Starting phenix.real_space_refine
on Mon Nov 17 13:44:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cmh_45748/11_2025/9cmh_45748.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cmh_45748/11_2025/9cmh_45748.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cmh_45748/11_2025/9cmh_45748.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cmh_45748/11_2025/9cmh_45748.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cmh_45748/11_2025/9cmh_45748.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cmh_45748/11_2025/9cmh_45748.map"
  }
  resolution = 4.0
  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=   0.010
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      18      5.16       5
     C    2270      2.51       5
     N     582      2.21       5
     O     683      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3553
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1324
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 4, 'TRANS': 175}
    Chain: "B"
      Number of atoms: 2229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2229
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 7, 'TRANS': 278}
  Time building chain proxies: 1.06, per 1000 atoms: 0.30
  Number of scatterers: 3553
  At special positions: 0
  Unit cell: (65.994, 51.76, 148.81, 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      18     16.00
     O     683      8.00
     N     582      7.00
     C    2270      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  64 " 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: 0.21
  Conformation dependent library (CDL) restraints added in 134.2 milliseconds
  

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  850

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      31.5% alpha, 25.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 27
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.928A  pdb=" N   ALA A  72 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU A  73 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 69 through 73'
    Processing helix  chain 'A' and resid 77 through 104
      removed outlier: 3.593A  pdb=" N   CYS A 104 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 149
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 161 through 184
    Processing helix  chain 'B' and resid 92 through 104
    Processing helix  chain 'B' and resid 170 through 174
      removed outlier: 3.624A  pdb=" N   ILE B 174 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 218
      removed outlier: 3.788A  pdb=" N   ASN B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 61
      removed outlier: 6.313A  pdb=" N   VAL B  57 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ALA B 134 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   SER B  59 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN B  61 " --> pdb=" O   TYR B 130 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   LYS B 138 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE B 195 " --> pdb=" O   ASP B  45 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 83
      removed outlier: 4.571A  pdb=" N   GLY B 153 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ILE B 155 " --> pdb=" O   TYR B 139 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TYR B 139 " --> pdb=" O   ILE B 155 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   THR B 135 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ILE B 161 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   TYR B 133 " --> pdb=" O   ILE B 161 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   LEU B 163 " --> pdb=" O   LYS B 131 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   LYS B 131 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   LYS B 165 " --> pdb=" O   TYR B 129 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   TYR B 129 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   SER B 167 " --> pdb=" O   TYR B 127 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   TYR B 127 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   LYS B 138 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 51
    Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 71
    Processing sheet with id=AA6, first strand: chain 'B' and resid 208 through 209
      removed outlier: 3.575A  pdb=" N   LEU B 240 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ILE B 263 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 225 through 227
    Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 254
      removed outlier: 3.788A  pdb=" N   LEU B 291 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    468 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: 0.38

  Time building geometry restraints manager: 0.32 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: 1133
        1.34 -     1.46: 688
        1.46 -     1.58: 1771
        1.58 -     1.70: 0
        1.70 -     1.81: 27
  Bond restraints: 3619
  Sorted by residual:
  bond pdb=" CB  VAL A  90 "
       pdb=" CG1 VAL A  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.58e+00
  bond pdb=" CG  LEU A 130 "
       pdb=" CD2 LEU A 130 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.95e+00
  bond pdb=" CB  GLN A 156 "
       pdb=" CG  GLN A 156 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.63e+00
  bond pdb=" CA  MET A  22 "
       pdb=" CB  MET A  22 "
    ideal  model  delta    sigma   weight residual
    1.528  1.548 -0.019 1.56e-02 4.11e+03 1.55e+00
  bond pdb=" CB  MET A  62 "
       pdb=" CG  MET A  62 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.47e+00
  ... (remaining 3614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.89: 4856
        2.89 -     5.78: 53
        5.78 -     8.68: 8
        8.68 -    11.57: 5
       11.57 -    14.46: 1
  Bond angle restraints: 4923
  Sorted by residual:
  angle pdb=" CB  MET A  22 "
        pdb=" CG  MET A  22 "
        pdb=" SD  MET A  22 "
      ideal   model   delta    sigma   weight residual
     112.70  127.16  -14.46 3.00e+00 1.11e-01 2.32e+01
  angle pdb=" CA  MET A  22 "
        pdb=" CB  MET A  22 "
        pdb=" CG  MET A  22 "
      ideal   model   delta    sigma   weight residual
     114.10  122.94   -8.84 2.00e+00 2.50e-01 1.95e+01
  angle pdb=" N   MET A  22 "
        pdb=" CA  MET A  22 "
        pdb=" CB  MET A  22 "
      ideal   model   delta    sigma   weight residual
     110.12  115.80   -5.68 1.47e+00 4.63e-01 1.50e+01
  angle pdb=" CB  MET A  62 "
        pdb=" CG  MET A  62 "
        pdb=" SD  MET A  62 "
      ideal   model   delta    sigma   weight residual
     112.70  123.91  -11.21 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" CA  GLN A 156 "
        pdb=" CB  GLN A 156 "
        pdb=" CG  GLN A 156 "
      ideal   model   delta    sigma   weight residual
     114.10  121.23   -7.13 2.00e+00 2.50e-01 1.27e+01
  ... (remaining 4918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.05: 1827
       14.05 -    28.10: 203
       28.10 -    42.15: 70
       42.15 -    56.20: 13
       56.20 -    70.25: 15
  Dihedral angle restraints: 2128
    sinusoidal: 793
      harmonic: 1335
  Sorted by residual:
  dihedral pdb=" CA  MET A 131 "
           pdb=" C   MET A 131 "
           pdb=" N   VAL A 132 "
           pdb=" CA  VAL A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.93   19.07     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  PRO A  28 "
           pdb=" C   PRO A  28 "
           pdb=" N   MET A  29 "
           pdb=" CA  MET A  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.19  -17.81     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  MET A  62 "
           pdb=" C   MET A  62 "
           pdb=" N   GLN A  63 "
           pdb=" CA  GLN A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.24   17.76     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 2125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 358
       0.034 -    0.067: 145
       0.067 -    0.100: 46
       0.100 -    0.134: 22
       0.134 -    0.167: 8
  Chirality restraints: 579
  Sorted by residual:
  chirality pdb=" CA  MET A  22 "
            pdb=" N   MET A  22 "
            pdb=" C   MET A  22 "
            pdb=" CB  MET A  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.00e-01
  chirality pdb=" CB  VAL B 118 "
            pdb=" CA  VAL B 118 "
            pdb=" CG1 VAL B 118 "
            pdb=" CG2 VAL B 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 6.89e-01
  chirality pdb=" CB  VAL A 132 "
            pdb=" CA  VAL A 132 "
            pdb=" CG1 VAL A 132 "
            pdb=" CG2 VAL A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.39e-01
  ... (remaining 576 not shown)

  Planarity restraints: 618
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  75 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.77e+00
        pdb=" C   GLN A  75 "    0.045 2.00e-02 2.50e+03
        pdb=" O   GLN A  75 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP A  76 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  81 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" C   VAL B  81 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   VAL B  81 "    0.012 2.00e-02 2.50e+03
        pdb=" N   SER B  82 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 224 "    0.010 2.00e-02 2.50e+03   1.01e-02 2.04e+00
        pdb=" CG  TYR B 224 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 224 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 224 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 224 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 224 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 224 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 224 "    0.000 2.00e-02 2.50e+03
  ... (remaining 615 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 71
        2.65 -     3.22: 3684
        3.22 -     3.78: 6189
        3.78 -     4.34: 8430
        4.34 -     4.90: 12976
  Nonbonded interactions: 31350
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  60 "
            pdb=" OH  TYR B 129 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" O   TYR B 232 "
            pdb=" OH  TYR B 306 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" NE2 GLN B 140 "
            pdb=" OD1 ASP B 152 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" O   ASP B  39 "
            pdb=" OH  TYR B 264 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OG1 THR B 135 "
            pdb=" O   THR B 159 "
     model   vdw
     2.166 3.040
  ... (remaining 31345 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:             1.310
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.720
  Find NCS groups from input model:        0.000
  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:0.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   3620  Z= 0.189
  Angle     :  0.873  14.461   4925  Z= 0.477
  Chirality :  0.046   0.167    579
  Planarity :  0.004   0.029    618
  Dihedral  : 14.789  70.254   1275
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 27.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 24.81 %
    Favored  : 74.42 %
  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: -1.26 (0.39), residues: 462
  helix:  1.65 (0.44), residues: 138
  sheet: -2.12 (0.44), residues: 116
  loop : -1.76 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 227 
 TYR   0.025   0.002   TYR B 224 
 PHE   0.014   0.002   PHE B 268 
 TRP   0.011   0.001   TRP A  30 
 HIS   0.002   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3619)
  covalent geometry    : angle       0.87276 ( 4923)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       1.39668 (    2)
  hydrogen bonds       : bond        0.11278 (  161)
  hydrogen bonds       : angle       7.19779 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.8544 (mm) cc_final: 0.8105 (pp)
REVERT: A   48 GLU cc_start: 0.6256 (tt0) cc_final: 0.5640 (tt0)
REVERT: A  144 ILE cc_start: 0.6878 (mm) cc_final: 0.6590 (tt)
  outliers start: 3
  outliers final: 3
  residues processed: 49
  average time/residue: 0.0814
  time to fit residues: 4.7344
Evaluate side-chains
  43 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain B residue  247 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0050
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 112 ASN
B 140 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.090772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.079275 restraints weight = 22263.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.080965 restraints weight = 13765.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.082128 restraints weight = 9781.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.082883 restraints weight = 7642.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.083362 restraints weight = 6412.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6610
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3620  Z= 0.136
  Angle     :  0.621   8.647   4925  Z= 0.324
  Chirality :  0.043   0.135    579
  Planarity :  0.004   0.047    618
  Dihedral  :  5.504  52.114    500
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 22.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 21.23 %
    Favored  : 76.98 %
  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: -1.09 (0.40), residues: 462
  helix:  2.01 (0.45), residues: 138
  sheet: -1.96 (0.50), residues: 103
  loop : -1.93 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 137 
 TYR   0.011   0.002   TYR B 130 
 PHE   0.012   0.001   PHE B 268 
 TRP   0.006   0.001   TRP B 162 
 HIS   0.002   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3619)
  covalent geometry    : angle       0.62156 ( 4923)
  SS BOND              : bond        0.00098 (    1)
  SS BOND              : angle       0.43760 (    2)
  hydrogen bonds       : bond        0.04195 (  161)
  hydrogen bonds       : angle       5.81626 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.6840 (tt0) cc_final: 0.6535 (tt0)
REVERT: A  118 MET cc_start: 0.4429 (ptt) cc_final: 0.3895 (ptt)
REVERT: B  157 LYS cc_start: 0.8054 (tttt) cc_final: 0.7716 (ptmt)
  outliers start: 7
  outliers final: 3
  residues processed: 47
  average time/residue: 0.0848
  time to fit residues: 4.8940
Evaluate side-chains
  39 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  296 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0030
   chunk 6 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    0.1980
   overall best weight:    0.5790

-------------------------------------------------------------------------------
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 111 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.090578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.079116 restraints weight = 22529.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.080929 restraints weight = 13715.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.082075 restraints weight = 9582.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.082766 restraints weight = 7438.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.083293 restraints weight = 6258.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3620  Z= 0.124
  Angle     :  0.630  10.590   4925  Z= 0.322
  Chirality :  0.045   0.293    579
  Planarity :  0.003   0.026    618
  Dihedral  :  4.572  16.614    496
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 20.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.48 %
    Favored  : 75.45 %
  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: -1.08 (0.40), residues: 462
  helix:  1.98 (0.44), residues: 139
  sheet: -2.06 (0.47), residues: 113
  loop : -1.81 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  31 
 TYR   0.008   0.001   TYR B 136 
 PHE   0.009   0.001   PHE B 268 
 TRP   0.008   0.001   TRP B 162 
 HIS   0.001   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3619)
  covalent geometry    : angle       0.63054 ( 4923)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.26662 (    2)
  hydrogen bonds       : bond        0.04043 (  161)
  hydrogen bonds       : angle       5.44370 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.9451 (tp) cc_final: 0.9218 (tp)
REVERT: A   18 TRP cc_start: 0.6193 (t60) cc_final: 0.5795 (t60)
REVERT: A   19 LEU cc_start: 0.8781 (mm) cc_final: 0.8338 (pp)
REVERT: A  118 MET cc_start: 0.4230 (ptt) cc_final: 0.3645 (ptt)
REVERT: B  186 CYS cc_start: 0.7796 (t) cc_final: 0.6551 (p)
REVERT: B  209 LEU cc_start: 0.5779 (tp) cc_final: 0.5504 (tp)
REVERT: B  315 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6499 (pp)
  outliers start: 12
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0754
  time to fit residues: 4.8040
Evaluate side-chains
  46 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 44 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   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 145 GLN
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.089074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.077614 restraints weight = 22530.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.079320 restraints weight = 13746.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.080451 restraints weight = 9695.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.081194 restraints weight = 7572.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.081625 restraints weight = 6347.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3620  Z= 0.134
  Angle     :  0.629   9.390   4925  Z= 0.324
  Chirality :  0.043   0.229    579
  Planarity :  0.004   0.038    618
  Dihedral  :  4.488  16.081    496
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 20.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 22.76 %
    Favored  : 73.91 %
  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: -0.82 (0.40), residues: 462
  helix:  2.38 (0.45), residues: 133
  sheet: -1.76 (0.49), residues: 108
  loop : -1.79 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  31 
 TYR   0.007   0.001   TYR B 130 
 PHE   0.009   0.001   PHE B 104 
 TRP   0.007   0.001   TRP B 162 
 HIS   0.002   0.001   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3619)
  covalent geometry    : angle       0.62939 ( 4923)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.32244 (    2)
  hydrogen bonds       : bond        0.03874 (  161)
  hydrogen bonds       : angle       5.22277 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 TRP cc_start: 0.6185 (t60) cc_final: 0.5709 (t60)
REVERT: A   19 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8309 (tp)
REVERT: A   48 GLU cc_start: 0.6687 (tt0) cc_final: 0.6434 (tm-30)
REVERT: A   52 MET cc_start: 0.8978 (ppp) cc_final: 0.8569 (ppp)
  outliers start: 13
  outliers final: 6
  residues processed: 48
  average time/residue: 0.0741
  time to fit residues: 4.4599
Evaluate side-chains
  45 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  296 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 241 HIS
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.084466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.073198 restraints weight = 23054.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.074786 restraints weight = 14311.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.075771 restraints weight = 10216.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.076495 restraints weight = 8094.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.076917 restraints weight = 6799.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3620  Z= 0.208
  Angle     :  0.701   9.940   4925  Z= 0.361
  Chirality :  0.046   0.251    579
  Planarity :  0.004   0.042    618
  Dihedral  :  4.866  17.227    496
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 27.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 20.97 %
    Favored  : 73.91 %
  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: -1.05 (0.39), residues: 462
  helix:  2.00 (0.44), residues: 133
  sheet: -1.76 (0.53), residues: 99
  loop : -1.89 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 185 
 TYR   0.017   0.002   TYR B 306 
 PHE   0.030   0.002   PHE B 316 
 TRP   0.016   0.002   TRP B 162 
 HIS   0.005   0.001   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 3619)
  covalent geometry    : angle       0.70142 ( 4923)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       0.28011 (    2)
  hydrogen bonds       : bond        0.04281 (  161)
  hydrogen bonds       : angle       5.62357 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 37
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8349 (tp)
REVERT: A   35 PHE cc_start: 0.0790 (OUTLIER) cc_final: 0.0572 (t80)
REVERT: A   48 GLU cc_start: 0.6871 (tt0) cc_final: 0.6647 (tm-30)
REVERT: A   52 MET cc_start: 0.8901 (ppp) cc_final: 0.8468 (ppp)
REVERT: B  291 LEU cc_start: 0.7900 (mt) cc_final: 0.7615 (mt)
REVERT: B  300 MET cc_start: 0.7944 (pmm) cc_final: 0.7565 (pmm)
  outliers start: 20
  outliers final: 12
  residues processed: 52
  average time/residue: 0.0711
  time to fit residues: 4.5833
Evaluate side-chains
  49 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  194 ASP
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 40 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.085196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.073973 restraints weight = 23110.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.075561 restraints weight = 14333.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.076621 restraints weight = 10203.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.077320 restraints weight = 7976.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.077737 restraints weight = 6700.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3620  Z= 0.155
  Angle     :  0.640  10.266   4925  Z= 0.329
  Chirality :  0.044   0.233    579
  Planarity :  0.004   0.031    618
  Dihedral  :  4.726  16.765    496
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 24.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 23.27 %
    Favored  : 72.89 %
  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: -1.00 (0.40), residues: 462
  helix:  2.12 (0.45), residues: 133
  sheet: -1.75 (0.52), residues: 98
  loop : -1.91 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 158 
 TYR   0.010   0.002   TYR B 156 
 PHE   0.012   0.001   PHE B 316 
 TRP   0.009   0.001   TRP B 162 
 HIS   0.002   0.001   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3619)
  covalent geometry    : angle       0.63949 ( 4923)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       0.82073 (    2)
  hydrogen bonds       : bond        0.03964 (  161)
  hydrogen bonds       : angle       5.38290 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8378 (tp)
REVERT: A   52 MET cc_start: 0.8902 (ppp) cc_final: 0.8586 (ppp)
REVERT: B  252 ARG cc_start: 0.4426 (OUTLIER) cc_final: 0.2766 (ptm160)
REVERT: B  291 LEU cc_start: 0.7805 (mt) cc_final: 0.7380 (mt)
  outliers start: 15
  outliers final: 10
  residues processed: 47
  average time/residue: 0.0643
  time to fit residues: 3.8234
Evaluate side-chains
  45 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   48 ASP
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 ARG
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0010
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.8792

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.085733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.074598 restraints weight = 23125.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.076191 restraints weight = 14210.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.077227 restraints weight = 10064.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.077906 restraints weight = 7876.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.078379 restraints weight = 6636.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3620  Z= 0.136
  Angle     :  0.632   9.794   4925  Z= 0.321
  Chirality :  0.043   0.192    579
  Planarity :  0.003   0.025    618
  Dihedral  :  4.569  17.132    496
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 21.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.79 %
    Favored  : 70.84 %
  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: -0.92 (0.40), residues: 462
  helix:  2.17 (0.45), residues: 133
  sheet: -1.69 (0.52), residues: 98
  loop : -1.85 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 158 
 TYR   0.010   0.001   TYR B 156 
 PHE   0.011   0.001   PHE B 316 
 TRP   0.034   0.002   TRP A  18 
 HIS   0.001   0.001   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3619)
  covalent geometry    : angle       0.63154 ( 4923)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.75174 (    2)
  hydrogen bonds       : bond        0.03872 (  161)
  hydrogen bonds       : angle       5.25265 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 37
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8377 (tp)
REVERT: A   35 PHE cc_start: 0.0740 (OUTLIER) cc_final: 0.0516 (t80)
REVERT: B  252 ARG cc_start: 0.4459 (OUTLIER) cc_final: 0.2863 (ptm160)
REVERT: B  291 LEU cc_start: 0.7951 (mt) cc_final: 0.7579 (mt)
  outliers start: 21
  outliers final: 11
  residues processed: 54
  average time/residue: 0.0741
  time to fit residues: 4.9622
Evaluate side-chains
  48 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 34
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   48 ASP
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 ARG
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.083934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.072854 restraints weight = 23800.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.074379 restraints weight = 14730.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.075396 restraints weight = 10550.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.076082 restraints weight = 8314.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.076488 restraints weight = 6971.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3620  Z= 0.171
  Angle     :  0.679  10.158   4925  Z= 0.343
  Chirality :  0.044   0.202    579
  Planarity :  0.004   0.031    618
  Dihedral  :  4.722  18.108    496
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 25.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 23.79 %
    Favored  : 71.10 %
  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: -1.04 (0.40), residues: 462
  helix:  2.10 (0.45), residues: 133
  sheet: -2.06 (0.45), residues: 123
  loop : -1.67 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 158 
 TYR   0.012   0.002   TYR B 156 
 PHE   0.006   0.001   PHE B 104 
 TRP   0.032   0.002   TRP A  18 
 HIS   0.003   0.001   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3619)
  covalent geometry    : angle       0.67904 ( 4923)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.77719 (    2)
  hydrogen bonds       : bond        0.03919 (  161)
  hydrogen bonds       : angle       5.41733 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 35
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8414 (tp)
REVERT: A   35 PHE cc_start: 0.0592 (OUTLIER) cc_final: 0.0327 (t80)
REVERT: B  252 ARG cc_start: 0.4505 (OUTLIER) cc_final: 0.2890 (ptm160)
REVERT: B  291 LEU cc_start: 0.8021 (mt) cc_final: 0.7693 (mt)
  outliers start: 20
  outliers final: 14
  residues processed: 51
  average time/residue: 0.0693
  time to fit residues: 4.4633
Evaluate side-chains
  50 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 33
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   48 ASP
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  252 ARG
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.079578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.069129 restraints weight = 23084.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.070467 restraints weight = 14774.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.071347 restraints weight = 10794.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.071973 restraints weight = 8609.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.072377 restraints weight = 7270.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   3620  Z= 0.303
  Angle     :  0.842  11.435   4925  Z= 0.437
  Chirality :  0.048   0.181    579
  Planarity :  0.005   0.049    618
  Dihedral  :  5.529  20.404    496
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 33.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 23.79 %
    Favored  : 72.12 %
  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: -1.47 (0.40), residues: 462
  helix:  1.54 (0.45), residues: 131
  sheet: -2.36 (0.45), residues: 113
  loop : -1.75 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 143 
 TYR   0.021   0.003   TYR B 156 
 PHE   0.012   0.002   PHE A  35 
 TRP   0.044   0.004   TRP A  18 
 HIS   0.006   0.002   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 3619)
  covalent geometry    : angle       0.84161 ( 4923)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       1.18574 (    2)
  hydrogen bonds       : bond        0.04978 (  161)
  hydrogen bonds       : angle       6.23556 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 37
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.1327 (OUTLIER) cc_final: 0.0639 (t80)
REVERT: B  252 ARG cc_start: 0.5113 (OUTLIER) cc_final: 0.3254 (ptm160)
REVERT: B  315 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7709 (pp)
  outliers start: 16
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0663
  time to fit residues: 4.1379
Evaluate side-chains
  46 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 PHE
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  252 ARG
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0020
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
** B 285 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 = 0.4097 r_free = 0.4097 target = 0.084388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.073696 restraints weight = 22604.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.075281 restraints weight = 14045.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.076285 restraints weight = 9897.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.076968 restraints weight = 7695.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.077412 restraints weight = 6402.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3620  Z= 0.144
  Angle     :  0.822  15.853   4925  Z= 0.391
  Chirality :  0.049   0.340    579
  Planarity :  0.003   0.034    618
  Dihedral  :  4.914  16.928    495
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 23.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 25.58 %
    Favored  : 71.87 %
  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: -1.18 (0.40), residues: 462
  helix:  1.71 (0.46), residues: 131
  sheet: -1.95 (0.47), residues: 110
  loop : -1.70 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 158 
 TYR   0.041   0.002   TYR B 296 
 PHE   0.012   0.001   PHE B 316 
 TRP   0.030   0.002   TRP A  18 
 HIS   0.002   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3619)
  covalent geometry    : angle       0.82190 ( 4923)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.80614 (    2)
  hydrogen bonds       : bond        0.04318 (  161)
  hydrogen bonds       : angle       5.55672 (  468)

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

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

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  924 Ramachandran restraints generated.
    462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.8787 (mm) cc_final: 0.8325 (pp)
REVERT: A   48 GLU cc_start: 0.6537 (tp30) cc_final: 0.6309 (tp30)
REVERT: B  252 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.3156 (ptm160)
  outliers start: 10
  outliers final: 8
  residues processed: 47
  average time/residue: 0.0775
  time to fit residues: 4.5087
Evaluate side-chains
  45 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  252 ARG
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0370
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.7860

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.084204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.073557 restraints weight = 22355.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.075100 restraints weight = 13993.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.076061 restraints weight = 9943.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.076735 restraints weight = 7837.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.077151 restraints weight = 6553.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.4760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3620  Z= 0.144
  Angle     :  0.784  14.870   4925  Z= 0.377
  Chirality :  0.046   0.220    579
  Planarity :  0.004   0.032    618
  Dihedral  :  4.822  16.739    495
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 23.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 25.58 %
    Favored  : 71.61 %
  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: -1.09 (0.40), residues: 462
  helix:  1.78 (0.46), residues: 133
  sheet: -1.80 (0.48), residues: 109
  loop : -1.74 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 158 
 TYR   0.052   0.002   TYR B 296 
 PHE   0.043   0.002   PHE B 316 
 TRP   0.027   0.002   TRP A  18 
 HIS   0.002   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3619)
  covalent geometry    : angle       0.78387 ( 4923)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.76130 (    2)
  hydrogen bonds       : bond        0.04198 (  161)
  hydrogen bonds       : angle       5.41535 (  468)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 826.70 seconds
wall clock time: 14 minutes 57.24 seconds (897.24 seconds total)