Starting phenix.real_space_refine
on Wed Sep 17 04:04:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g2u_50984/09_2025/9g2u_50984.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g2u_50984/09_2025/9g2u_50984.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g2u_50984/09_2025/9g2u_50984.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g2u_50984/09_2025/9g2u_50984.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g2u_50984/09_2025/9g2u_50984.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g2u_50984/09_2025/9g2u_50984.cif"
  }
  resolution = 3.45
  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=   0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2272      2.51       5
     N     640      2.21       5
     O     706      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3634
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1817
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 5, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1817
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 5, 'TRANS': 222}
          Chain breaks: 1
  Time building chain proxies: 0.99, per 1000 atoms: 0.27
  Number of scatterers: 3634
  At special positions: 0
  Unit cell: (100.928, 83.664, 131.472, 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      16     16.00
     O     706      8.00
     N     640      7.00
     C    2272      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: 0.29
  Conformation dependent library (CDL) restraints added in 112.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  868

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      95.2% 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 11 through 31
      removed outlier: 3.851A  pdb=" N   ALA A  15 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 68
    Processing helix  chain 'A' and resid 70 through 76
    Processing helix  chain 'A' and resid 92 through 109
    Processing helix  chain 'A' and resid 112 through 143
    Processing helix  chain 'A' and resid 143 through 154
      removed outlier: 3.688A  pdb=" N   ILE A 151 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 181
    Processing helix  chain 'A' and resid 184 through 252
      removed outlier: 3.864A  pdb=" N   ILE A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   SER A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   SER A 218 " --> pdb=" O   GLU A 214 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR A 219 " --> pdb=" O   GLY A 215 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 31
    Processing helix  chain 'B' and resid 39 through 68
    Processing helix  chain 'B' and resid 70 through 76
    Processing helix  chain 'B' and resid 92 through 109
    Processing helix  chain 'B' and resid 112 through 143
    Processing helix  chain 'B' and resid 143 through 153
    Processing helix  chain 'B' and resid 153 through 182
    Processing helix  chain 'B' and resid 184 through 252
      removed outlier: 3.820A  pdb=" N   ILE B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   SER B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)

    359 hydrogen bonds defined for protein.
    1077 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: 0.48

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 787
        1.33 -     1.45: 731
        1.45 -     1.57: 2138
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 3680
  Sorted by residual:
  bond pdb=" N   THR A 145 "
       pdb=" CA  THR A 145 "
    ideal  model  delta    sigma   weight residual
    1.462  1.488 -0.026 7.70e-03 1.69e+04 1.15e+01
  bond pdb=" N   ASN B  93 "
       pdb=" CA  ASN B  93 "
    ideal  model  delta    sigma   weight residual
    1.461  1.488 -0.027 9.20e-03 1.18e+04 8.53e+00
  bond pdb=" N   LEU B  38 "
       pdb=" CA  LEU B  38 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.033 1.16e-02 7.43e+03 8.29e+00
  bond pdb=" N   ILE A 216 "
       pdb=" CA  ILE A 216 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.24e-02 6.50e+03 8.03e+00
  bond pdb=" N   GLU B  37 "
       pdb=" CA  GLU B  37 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.034 1.22e-02 6.72e+03 7.97e+00
  ... (remaining 3675 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 2935
        1.00 -     2.00: 894
        2.00 -     3.00: 1074
        3.00 -     4.00: 40
        4.00 -     5.00: 9
  Bond angle restraints: 4952
  Sorted by residual:
  angle pdb=" N   GLN A  32 "
        pdb=" CA  GLN A  32 "
        pdb=" C   GLN A  32 "
      ideal   model   delta    sigma   weight residual
     113.20  108.89    4.31 1.21e+00 6.83e-01 1.27e+01
  angle pdb=" N   GLY B  31 "
        pdb=" CA  GLY B  31 "
        pdb=" C   GLY B  31 "
      ideal   model   delta    sigma   weight residual
     115.21  110.77    4.44 1.30e+00 5.92e-01 1.17e+01
  angle pdb=" CA  ALA B 182 "
        pdb=" C   ALA B 182 "
        pdb=" O   ALA B 182 "
      ideal   model   delta    sigma   weight residual
     122.41  118.33    4.08 1.21e+00 6.83e-01 1.14e+01
  angle pdb=" N   GLY A  31 "
        pdb=" CA  GLY A  31 "
        pdb=" C   GLY A  31 "
      ideal   model   delta    sigma   weight residual
     115.21  110.86    4.35 1.30e+00 5.92e-01 1.12e+01
  angle pdb=" N   LYS A 183 "
        pdb=" CA  LYS A 183 "
        pdb=" C   LYS A 183 "
      ideal   model   delta    sigma   weight residual
     114.39  109.58    4.81 1.45e+00 4.76e-01 1.10e+01
  ... (remaining 4947 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.96: 2100
       15.96 -    31.92: 142
       31.92 -    47.88: 13
       47.88 -    63.85: 26
       63.85 -    79.81: 1
  Dihedral angle restraints: 2282
    sinusoidal: 948
      harmonic: 1334
  Sorted by residual:
  dihedral pdb=" CD  ARG A 225 "
           pdb=" NE  ARG A 225 "
           pdb=" CZ  ARG A 225 "
           pdb=" NH1 ARG A 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -30.30   30.30     1      1.00e+01 1.00e-02 1.31e+01
  dihedral pdb=" CD  ARG B 225 "
           pdb=" NE  ARG B 225 "
           pdb=" CZ  ARG B 225 "
           pdb=" NH1 ARG B 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -26.50   26.50     1      1.00e+01 1.00e-02 1.01e+01
  dihedral pdb=" CB  MET A 245 "
           pdb=" CG  MET A 245 "
           pdb=" SD  MET A 245 "
           pdb=" CE  MET A 245 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  112.23  -52.23     3      1.50e+01 4.44e-03 9.09e+00
  ... (remaining 2279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 128
       0.044 -    0.088: 161
       0.088 -    0.132: 161
       0.132 -    0.176: 94
       0.176 -    0.220: 20
  Chirality restraints: 564
  Sorted by residual:
  chirality pdb=" CA  ILE A  75 "
            pdb=" N   ILE A  75 "
            pdb=" C   ILE A  75 "
            pdb=" CB  ILE A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ILE A 208 "
            pdb=" N   ILE A 208 "
            pdb=" C   ILE A 208 "
            pdb=" CB  ILE A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ILE B  75 "
            pdb=" N   ILE B  75 "
            pdb=" C   ILE B  75 "
            pdb=" CB  ILE B  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 561 not shown)

  Planarity restraints: 644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 225 "    0.542 9.50e-02 1.11e+02   2.43e-01 3.61e+01
        pdb=" NE  ARG A 225 "   -0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 225 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 225 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 225 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 225 "    0.478 9.50e-02 1.11e+02   2.14e-01 2.81e+01
        pdb=" NE  ARG B 225 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 225 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 225 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 225 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 204 "   -0.378 9.50e-02 1.11e+02   1.69e-01 1.76e+01
        pdb=" NE  ARG B 204 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 204 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 204 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 204 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 641 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 59
        2.68 -     3.24: 3938
        3.24 -     3.79: 6011
        3.79 -     4.35: 7726
        4.35 -     4.90: 12141
  Nonbonded interactions: 29875
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP A  55 "
            pdb=" OE1 GLU B 107 "
     model   vdw
     2.127 3.120
  nonbonded pdb=" CB  CYS A  51 "
            pdb=" OE2 GLU B 107 "
     model   vdw
     2.208 3.440
  nonbonded pdb=" CD1 PHE B 150 "
            pdb=" CG2 THR B 219 "
     model   vdw
     2.370 3.760
  nonbonded pdb=" SG  CYS A  51 "
            pdb=" OE2 GLU B 107 "
     model   vdw
     2.375 3.400
  nonbonded pdb=" ND1 HIS A 222 "
            pdb=" NH2 ARG A 225 "
     model   vdw
     2.431 3.200
  ... (remaining 29870 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.670
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
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      :  0.011   0.036   3680  Z= 0.892
  Angle     :  1.371   4.996   4952  Z= 1.172
  Chirality :  0.101   0.220    564
  Planarity :  0.021   0.243    644
  Dihedral  : 12.819  79.808   1414
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.55 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.32), residues: 448
  helix:  1.26 (0.20), residues: 414
  sheet:  None (None), residues: 0
  loop : -2.64 (0.68), residues: 34

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 210 
 TYR   0.005   0.001   TYR A 244 
 PHE   0.006   0.001   PHE B 150 
 TRP   0.002   0.001   TRP A  55 
 HIS   0.003   0.001   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.01134 ( 3680)
  covalent geometry    : angle       1.37110 ( 4952)
  hydrogen bonds       : bond        0.19360 (  359)
  hydrogen bonds       : angle       6.21174 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 LEU cc_start: 0.9197 (tp) cc_final: 0.8701 (tt)
REVERT: A  101 MET cc_start: 0.8470 (mtt) cc_final: 0.8120 (mtt)
REVERT: A  190 SER cc_start: 0.8445 (t) cc_final: 0.7725 (p)
REVERT: A  216 ILE cc_start: 0.9283 (mm) cc_final: 0.8862 (tt)
REVERT: B   46 LEU cc_start: 0.9394 (mt) cc_final: 0.9119 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1338
  time to fit residues: 16.0465
Evaluate side-chains
  54 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 251 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.076771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.062347 restraints weight = 14162.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 3.41
r_work: 0.3246 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.4532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3680  Z= 0.186
  Angle     :  0.580   5.166   4952  Z= 0.318
  Chirality :  0.034   0.123    564
  Planarity :  0.004   0.042    644
  Dihedral  :  2.910  15.528    492
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  6.96 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.32 (0.34), residues: 448
  helix:  3.74 (0.21), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.65 (0.78), residues: 28

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 188 
 TYR   0.015   0.001   TYR A 155 
 PHE   0.012   0.002   PHE A 108 
 TRP   0.020   0.003   TRP A  55 
 HIS   0.002   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3680)
  covalent geometry    : angle       0.58024 ( 4952)
  hydrogen bonds       : bond        0.07909 (  359)
  hydrogen bonds       : angle       4.07375 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   26 THR cc_start: 0.9269 (m) cc_final: 0.9056 (p)
REVERT: A  101 MET cc_start: 0.8848 (mtt) cc_final: 0.8528 (mtm)
REVERT: A  171 ASP cc_start: 0.8150 (m-30) cc_final: 0.7618 (m-30)
REVERT: A  178 ARG cc_start: 0.8572 (ttt-90) cc_final: 0.8063 (tpt-90)
REVERT: B   26 THR cc_start: 0.9272 (m) cc_final: 0.9038 (p)
REVERT: B  188 ARG cc_start: 0.6868 (ttt90) cc_final: 0.6150 (mtm-85)
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0624
  time to fit residues: 4.8776
Evaluate side-chains
  46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 CYS
Chi-restraints excluded: chain A residue  132 ASP
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   19 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0570
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 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 = 0.3656 r_free = 0.3656 target = 0.075131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.060504 restraints weight = 14269.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 3.68
r_work: 0.3171 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3680  Z= 0.161
  Angle     :  0.496   5.960   4952  Z= 0.276
  Chirality :  0.032   0.126    564
  Planarity :  0.003   0.026    644
  Dihedral  :  2.792  16.971    492
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  8.76 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.15 (0.34), residues: 448
  helix:  4.29 (0.21), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.71 (0.83), residues: 28

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 162 
 TYR   0.015   0.001   TYR B 155 
 PHE   0.020   0.002   PHE B  18 
 TRP   0.015   0.002   TRP A  55 
 HIS   0.002   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3680)
  covalent geometry    : angle       0.49554 ( 4952)
  hydrogen bonds       : bond        0.07228 (  359)
  hydrogen bonds       : angle       3.72458 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 THR cc_start: 0.9330 (m) cc_final: 0.9124 (p)
REVERT: A  101 MET cc_start: 0.8872 (mtt) cc_final: 0.8524 (mtm)
REVERT: A  171 ASP cc_start: 0.8395 (m-30) cc_final: 0.8177 (m-30)
REVERT: A  178 ARG cc_start: 0.8606 (ttt-90) cc_final: 0.8154 (tpt-90)
REVERT: B  103 ASP cc_start: 0.9108 (m-30) cc_final: 0.8728 (m-30)
REVERT: B  134 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8834 (tm-30)
REVERT: B  232 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8456 (tm-30)
REVERT: B  235 MET cc_start: 0.9095 (tmm) cc_final: 0.8422 (tmm)
  outliers start: 10
  outliers final: 7
  residues processed: 53
  average time/residue: 0.0662
  time to fit residues: 4.4675
Evaluate side-chains
  47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ASP
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   51 CYS
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  199 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B 205 GLN
B 249 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.072410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.057922 restraints weight = 14432.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 3.68
r_work: 0.3112 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.5981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3680  Z= 0.178
  Angle     :  0.520   5.576   4952  Z= 0.282
  Chirality :  0.033   0.124    564
  Planarity :  0.003   0.024    644
  Dihedral  :  2.793  11.942    492
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  :  8.76 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  5.90 (0.34), residues: 448
  helix:  4.12 (0.21), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.60 (0.84), residues: 28

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  21 
 TYR   0.016   0.001   TYR B 155 
 PHE   0.018   0.002   PHE B 202 
 TRP   0.012   0.002   TRP A  55 
 HIS   0.002   0.000   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3680)
  covalent geometry    : angle       0.51997 ( 4952)
  hydrogen bonds       : bond        0.07503 (  359)
  hydrogen bonds       : angle       3.74811 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 THR cc_start: 0.9322 (m) cc_final: 0.9111 (p)
REVERT: A  101 MET cc_start: 0.8844 (mtt) cc_final: 0.8487 (mtm)
REVERT: A  125 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8241 (mp10)
REVERT: A  171 ASP cc_start: 0.8301 (m-30) cc_final: 0.7954 (m-30)
REVERT: B  103 ASP cc_start: 0.9193 (m-30) cc_final: 0.8843 (m-30)
REVERT: B  134 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8893 (tm-30)
REVERT: B  188 ARG cc_start: 0.7399 (ttt90) cc_final: 0.6683 (mtm-85)
REVERT: B  232 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8527 (tm-30)
REVERT: B  235 MET cc_start: 0.9081 (tmm) cc_final: 0.8400 (tmm)
  outliers start: 11
  outliers final: 7
  residues processed: 54
  average time/residue: 0.0528
  time to fit residues: 3.7444
Evaluate side-chains
  47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  132 ASP
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   51 CYS
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 27 optimal weight:    0.0070
   chunk 16 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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 = 0.3647 r_free = 0.3647 target = 0.074804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.059987 restraints weight = 14520.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 3.80
r_work: 0.3159 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.6410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3680  Z= 0.148
  Angle     :  0.465   6.158   4952  Z= 0.250
  Chirality :  0.030   0.125    564
  Planarity :  0.003   0.025    644
  Dihedral  :  2.708  12.195    492
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 10.05 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.35 (0.35), residues: 448
  helix:  4.42 (0.21), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.62 (0.88), residues: 28

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  21 
 TYR   0.015   0.001   TYR B 155 
 PHE   0.022   0.002   PHE B  18 
 TRP   0.009   0.002   TRP A  55 
 HIS   0.001   0.000   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3680)
  covalent geometry    : angle       0.46506 ( 4952)
  hydrogen bonds       : bond        0.06684 (  359)
  hydrogen bonds       : angle       3.35782 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   26 THR cc_start: 0.9311 (m) cc_final: 0.9099 (p)
REVERT: A  101 MET cc_start: 0.8880 (mtt) cc_final: 0.8544 (mtm)
REVERT: B  103 ASP cc_start: 0.9173 (m-30) cc_final: 0.8817 (m-30)
REVERT: B  134 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8889 (tm-30)
REVERT: B  188 ARG cc_start: 0.7354 (ttt90) cc_final: 0.6681 (mtm-85)
REVERT: B  232 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8612 (tm-30)
REVERT: B  235 MET cc_start: 0.9102 (tmm) cc_final: 0.8489 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 50
  average time/residue: 0.0416
  time to fit residues: 3.0002
Evaluate side-chains
  46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ASP
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   51 CYS
Chi-restraints excluded: chain B residue  134 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.073686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.059016 restraints weight = 14557.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 3.80
r_work: 0.3135 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.6568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3680  Z= 0.157
  Angle     :  0.497   6.314   4952  Z= 0.264
  Chirality :  0.031   0.123    564
  Planarity :  0.003   0.024    644
  Dihedral  :  2.717  11.145    492
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 11.60 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.17 (0.34), residues: 448
  helix:  4.29 (0.21), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.50 (0.92), residues: 28

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 162 
 TYR   0.015   0.001   TYR B 155 
 PHE   0.015   0.002   PHE A  18 
 TRP   0.008   0.002   TRP A  55 
 HIS   0.002   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3680)
  covalent geometry    : angle       0.49700 ( 4952)
  hydrogen bonds       : bond        0.06896 (  359)
  hydrogen bonds       : angle       3.44889 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 THR cc_start: 0.9311 (m) cc_final: 0.9095 (p)
REVERT: A  101 MET cc_start: 0.8834 (mtt) cc_final: 0.8471 (mtm)
REVERT: B  103 ASP cc_start: 0.9185 (m-30) cc_final: 0.8828 (m-30)
REVERT: B  134 GLU cc_start: 0.9109 (tt0) cc_final: 0.8903 (tm-30)
REVERT: B  232 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8638 (tm-30)
REVERT: B  235 MET cc_start: 0.9214 (tmm) cc_final: 0.8442 (tmm)
  outliers start: 11
  outliers final: 7
  residues processed: 47
  average time/residue: 0.0468
  time to fit residues: 3.0864
Evaluate side-chains
  46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ASP
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  216 ILE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   51 CYS
Chi-restraints excluded: chain B residue   60 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0870
   chunk 29 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0770
   chunk 35 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
B 234 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.075771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.060882 restraints weight = 14756.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 3.87
r_work: 0.3186 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.6919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3680  Z= 0.139
  Angle     :  0.458   6.214   4952  Z= 0.245
  Chirality :  0.031   0.153    564
  Planarity :  0.003   0.024    644
  Dihedral  :  2.686  11.732    492
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.11 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.32 (0.35), residues: 448
  helix:  4.39 (0.21), residues: 420
  sheet:  None (None), residues: 0
  loop : -1.46 (0.96), residues: 28

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 188 
 TYR   0.013   0.001   TYR B 155 
 PHE   0.020   0.001   PHE B  18 
 TRP   0.007   0.002   TRP B  55 
 HIS   0.001   0.000   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3680)
  covalent geometry    : angle       0.45838 ( 4952)
  hydrogen bonds       : bond        0.06267 (  359)
  hydrogen bonds       : angle       3.23095 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   26 THR cc_start: 0.9268 (m) cc_final: 0.9051 (p)
REVERT: A  101 MET cc_start: 0.8803 (mtt) cc_final: 0.8464 (mtm)
REVERT: B  103 ASP cc_start: 0.9190 (m-30) cc_final: 0.8818 (m-30)
REVERT: B  134 GLU cc_start: 0.9130 (tt0) cc_final: 0.8927 (tm-30)
REVERT: B  232 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8617 (tm-30)
REVERT: B  235 MET cc_start: 0.9185 (tmm) cc_final: 0.8412 (tmm)
  outliers start: 8
  outliers final: 3
  residues processed: 48
  average time/residue: 0.0470
  time to fit residues: 3.1605
Evaluate side-chains
  37 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 CYS
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.074083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.059440 restraints weight = 14641.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 3.85
r_work: 0.3153 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.6930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3680  Z= 0.156
  Angle     :  0.530  10.029   4952  Z= 0.276
  Chirality :  0.032   0.137    564
  Planarity :  0.003   0.023    644
  Dihedral  :  2.785  11.524    492
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.40 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.11 (0.35), residues: 448
  helix:  4.19 (0.22), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.27 (1.07), residues: 24

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 210 
 TYR   0.014   0.001   TYR B 155 
 PHE   0.021   0.002   PHE B  25 
 TRP   0.006   0.001   TRP A  55 
 HIS   0.001   0.000   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3680)
  covalent geometry    : angle       0.52989 ( 4952)
  hydrogen bonds       : bond        0.06614 (  359)
  hydrogen bonds       : angle       3.39770 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   26 THR cc_start: 0.9283 (m) cc_final: 0.9055 (p)
REVERT: A  101 MET cc_start: 0.8815 (mtt) cc_final: 0.8471 (mtm)
REVERT: B  103 ASP cc_start: 0.9211 (m-30) cc_final: 0.8859 (m-30)
REVERT: B  134 GLU cc_start: 0.9116 (tt0) cc_final: 0.8915 (tm-30)
REVERT: B  173 ASP cc_start: 0.8569 (m-30) cc_final: 0.8065 (t0)
REVERT: B  188 ARG cc_start: 0.7499 (ttt90) cc_final: 0.7137 (mtt-85)
REVERT: B  232 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8653 (tm-30)
REVERT: B  235 MET cc_start: 0.9212 (tmm) cc_final: 0.8457 (tmm)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0503
  time to fit residues: 2.6852
Evaluate side-chains
  38 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   51 CYS
Chi-restraints excluded: chain B residue   60 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.073424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.058593 restraints weight = 14512.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 3.89
r_work: 0.3132 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.7024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3680  Z= 0.157
  Angle     :  0.513   9.438   4952  Z= 0.275
  Chirality :  0.032   0.120    564
  Planarity :  0.003   0.022    644
  Dihedral  :  2.767  11.805    492
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.14 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.08 (0.35), residues: 448
  helix:  4.17 (0.22), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.25 (1.07), residues: 24

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 188 
 TYR   0.014   0.001   TYR B 155 
 PHE   0.022   0.002   PHE B  18 
 TRP   0.006   0.001   TRP B  55 
 HIS   0.001   0.000   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3680)
  covalent geometry    : angle       0.51302 ( 4952)
  hydrogen bonds       : bond        0.06779 (  359)
  hydrogen bonds       : angle       3.42279 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   26 THR cc_start: 0.9268 (m) cc_final: 0.9041 (p)
REVERT: B  103 ASP cc_start: 0.9210 (m-30) cc_final: 0.8859 (m-30)
REVERT: B  171 ASP cc_start: 0.9117 (p0) cc_final: 0.8819 (m-30)
REVERT: B  188 ARG cc_start: 0.7589 (ttt90) cc_final: 0.7153 (ttm170)
REVERT: B  232 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8639 (tm-30)
REVERT: B  235 MET cc_start: 0.9223 (tmm) cc_final: 0.8454 (tmm)
  outliers start: 5
  outliers final: 4
  residues processed: 37
  average time/residue: 0.0499
  time to fit residues: 2.5873
Evaluate side-chains
  38 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   51 CYS
Chi-restraints excluded: chain B residue   60 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0270
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.074040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.059280 restraints weight = 14694.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 3.88
r_work: 0.3147 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.7153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3680  Z= 0.149
  Angle     :  0.520   9.502   4952  Z= 0.272
  Chirality :  0.031   0.124    564
  Planarity :  0.003   0.022    644
  Dihedral  :  2.751  12.020    492
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 13.14 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.15 (0.35), residues: 448
  helix:  4.22 (0.22), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.28 (1.08), residues: 24

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 162 
 TYR   0.014   0.001   TYR B 155 
 PHE   0.018   0.002   PHE A  18 
 TRP   0.006   0.001   TRP B  55 
 HIS   0.001   0.000   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3680)
  covalent geometry    : angle       0.51971 ( 4952)
  hydrogen bonds       : bond        0.06518 (  359)
  hydrogen bonds       : angle       3.34301 ( 1077)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 THR cc_start: 0.9263 (m) cc_final: 0.9036 (p)
REVERT: B  103 ASP cc_start: 0.9217 (m-30) cc_final: 0.8865 (m-30)
REVERT: B  171 ASP cc_start: 0.9164 (p0) cc_final: 0.8858 (m-30)
REVERT: B  188 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7531 (ttm-80)
REVERT: B  232 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8635 (tm-30)
REVERT: B  235 MET cc_start: 0.9227 (tmm) cc_final: 0.8462 (tmm)
  outliers start: 4
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0635
  time to fit residues: 3.2123
Evaluate side-chains
  40 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   51 CYS
Chi-restraints excluded: chain B residue   60 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.074200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.059221 restraints weight = 14190.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 3.90
r_work: 0.3129 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.7234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3680  Z= 0.150
  Angle     :  0.518   8.990   4952  Z= 0.272
  Chirality :  0.031   0.121    564
  Planarity :  0.003   0.022    644
  Dihedral  :  2.751  11.906    492
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.63 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.15 (0.35), residues: 448
  helix:  4.22 (0.22), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.32 (1.06), residues: 24

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 188 
 TYR   0.014   0.001   TYR B 155 
 PHE   0.023   0.002   PHE B  18 
 TRP   0.006   0.001   TRP B  55 
 HIS   0.001   0.000   HIS B 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3680)
  covalent geometry    : angle       0.51818 ( 4952)
  hydrogen bonds       : bond        0.06516 (  359)
  hydrogen bonds       : angle       3.34089 ( 1077)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1089.68 seconds
wall clock time: 19 minutes 19.92 seconds (1159.92 seconds total)