Starting phenix.real_space_refine
on Sat Apr  4 21:17:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vj4_65103/04_2026/9vj4_65103.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vj4_65103/04_2026/9vj4_65103.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vj4_65103/04_2026/9vj4_65103.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vj4_65103/04_2026/9vj4_65103.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vj4_65103/04_2026/9vj4_65103.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vj4_65103/04_2026/9vj4_65103.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.064
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      21      5.16       5
     C    2565      2.51       5
     N     539      2.21       5
     O     609      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3735
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2259
          Classifications: {'peptide': 280}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 259}
    Chain: "B"
      Number of atoms: 1372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1372
          Classifications: {'peptide': 165}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 159}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 90
          Unusual residues: {'46E': 1, 'C14': 1, 'UJO': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'C14': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.13, per 1000 atoms: 0.30
  Number of scatterers: 3735
  At special positions: 0
  Unit cell: (75.932, 60.19, 87.044, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P       1     15.00
     O     609      8.00
     N     539      7.00
     C    2565      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.39
  Conformation dependent library (CDL) restraints added in 155.4 milliseconds
  

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  844

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      76.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 62
    Processing helix  chain 'A' and resid 65 through 82
      removed outlier: 3.648A  pdb=" N   LYS A  69 " --> pdb=" O   PRO A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 92
    Processing helix  chain 'A' and resid 92 through 107
      removed outlier: 3.576A  pdb=" N   SER A 106 " --> pdb=" O   TYR A 102 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   TYR A 107 " --> pdb=" O   PHE A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 129
    Processing helix  chain 'A' and resid 142 through 156
      Proline residue:  A 152  - end of helix
    Processing helix  chain 'A' and resid 160 through 171
    Processing helix  chain 'A' and resid 175 through 198
      removed outlier: 4.229A  pdb=" N   GLY A 179 " --> pdb=" O   THR A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 209
      removed outlier: 4.129A  pdb=" N   LYS A 206 " --> pdb=" O   PRO A 202 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE A 207 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 208 " --> pdb=" O   TRP A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 230
      removed outlier: 4.130A  pdb=" N   ILE A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 243
      removed outlier: 4.116A  pdb=" N   THR A 239 " --> pdb=" O   ASN A 235 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 268
    Processing helix  chain 'A' and resid 274 through 291
    Processing helix  chain 'A' and resid 295 through 303
      removed outlier: 3.901A  pdb=" N   LEU A 299 " --> pdb=" O   TYR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 315
    Processing helix  chain 'B' and resid 17 through 42
      removed outlier: 3.555A  pdb=" N   LYS B  33 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   GLY B  36 " --> pdb=" O   ASN B  32 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ALA B  37 " --> pdb=" O   LYS B  33 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR B  38 " --> pdb=" O   CYS B  34 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY B  39 " --> pdb=" O   SER B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 73
      removed outlier: 4.238A  pdb=" N   LEU B  73 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 110
      removed outlier: 3.869A  pdb=" N   SER B  83 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   GLN B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LEU B 101 " --> pdb=" O   CYS B  97 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR B 104 " --> pdb=" O   THR B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 181
      removed outlier: 3.608A  pdb=" N   LEU B 161 " --> pdb=" O   THR B 157 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE B 163 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG B 164 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 221
      removed outlier: 3.714A  pdb=" N   GLU B 221 " --> pdb=" O   LYS B 217 " (cutoff:3.500A)

    233 hydrogen bonds defined for protein.
    699 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: 0.53

  Time building geometry restraints manager: 0.50 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: 513
        1.31 -     1.43: 1212
        1.43 -     1.56: 2107
        1.56 -     1.68: 2
        1.68 -     1.81: 32
  Bond restraints: 3866
  Sorted by residual:
  bond pdb=" C31 46E A 503 "
       pdb=" O31 46E A 503 "
    ideal  model  delta    sigma   weight residual
    1.327  1.449 -0.122 2.00e-02 2.50e+03 3.71e+01
  bond pdb=" C21 46E A 503 "
       pdb=" O21 46E A 503 "
    ideal  model  delta    sigma   weight residual
    1.331  1.451 -0.120 2.00e-02 2.50e+03 3.63e+01
  bond pdb=" C12 UJO A 501 "
       pdb=" O13 UJO A 501 "
    ideal  model  delta    sigma   weight residual
    1.231  1.182  0.049 2.00e-02 2.50e+03 6.07e+00
  bond pdb=" C15 UJO A 501 "
       pdb=" C18 UJO A 501 "
    ideal  model  delta    sigma   weight residual
    1.549  1.504  0.045 2.00e-02 2.50e+03 4.96e+00
  bond pdb=" C24 UJO A 501 "
       pdb=" C25 UJO A 501 "
    ideal  model  delta    sigma   weight residual
    1.525  1.487  0.038 2.00e-02 2.50e+03 3.69e+00
  ... (remaining 3861 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 5138
        2.98 -     5.96: 93
        5.96 -     8.95: 13
        8.95 -    11.93: 5
       11.93 -    14.91: 3
  Bond angle restraints: 5252
  Sorted by residual:
  angle pdb=" C20 UJO A 501 "
        pdb=" C21 UJO A 501 "
        pdb=" C22 UJO A 501 "
      ideal   model   delta    sigma   weight residual
     112.69   97.78   14.91 3.00e+00 1.11e-01 2.47e+01
  angle pdb=" C18 UJO A 501 "
        pdb=" C19 UJO A 501 "
        pdb=" C20 UJO A 501 "
      ideal   model   delta    sigma   weight residual
     129.28  114.38   14.90 3.00e+00 1.11e-01 2.47e+01
  angle pdb=" C19 UJO A 501 "
        pdb=" C20 UJO A 501 "
        pdb=" C21 UJO A 501 "
      ideal   model   delta    sigma   weight residual
     130.75  118.59   12.16 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" N   ILE A 136 "
        pdb=" CA  ILE A 136 "
        pdb=" C   ILE A 136 "
      ideal   model   delta    sigma   weight residual
     112.50  107.04    5.46 1.39e+00 5.18e-01 1.54e+01
  angle pdb=" O11 46E A 503 "
        pdb=" P   46E A 503 "
        pdb=" O13 46E A 503 "
      ideal   model   delta    sigma   weight residual
      93.37  104.86  -11.49 3.00e+00 1.11e-01 1.47e+01
  ... (remaining 5247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.65: 2075
       27.65 -    55.29: 99
       55.29 -    82.93: 12
       82.93 -   110.57: 11
      110.57 -   138.22: 5
  Dihedral angle restraints: 2202
    sinusoidal: 888
      harmonic: 1314
  Sorted by residual:
  dihedral pdb=" C24 46E A 503 "
           pdb=" C25 46E A 503 "
           pdb=" C26 46E A 503 "
           pdb=" C27 46E A 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -179.47  -41.25 -138.22     1      3.00e+01 1.11e-03 1.86e+01
  dihedral pdb=" CA  MET A 300 "
           pdb=" C   MET A 300 "
           pdb=" N   ALA A 301 "
           pdb=" CA  ALA A 301 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.89   21.11     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" C07 UJO A 501 "
           pdb=" C08 UJO A 501 "
           pdb=" C09 UJO A 501 "
           pdb=" C10 UJO A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      72.13 -157.93 -129.94     1      3.00e+01 1.11e-03 1.75e+01
  ... (remaining 2199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 310
       0.032 -    0.064: 168
       0.064 -    0.096: 68
       0.096 -    0.128: 26
       0.128 -    0.160: 5
  Chirality restraints: 577
  Sorted by residual:
  chirality pdb=" C15 UJO A 501 "
            pdb=" C16 UJO A 501 "
            pdb=" C18 UJO A 501 "
            pdb=" N14 UJO A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.34   -0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  LYS A 274 "
            pdb=" N   LYS A 274 "
            pdb=" C   LYS A 274 "
            pdb=" CB  LYS A 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  ILE A 234 "
            pdb=" N   ILE A 234 "
            pdb=" C   ILE A 234 "
            pdb=" CB  ILE A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.30e-01
  ... (remaining 574 not shown)

  Planarity restraints: 619
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 UJO A 501 "    0.166 2.00e-02 2.50e+03   2.90e-01 1.05e+03
        pdb=" C12 UJO A 501 "   -0.087 2.00e-02 2.50e+03
        pdb=" C15 UJO A 501 "    0.343 2.00e-02 2.50e+03
        pdb=" N14 UJO A 501 "   -0.511 2.00e-02 2.50e+03
        pdb=" O13 UJO A 501 "    0.089 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  73 "    0.013 2.00e-02 2.50e+03   1.27e-02 3.23e+00
        pdb=" CG  TYR A  73 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  73 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  73 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  73 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  73 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  73 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  73 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  64 "   -0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO A  65 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  65 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  65 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 616 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 23
        2.56 -     3.15: 3130
        3.15 -     3.73: 5836
        3.73 -     4.32: 7605
        4.32 -     4.90: 12518
  Nonbonded interactions: 29112
  Sorted by model distance:
  nonbonded pdb=" O17 UJO A 501 "
            pdb=" O33 UJO A 501 "
     model   vdw
     1.980 3.040
  nonbonded pdb=" OH  TYR A 268 "
            pdb=" O   PRO A 319 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ALA A 149 "
            pdb=" OG  SER A 287 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   VAL A 192 "
            pdb=" ND2 ASN A 196 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" CD2 LEU A 177 "
            pdb=" C32 UJO A 501 "
     model   vdw
     2.249 3.880
  ... (remaining 29107 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.650
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
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      :  0.007   0.122   3866  Z= 0.310
  Angle     :  1.029  14.909   5252  Z= 0.473
  Chirality :  0.047   0.160    577
  Planarity :  0.013   0.290    619
  Dihedral  : 19.026 138.217   1358
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.18 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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: -0.55 (0.40), residues: 437
  helix:  0.15 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.70 (0.61), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 227 
 TYR   0.031   0.003   TYR A  73 
 PHE   0.018   0.002   PHE A  90 
 TRP   0.025   0.002   TRP A  98 
 HIS   0.006   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00704 ( 3866)
  covalent geometry    : angle       1.02876 ( 5252)
  hydrogen bonds       : bond        0.13451 (  233)
  hydrogen bonds       : angle       5.89560 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  217 ASP cc_start: 0.8469 (t70) cc_final: 0.8253 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0549
  time to fit residues: 5.3662
Evaluate side-chains
  68 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 196 ASN
B 168 ASN
B 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.215135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.181028 restraints weight = 4535.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.184347 restraints weight = 2915.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.186287 restraints weight = 2022.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.186989 restraints weight = 1672.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.187521 restraints weight = 1540.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3866  Z= 0.156
  Angle     :  0.671   8.123   5252  Z= 0.330
  Chirality :  0.043   0.142    577
  Planarity :  0.004   0.040    619
  Dihedral  : 20.134 158.853    571
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.49 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.18 %
    Favored  : 89.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 (0.40), residues: 437
  helix:  0.70 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop : -1.65 (0.61), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.026   0.002   TYR A  73 
 PHE   0.021   0.002   PHE B  98 
 TRP   0.013   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3866)
  covalent geometry    : angle       0.67123 ( 5252)
  hydrogen bonds       : bond        0.04817 (  233)
  hydrogen bonds       : angle       4.60200 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  196 ASN cc_start: 0.8221 (m-40) cc_final: 0.7921 (m110)
REVERT: A  212 GLN cc_start: 0.6113 (pp30) cc_final: 0.5366 (pt0)
REVERT: A  217 ASP cc_start: 0.8370 (t70) cc_final: 0.8158 (t70)
REVERT: B  217 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7554 (mttt)
  outliers start: 3
  outliers final: 1
  residues processed: 74
  average time/residue: 0.0524
  time to fit residues: 5.0956
Evaluate side-chains
  70 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    9.9990
   chunk 39 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0270
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
A 293 HIS
B  84 GLN
B 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.216553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.183074 restraints weight = 4436.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.186594 restraints weight = 2766.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.188546 restraints weight = 1968.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.190022 restraints weight = 1569.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.190513 restraints weight = 1414.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3866  Z= 0.137
  Angle     :  0.615   6.923   5252  Z= 0.301
  Chirality :  0.041   0.133    577
  Planarity :  0.004   0.038    619
  Dihedral  : 19.021 172.696    571
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.26 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.74 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.46 (0.42), residues: 437
  helix:  0.93 (0.29), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.59 (0.65), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.028   0.002   TYR B 148 
 PHE   0.018   0.001   PHE B  98 
 TRP   0.011   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3866)
  covalent geometry    : angle       0.61486 ( 5252)
  hydrogen bonds       : bond        0.04351 (  233)
  hydrogen bonds       : angle       4.37452 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  129 TYR cc_start: 0.8545 (m-80) cc_final: 0.8325 (m-80)
REVERT: A  196 ASN cc_start: 0.8192 (m-40) cc_final: 0.7811 (m110)
REVERT: A  212 GLN cc_start: 0.5940 (pp30) cc_final: 0.5706 (pt0)
REVERT: A  217 ASP cc_start: 0.8335 (t70) cc_final: 0.8108 (t70)
REVERT: A  241 PHE cc_start: 0.7391 (m-80) cc_final: 0.7183 (m-10)
REVERT: A  273 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8040 (tt)
REVERT: B  217 LYS cc_start: 0.7717 (mtmt) cc_final: 0.7304 (mttt)
  outliers start: 8
  outliers final: 2
  residues processed: 82
  average time/residue: 0.0526
  time to fit residues: 5.7219
Evaluate side-chains
  72 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  175 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0070
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    8.9990
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
B  32 ASN
B  84 GLN
B 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.215917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.183197 restraints weight = 4432.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.186264 restraints weight = 2770.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.188263 restraints weight = 2024.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.189793 restraints weight = 1620.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.189955 restraints weight = 1458.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3866  Z= 0.133
  Angle     :  0.589   6.426   5252  Z= 0.292
  Chirality :  0.040   0.133    577
  Planarity :  0.004   0.037    619
  Dihedral  : 17.893 154.087    571
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.03 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.03 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.66 (0.42), residues: 437
  helix:  1.06 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.47 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 113 
 TYR   0.019   0.001   TYR A  73 
 PHE   0.013   0.001   PHE B  51 
 TRP   0.010   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3866)
  covalent geometry    : angle       0.58915 ( 5252)
  hydrogen bonds       : bond        0.04204 (  233)
  hydrogen bonds       : angle       4.22847 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  196 ASN cc_start: 0.8112 (m-40) cc_final: 0.7801 (m-40)
REVERT: A  217 ASP cc_start: 0.8287 (t70) cc_final: 0.8061 (t70)
REVERT: A  261 MET cc_start: 0.8629 (tpp) cc_final: 0.7783 (tpp)
REVERT: B  217 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7161 (mtmt)
  outliers start: 6
  outliers final: 3
  residues processed: 78
  average time/residue: 0.0522
  time to fit residues: 5.4163
Evaluate side-chains
  75 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  175 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0010
   chunk 17 optimal weight:    6.9990
   chunk 42 optimal weight:   20.0000
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN
B 168 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.213949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.178317 restraints weight = 4520.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.181598 restraints weight = 2944.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.184457 restraints weight = 2023.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.187133 restraints weight = 1595.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.187492 restraints weight = 1425.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3866  Z= 0.129
  Angle     :  0.592  12.897   5252  Z= 0.286
  Chirality :  0.040   0.132    577
  Planarity :  0.003   0.037    619
  Dihedral  : 17.054 131.790    571
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.49 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 17.56 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.82 (0.42), residues: 437
  helix:  1.15 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.33 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 113 
 TYR   0.017   0.001   TYR A  73 
 PHE   0.015   0.001   PHE B  51 
 TRP   0.010   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3866)
  covalent geometry    : angle       0.59244 ( 5252)
  hydrogen bonds       : bond        0.04068 (  233)
  hydrogen bonds       : angle       4.09939 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  196 ASN cc_start: 0.8217 (m-40) cc_final: 0.7866 (m-40)
REVERT: A  217 ASP cc_start: 0.8337 (t70) cc_final: 0.8100 (t70)
REVERT: A  268 TYR cc_start: 0.7983 (t80) cc_final: 0.7379 (t80)
REVERT: B  217 LYS cc_start: 0.7422 (mtmt) cc_final: 0.6980 (mttt)
  outliers start: 4
  outliers final: 3
  residues processed: 74
  average time/residue: 0.0419
  time to fit residues: 4.1840
Evaluate side-chains
  71 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  175 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 11 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.216173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.182478 restraints weight = 4540.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.185633 restraints weight = 2848.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.187844 restraints weight = 2068.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.189066 restraints weight = 1661.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.189627 restraints weight = 1513.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3866  Z= 0.125
  Angle     :  0.578  10.236   5252  Z= 0.281
  Chirality :  0.040   0.151    577
  Planarity :  0.003   0.036    619
  Dihedral  : 16.676 124.638    571
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.03 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.07 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.98 (0.43), residues: 437
  helix:  1.30 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.39 (0.68), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 113 
 TYR   0.017   0.001   TYR A  73 
 PHE   0.029   0.001   PHE B  98 
 TRP   0.010   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3866)
  covalent geometry    : angle       0.57818 ( 5252)
  hydrogen bonds       : bond        0.03970 (  233)
  hydrogen bonds       : angle       4.03583 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  196 ASN cc_start: 0.8090 (m-40) cc_final: 0.7777 (m-40)
REVERT: A  217 ASP cc_start: 0.8269 (t70) cc_final: 0.8034 (t70)
REVERT: A  261 MET cc_start: 0.8593 (tpp) cc_final: 0.7738 (tpp)
REVERT: B  217 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7080 (mtmt)
  outliers start: 9
  outliers final: 4
  residues processed: 78
  average time/residue: 0.0484
  time to fit residues: 5.1230
Evaluate side-chains
  72 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   97 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  32 ASN
B  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.218640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.185313 restraints weight = 4484.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.187487 restraints weight = 2743.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.189837 restraints weight = 2180.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.192234 restraints weight = 1614.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.192462 restraints weight = 1482.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3866  Z= 0.129
  Angle     :  0.576   9.448   5252  Z= 0.282
  Chirality :  0.041   0.163    577
  Planarity :  0.004   0.036    619
  Dihedral  : 16.446 119.931    571
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.03 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.32 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.02 (0.43), residues: 437
  helix:  1.32 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.34 (0.68), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.016   0.001   TYR A  73 
 PHE   0.026   0.001   PHE B  98 
 TRP   0.010   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3866)
  covalent geometry    : angle       0.57557 ( 5252)
  hydrogen bonds       : bond        0.03963 (  233)
  hydrogen bonds       : angle       4.03530 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  217 ASP cc_start: 0.8323 (t70) cc_final: 0.8085 (t70)
REVERT: A  268 TYR cc_start: 0.7942 (t80) cc_final: 0.7423 (t80)
REVERT: B   52 MET cc_start: 0.7261 (tpt) cc_final: 0.7010 (tpp)
REVERT: B  217 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7015 (mtmt)
  outliers start: 7
  outliers final: 6
  residues processed: 75
  average time/residue: 0.0470
  time to fit residues: 4.8069
Evaluate side-chains
  74 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  175 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0670
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.217810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.183820 restraints weight = 4530.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.187348 restraints weight = 2875.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.189285 restraints weight = 2049.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.189867 restraints weight = 1663.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.191657 restraints weight = 1552.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3866  Z= 0.126
  Angle     :  0.572   8.405   5252  Z= 0.281
  Chirality :  0.040   0.145    577
  Planarity :  0.004   0.036    619
  Dihedral  : 16.254 141.461    571
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.81 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.07 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.10 (0.43), residues: 437
  helix:  1.37 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.28 (0.69), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.015   0.001   TYR A  73 
 PHE   0.011   0.001   PHE B  51 
 TRP   0.009   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3866)
  covalent geometry    : angle       0.57244 ( 5252)
  hydrogen bonds       : bond        0.03917 (  233)
  hydrogen bonds       : angle       4.01646 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  217 ASP cc_start: 0.8239 (t70) cc_final: 0.8024 (t70)
REVERT: A  261 MET cc_start: 0.8608 (tpp) cc_final: 0.8405 (tpp)
REVERT: A  268 TYR cc_start: 0.7860 (t80) cc_final: 0.7447 (t80)
REVERT: B  217 LYS cc_start: 0.7434 (mtmt) cc_final: 0.6998 (mtmt)
  outliers start: 10
  outliers final: 8
  residues processed: 76
  average time/residue: 0.0456
  time to fit residues: 4.7089
Evaluate side-chains
  75 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   97 CYS
Chi-restraints excluded: chain B residue  175 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0000
   chunk 4 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.217638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.184085 restraints weight = 4466.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.188065 restraints weight = 2722.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.189901 restraints weight = 1906.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.191246 restraints weight = 1513.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.191520 restraints weight = 1378.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.2537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3866  Z= 0.127
  Angle     :  0.590   8.022   5252  Z= 0.289
  Chirality :  0.040   0.150    577
  Planarity :  0.004   0.037    619
  Dihedral  : 16.215 162.552    571
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.58 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.07 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.14 (0.43), residues: 437
  helix:  1.38 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.21 (0.69), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.022   0.001   TYR A 209 
 PHE   0.010   0.001   PHE B  51 
 TRP   0.010   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3866)
  covalent geometry    : angle       0.59029 ( 5252)
  hydrogen bonds       : bond        0.03865 (  233)
  hydrogen bonds       : angle       3.97867 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  212 GLN cc_start: 0.5621 (pp30) cc_final: 0.4621 (pt0)
REVERT: A  261 MET cc_start: 0.8624 (tpp) cc_final: 0.8364 (tpp)
REVERT: A  268 TYR cc_start: 0.7866 (t80) cc_final: 0.7459 (t80)
REVERT: B   52 MET cc_start: 0.7315 (tpt) cc_final: 0.6864 (tpp)
REVERT: B  217 LYS cc_start: 0.7394 (mtmt) cc_final: 0.6968 (mtmt)
  outliers start: 10
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0431
  time to fit residues: 4.3562
Evaluate side-chains
  76 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain A residue  186 TYR
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   97 CYS
Chi-restraints excluded: chain B residue  175 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   chunk 8 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 42 optimal weight:   20.0000
   chunk 26 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 29 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:
B  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.218333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.184501 restraints weight = 4535.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.186752 restraints weight = 2810.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.189114 restraints weight = 2238.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.191340 restraints weight = 1639.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.191514 restraints weight = 1532.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3866  Z= 0.129
  Angle     :  0.600   7.775   5252  Z= 0.293
  Chirality :  0.040   0.157    577
  Planarity :  0.004   0.037    619
  Dihedral  : 16.267 174.581    571
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  4.58 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.32 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.19 (0.43), residues: 437
  helix:  1.42 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.22 (0.70), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 113 
 TYR   0.015   0.001   TYR A 209 
 PHE   0.010   0.001   PHE B  51 
 TRP   0.009   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3866)
  covalent geometry    : angle       0.59982 ( 5252)
  hydrogen bonds       : bond        0.03874 (  233)
  hydrogen bonds       : angle       3.94603 (  699)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   59 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.6228 (m-10)
REVERT: A  261 MET cc_start: 0.8598 (tpp) cc_final: 0.7778 (tpp)
REVERT: A  268 TYR cc_start: 0.7869 (t80) cc_final: 0.7522 (t80)
REVERT: B   52 MET cc_start: 0.7354 (tpt) cc_final: 0.6903 (tpp)
REVERT: B  217 LYS cc_start: 0.7372 (mtmt) cc_final: 0.6947 (mtmt)
  outliers start: 10
  outliers final: 9
  residues processed: 77
  average time/residue: 0.0500
  time to fit residues: 5.1889
Evaluate side-chains
  77 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   59 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 TYR
Chi-restraints excluded: chain A residue  186 TYR
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   97 CYS
Chi-restraints excluded: chain B residue  175 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0470
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0670
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.220027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.187014 restraints weight = 4391.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.189298 restraints weight = 2680.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.191490 restraints weight = 2133.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.193599 restraints weight = 1595.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.193811 restraints weight = 1489.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3866  Z= 0.116
  Angle     :  0.579   7.447   5252  Z= 0.283
  Chirality :  0.040   0.152    577
  Planarity :  0.004   0.037    619
  Dihedral  : 15.886 171.015    571
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  3.89 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.58 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  1.30 (0.43), residues: 437
  helix:  1.51 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.19 (0.69), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 112 
 TYR   0.016   0.001   TYR A  73 
 PHE   0.010   0.001   PHE A  88 
 TRP   0.010   0.001   TRP A  45 
 HIS   0.002   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 3866)
  covalent geometry    : angle       0.57901 ( 5252)
  hydrogen bonds       : bond        0.03746 (  233)
  hydrogen bonds       : angle       3.87414 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 749.30 seconds
wall clock time: 13 minutes 36.61 seconds (816.61 seconds total)