0) cc_final: 0.6835 (t0)
REVERT: A   91 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7777 (pttm)
REVERT: B   42 HIS cc_start: 0.8267 (m170) cc_final: 0.7973 (m170)
REVERT: B   55 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8246 (ttmt)
REVERT: B   70 ASP cc_start: 0.7144 (t0) cc_final: 0.6552 (t0)
  outliers start: 4
  outliers final: 1
  residues processed: 81
  average time/residue: 0.1157
  time to fit residues: 11.3589
Evaluate side-chains
  67 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   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  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.100103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.082103 restraints weight = 12839.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.79
r_work: 0.3259 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5083  Z= 0.196
  Angle     :  0.667   9.249   6888  Z= 0.344
  Chirality :  0.047   0.163    756
  Planarity :  0.004   0.034    914
  Dihedral  :  4.668  19.668    686
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.80 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.85 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.34), residues: 610
  helix:  0.61 (0.42), residues: 174
  sheet: -3.21 (0.71), residues: 44
  loop : -2.03 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 283 
 TYR   0.016   0.002   TYR A 216 
 PHE   0.016   0.002   PHE A  26 
 TRP   0.014   0.003   TRP A  46 
 HIS   0.007   0.002   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 5080)
  covalent geometry    : angle       0.66595 ( 6882)
  SS BOND              : bond        0.00455 (    3)
  SS BOND              : angle       1.14734 (    6)
  hydrogen bonds       : bond        0.03825 (  153)
  hydrogen bonds       : angle       5.80491 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7952 (mmm) cc_final: 0.7547 (mpp)
REVERT: A   70 ASP cc_start: 0.7505 (t0) cc_final: 0.6952 (t0)
REVERT: A   82 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8320 (mm)
REVERT: A  273 LYS cc_start: 0.1911 (mptt) cc_final: 0.0609 (pttm)
REVERT: B   82 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8358 (mt)
REVERT: B  137 TYR cc_start: 0.7486 (m-80) cc_final: 0.7024 (m-10)
  outliers start: 12
  outliers final: 4
  residues processed: 77
  average time/residue: 0.1096
  time to fit residues: 10.2460
Evaluate side-chains
  69 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue   82 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0470
   chunk 59 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0370
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
B 106 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.101428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.083436 restraints weight = 13080.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 3.84
r_work: 0.3279 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5083  Z= 0.131
  Angle     :  0.616   8.095   6888  Z= 0.319
  Chirality :  0.046   0.163    756
  Planarity :  0.003   0.029    914
  Dihedral  :  4.467  17.403    686
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.51 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.37 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.34), residues: 610
  helix:  0.57 (0.42), residues: 174
  sheet: -3.26 (0.70), residues: 44
  loop : -2.00 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 283 
 TYR   0.013   0.001   TYR A 301 
 PHE   0.019   0.002   PHE A  47 
 TRP   0.006   0.001   TRP A  46 
 HIS   0.003   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 5080)
  covalent geometry    : angle       0.61553 ( 6882)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       0.94295 (    6)
  hydrogen bonds       : bond        0.03389 (  153)
  hydrogen bonds       : angle       5.55035 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   59 MET cc_start: 0.7817 (mmm) cc_final: 0.7484 (mpp)
REVERT: A   91 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7633 (pttm)
REVERT: A  273 LYS cc_start: 0.2193 (mptt) cc_final: 0.0671 (pttm)
REVERT: B   55 LYS cc_start: 0.8573 (tmtt) cc_final: 0.8270 (mtpt)
REVERT: B   70 ASP cc_start: 0.6577 (m-30) cc_final: 0.6356 (m-30)
REVERT: B  137 TYR cc_start: 0.7310 (m-80) cc_final: 0.6781 (m-10)
  outliers start: 8
  outliers final: 1
  residues processed: 75
  average time/residue: 0.1111
  time to fit residues: 10.1363
Evaluate side-chains
  65 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0870
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0070
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.2776

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 184 ASN
B 106 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.101520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.083902 restraints weight = 13114.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 3.83
r_work: 0.3295 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5083  Z= 0.119
  Angle     :  0.604   7.513   6888  Z= 0.313
  Chirality :  0.045   0.150    756
  Planarity :  0.003   0.031    914
  Dihedral  :  4.323  16.762    686
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.98 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.73 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.34), residues: 610
  helix:  0.99 (0.43), residues: 160
  sheet: -3.17 (0.70), residues: 44
  loop : -2.05 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 147 
 TYR   0.010   0.001   TYR A 137 
 PHE   0.016   0.001   PHE B  74 
 TRP   0.005   0.001   TRP B  46 
 HIS   0.016   0.002   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5080)
  covalent geometry    : angle       0.60335 ( 6882)
  SS BOND              : bond        0.00412 (    3)
  SS BOND              : angle       0.89456 (    6)
  hydrogen bonds       : bond        0.03219 (  153)
  hydrogen bonds       : angle       5.39841 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7730 (mmm) cc_final: 0.7447 (mpp)
REVERT: A   91 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7671 (pttm)
REVERT: A  273 LYS cc_start: 0.2283 (mptt) cc_final: 0.0698 (pttm)
REVERT: A  315 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6235 (t80)
REVERT: B   42 HIS cc_start: 0.8322 (m170) cc_final: 0.8019 (m170)
REVERT: B   55 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8276 (mtpt)
REVERT: B   82 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8150 (mt)
REVERT: B  137 TYR cc_start: 0.7287 (m-80) cc_final: 0.6737 (m-10)
  outliers start: 9
  outliers final: 3
  residues processed: 72
  average time/residue: 0.1198
  time to fit residues: 10.3667
Evaluate side-chains
  67 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  106 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0020
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 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 = 0.3756 r_free = 0.3756 target = 0.100992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.083022 restraints weight = 12921.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 3.88
r_work: 0.3281 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.4214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5083  Z= 0.136
  Angle     :  0.623   7.869   6888  Z= 0.321
  Chirality :  0.046   0.151    756
  Planarity :  0.004   0.028    914
  Dihedral  :  4.368  16.471    686
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.15 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 18.88 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.34), residues: 610
  helix:  1.02 (0.43), residues: 160
  sheet: -3.18 (0.72), residues: 44
  loop : -2.10 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 147 
 TYR   0.010   0.001   TYR B 216 
 PHE   0.017   0.001   PHE B  74 
 TRP   0.007   0.002   TRP B  46 
 HIS   0.013   0.002   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5080)
  covalent geometry    : angle       0.62250 ( 6882)
  SS BOND              : bond        0.00505 (    3)
  SS BOND              : angle       0.94731 (    6)
  hydrogen bonds       : bond        0.03297 (  153)
  hydrogen bonds       : angle       5.39796 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7764 (mmm) cc_final: 0.7439 (mpp)
REVERT: A   91 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7665 (pttm)
REVERT: A  147 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7574 (ttp80)
REVERT: A  273 LYS cc_start: 0.3122 (mptt) cc_final: 0.1668 (pttm)
REVERT: A  315 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6002 (t80)
REVERT: B   82 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8358 (mt)
REVERT: B  137 TYR cc_start: 0.7322 (m-80) cc_final: 0.6758 (m-10)
REVERT: B  157 LYS cc_start: 0.8551 (tppt) cc_final: 0.8231 (tppt)
  outliers start: 6
  outliers final: 2
  residues processed: 69
  average time/residue: 0.1169
  time to fit residues: 9.7125
Evaluate side-chains
  67 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain B residue   82 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    0.0070
   chunk 37 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 31 optimal weight:    0.2980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 ASN
B 106 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.100929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.083180 restraints weight = 12925.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 3.84
r_work: 0.3276 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5083  Z= 0.142
  Angle     :  0.638   8.350   6888  Z= 0.329
  Chirality :  0.046   0.149    756
  Planarity :  0.004   0.028    914
  Dihedral  :  4.420  19.466    686
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.60 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.34), residues: 610
  helix:  0.93 (0.42), residues: 160
  sheet: -3.28 (0.70), residues: 44
  loop : -2.11 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 279 
 TYR   0.010   0.002   TYR B 216 
 PHE   0.018   0.001   PHE B  74 
 TRP   0.007   0.002   TRP B  46 
 HIS   0.013   0.002   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5080)
  covalent geometry    : angle       0.63729 ( 6882)
  SS BOND              : bond        0.00473 (    3)
  SS BOND              : angle       0.92954 (    6)
  hydrogen bonds       : bond        0.03329 (  153)
  hydrogen bonds       : angle       5.39260 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7741 (mmm) cc_final: 0.7452 (mpp)
REVERT: A   91 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7647 (pttm)
REVERT: A  273 LYS cc_start: 0.3258 (mptt) cc_final: 0.1714 (pttm)
REVERT: A  315 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6469 (t80)
REVERT: B   82 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8429 (mt)
REVERT: B  137 TYR cc_start: 0.7337 (m-80) cc_final: 0.6766 (m-10)
  outliers start: 9
  outliers final: 3
  residues processed: 71
  average time/residue: 0.1167
  time to fit residues: 9.9594
Evaluate side-chains
  68 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain B residue   82 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.1980
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0570
   chunk 40 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0670
   chunk 14 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.3236

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  73 GLN
B 106 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.101555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.083997 restraints weight = 12783.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 3.82
r_work: 0.3295 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5083  Z= 0.126
  Angle     :  0.634   8.363   6888  Z= 0.325
  Chirality :  0.045   0.148    756
  Planarity :  0.003   0.027    914
  Dihedral  :  4.316  19.871    686
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 20.50 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.34), residues: 610
  helix:  0.99 (0.43), residues: 160
  sheet: -3.23 (0.72), residues: 44
  loop : -2.10 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 147 
 TYR   0.010   0.001   TYR B 294 
 PHE   0.019   0.001   PHE B  74 
 TRP   0.004   0.001   TRP B  46 
 HIS   0.011   0.002   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5080)
  covalent geometry    : angle       0.63369 ( 6882)
  SS BOND              : bond        0.00445 (    3)
  SS BOND              : angle       0.89121 (    6)
  hydrogen bonds       : bond        0.03157 (  153)
  hydrogen bonds       : angle       5.28361 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7656 (mmm) cc_final: 0.7402 (mpp)
REVERT: A   91 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7638 (pttm)
REVERT: A  273 LYS cc_start: 0.3276 (mptt) cc_final: 0.1671 (pttm)
REVERT: A  315 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6280 (t80)
REVERT: B   55 LYS cc_start: 0.8528 (tmtt) cc_final: 0.8212 (mtpt)
REVERT: B   82 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8348 (mt)
REVERT: B  137 TYR cc_start: 0.7307 (m-80) cc_final: 0.6731 (m-10)
REVERT: B  157 LYS cc_start: 0.8531 (tppt) cc_final: 0.8267 (tppt)
  outliers start: 9
  outliers final: 6
  residues processed: 69
  average time/residue: 0.1266
  time to fit residues: 10.4024
Evaluate side-chains
  70 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  106 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0050
   chunk 9 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0670
   chunk 34 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.3332

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

Flipped N/Q/H residues before XYZ refinement:
A  42 HIS
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  73 GLN
B 106 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.101513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.083803 restraints weight = 12870.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 3.88
r_work: 0.3288 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.4548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5083  Z= 0.130
  Angle     :  0.648   8.743   6888  Z= 0.332
  Chirality :  0.045   0.145    756
  Planarity :  0.004   0.028    914
  Dihedral  :  4.328  19.606    686
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.49 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 20.68 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.34), residues: 610
  helix:  0.99 (0.43), residues: 160
  sheet: -3.23 (0.71), residues: 44
  loop : -2.06 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 147 
 TYR   0.010   0.001   TYR B 216 
 PHE   0.021   0.001   PHE B  74 
 TRP   0.005   0.001   TRP B  46 
 HIS   0.011   0.002   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5080)
  covalent geometry    : angle       0.64828 ( 6882)
  SS BOND              : bond        0.00433 (    3)
  SS BOND              : angle       0.83032 (    6)
  hydrogen bonds       : bond        0.03114 (  153)
  hydrogen bonds       : angle       5.23709 (  393)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.7646 (mmm) cc_final: 0.7389 (mpp)
REVERT: A   91 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7634 (pttm)
REVERT: A  273 LYS cc_start: 0.2840 (mptt) cc_final: 0.1593 (pttm)
REVERT: A  315 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6376 (t80)
REVERT: B   55 LYS cc_start: 0.8545 (tmtt) cc_final: 0.8252 (mtmt)
REVERT: B   82 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8370 (mt)
REVERT: B  137 TYR cc_start: 0.7285 (m-80) cc_final: 0.6697 (m-10)
REVERT: B  157 LYS cc_start: 0.8549 (tppt) cc_final: 0.8254 (tppt)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.1289
  time to fit residues: 10.5829
Evaluate side-chains
  71 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  269 ARG
Chi-restraints excluded: chain A residue  315 PHE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  106 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.0470
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 57 optimal weight:    0.1980
   chunk 8 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  73 GLN
B 106 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.100713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.082987 restraints weight = 12845.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 3.84
r_work: 0.3274 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5083  Z= 0.144
  Angle     :  0.669   9.304   6888  Z= 0.342
  Chirality :  0.046   0.177    756
  Planarity :  0.004   0.028    914
  Dihedral  :  4.404  19.391    686
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.22 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.34), residues: 610
  helix:  0.96 (0.43), residues: 160
  sheet: -3.24 (0.71), residues: 44
  loop : -2.05 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 147 
 TYR   0.011   0.002   TYR B 294 
 PHE   0.020   0.002   PHE B  74 
 TRP   0.006   0.002   TRP B  46 
 HIS   0.004   0.001   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5080)
  covalent geometry    : angle       0.66894 ( 6882)
  SS BOND              : bond        0.00427 (    3)
  SS BOND              : angle       0.74043 (    6)
  hydrogen bonds       : bond        0.03247 (  153)
  hydrogen bonds       : angle       5.32748 (  393)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1623.96 seconds
wall clock time: 28 minutes 45.71 seconds (1725.71 seconds total)