Starting phenix.real_space_refine
on Wed Sep 17 05:09:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nxk_49902/09_2025/9nxk_49902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nxk_49902/09_2025/9nxk_49902.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nxk_49902/09_2025/9nxk_49902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nxk_49902/09_2025/9nxk_49902.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nxk_49902/09_2025/9nxk_49902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nxk_49902/09_2025/9nxk_49902.map"
  }
  resolution = 3.0
  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=   0.006
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      15      5.16       5
     C    2922      2.51       5
     N     819      2.21       5
     O     897      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 4653
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1551
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 200}
    Chain: "B"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1551
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 200}
    Chain: "C"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1551
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 200}
  Time building chain proxies: 1.54, per 1000 atoms: 0.33
  Number of scatterers: 4653
  At special positions: 0
  Unit cell: (104.06, 120.142, 154.198, 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      15     16.00
     O     897      8.00
     N     819      7.00
     C    2922      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: 0.42
  Conformation dependent library (CDL) restraints added in 153.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1116

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 6 sheets defined
      17.9% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 12
    Processing helix  chain 'A' and resid 22 through 24
      No H-bonds generated for 'chain 'A' and resid 22 through 24'
    Processing helix  chain 'A' and resid 25 through 41
    Processing helix  chain 'A' and resid 51 through 57
    Processing helix  chain 'A' and resid 58 through 60
      No H-bonds generated for 'chain 'A' and resid 58 through 60'
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 4.170A  pdb=" N   ILE A 142 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 12
    Processing helix  chain 'B' and resid 22 through 24
      No H-bonds generated for 'chain 'B' and resid 22 through 24'
    Processing helix  chain 'B' and resid 25 through 41
    Processing helix  chain 'B' and resid 51 through 57
    Processing helix  chain 'B' and resid 58 through 60
      No H-bonds generated for 'chain 'B' and resid 58 through 60'
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 4.130A  pdb=" N   ILE B 142 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 12
    Processing helix  chain 'C' and resid 22 through 24
      No H-bonds generated for 'chain 'C' and resid 22 through 24'
    Processing helix  chain 'C' and resid 25 through 41
    Processing helix  chain 'C' and resid 51 through 57
    Processing helix  chain 'C' and resid 58 through 60
      No H-bonds generated for 'chain 'C' and resid 58 through 60'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 73
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149
      removed outlier: 4.337A  pdb=" N   LEU A 179 " --> pdb=" O   TRP A 149 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 157
      removed outlier: 3.810A  pdb=" N   THR A 156 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151
      removed outlier: 4.432A  pdb=" N   LEU B 179 " --> pdb=" O   TRP B 149 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   SER B 151 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   THR B 177 " --> pdb=" O   SER B 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 157
      removed outlier: 3.626A  pdb=" N   THR B 156 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 151
      removed outlier: 4.414A  pdb=" N   LEU C 179 " --> pdb=" O   TRP C 149 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   SER C 151 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   THR C 177 " --> pdb=" O   SER C 151 " (cutoff:3.500A)

    61 hydrogen bonds defined for protein.
    159 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: 0.54

  Time building geometry restraints manager: 0.55 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: 1555
        1.34 -     1.46: 852
        1.46 -     1.58: 2330
        1.58 -     1.70: 0
        1.70 -     1.81: 24
  Bond restraints: 4761
  Sorted by residual:
  bond pdb=" CB  PRO C 183 "
       pdb=" CG  PRO C 183 "
    ideal  model  delta    sigma   weight residual
    1.492  1.555 -0.063 5.00e-02 4.00e+02 1.58e+00
  bond pdb=" CB  MET A 198 "
       pdb=" CG  MET A 198 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.00e+00
  bond pdb=" CA  GLY B 130 "
       pdb=" C   GLY B 130 "
    ideal  model  delta    sigma   weight residual
    1.519  1.512  0.007 7.00e-03 2.04e+04 1.00e+00
  bond pdb=" C   GLY B 109 "
       pdb=" O   GLY B 109 "
    ideal  model  delta    sigma   weight residual
    1.243  1.234  0.009 9.30e-03 1.16e+04 9.14e-01
  bond pdb=" CG  PRO C 183 "
       pdb=" CD  PRO C 183 "
    ideal  model  delta    sigma   weight residual
    1.503  1.472  0.031 3.40e-02 8.65e+02 8.41e-01
  ... (remaining 4756 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 6422
        2.09 -     4.17: 80
        4.17 -     6.26: 11
        6.26 -     8.35: 2
        8.35 -    10.43: 1
  Bond angle restraints: 6516
  Sorted by residual:
  angle pdb=" CB  MET A 198 "
        pdb=" CG  MET A 198 "
        pdb=" SD  MET A 198 "
      ideal   model   delta    sigma   weight residual
     112.70  123.13  -10.43 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" N   MET C 198 "
        pdb=" CA  MET C 198 "
        pdb=" C   MET C 198 "
      ideal   model   delta    sigma   weight residual
     109.81  116.98   -7.17 2.21e+00 2.05e-01 1.05e+01
  angle pdb=" CA  PRO C 183 "
        pdb=" N   PRO C 183 "
        pdb=" CD  PRO C 183 "
      ideal   model   delta    sigma   weight residual
     112.00  108.21    3.79 1.40e+00 5.10e-01 7.34e+00
  angle pdb=" N   PRO C 183 "
        pdb=" CD  PRO C 183 "
        pdb=" CG  PRO C 183 "
      ideal   model   delta    sigma   weight residual
     103.20   99.29    3.91 1.50e+00 4.44e-01 6.80e+00
  angle pdb=" N   ILE A 203 "
        pdb=" CA  ILE A 203 "
        pdb=" C   ILE A 203 "
      ideal   model   delta    sigma   weight residual
     107.56  109.90   -2.34 9.10e-01 1.21e+00 6.63e+00
  ... (remaining 6511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.79: 2419
       15.79 -    31.58: 264
       31.58 -    47.37: 50
       47.37 -    63.16: 9
       63.16 -    78.94: 6
  Dihedral angle restraints: 2748
    sinusoidal: 987
      harmonic: 1761
  Sorted by residual:
  dihedral pdb=" CG  ARG B 120 "
           pdb=" CD  ARG B 120 "
           pdb=" NE  ARG B 120 "
           pdb=" CZ  ARG B 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.74  -44.74     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CA  MET A 198 "
           pdb=" C   MET A 198 "
           pdb=" N   PRO A 199 "
           pdb=" CA  PRO A 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.76   16.24     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CG  ARG A 120 "
           pdb=" CD  ARG A 120 "
           pdb=" NE  ARG A 120 "
           pdb=" CZ  ARG A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.96  -41.96     2      1.50e+01 4.44e-03 9.54e+00
  ... (remaining 2745 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 501
       0.033 -    0.066: 162
       0.066 -    0.100: 57
       0.100 -    0.133: 34
       0.133 -    0.166: 2
  Chirality restraints: 756
  Sorted by residual:
  chirality pdb=" CA  ILE A  71 "
            pdb=" N   ILE A  71 "
            pdb=" C   ILE A  71 "
            pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.89e-01
  chirality pdb=" CA  ILE B  71 "
            pdb=" N   ILE B  71 "
            pdb=" C   ILE B  71 "
            pdb=" CB  ILE B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  MET A 198 "
            pdb=" N   MET A 198 "
            pdb=" C   MET A 198 "
            pdb=" CB  MET A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 753 not shown)

  Planarity restraints: 855
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 198 "    0.063 5.00e-02 4.00e+02   9.64e-02 1.49e+01
        pdb=" N   PRO B 199 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO B 199 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 199 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 182 "    0.042 5.00e-02 4.00e+02   6.24e-02 6.22e+00
        pdb=" N   PRO C 183 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO C 183 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 183 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 198 "    0.036 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO A 199 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 199 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 199 "    0.030 5.00e-02 4.00e+02
  ... (remaining 852 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 368
        2.73 -     3.27: 5192
        3.27 -     3.82: 8289
        3.82 -     4.36: 9674
        4.36 -     4.90: 15686
  Nonbonded interactions: 39209
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 152 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG1 THR B  93 "
            pdb=" OD1 ASN B  95 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG1 THR C 135 "
            pdb=" O   ASN C 191 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG1 THR C  93 "
            pdb=" OD1 ASN C  95 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR A 146 "
            pdb=" O   THR A 181 "
     model   vdw
     2.241 3.040
  ... (remaining 39204 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             9.770
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.500
  Find NCS groups from input model:        0.040
  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:6.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4761  Z= 0.149
  Angle     :  0.570  10.433   6516  Z= 0.295
  Chirality :  0.043   0.166    756
  Planarity :  0.006   0.096    855
  Dihedral  : 13.782  78.943   1632
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 13.29 %
    Favored  : 86.50 %
  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: -1.64 (0.33), residues: 636
  helix: -1.89 (0.45), residues: 93
  sheet: -2.54 (0.47), residues: 102
  loop : -0.48 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 152 
 TYR   0.016   0.002   TYR A  64 
 PHE   0.007   0.001   PHE B 206 
 TRP   0.010   0.001   TRP A  73 
 HIS   0.002   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4761)
  covalent geometry    : angle       0.57020 ( 6516)
  hydrogen bonds       : bond        0.21215 (   61)
  hydrogen bonds       : angle       9.96018 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.3145 (ppp) cc_final: 0.1085 (tpp)
REVERT: B  198 MET cc_start: 0.5474 (tpp) cc_final: 0.4429 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 13
  average time/residue: 0.6684
  time to fit residues: 9.2033
Evaluate side-chains
  10 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.0060
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0980
   chunk 61 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   overall best weight:    2.4000

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 GLN
B 197 ASN
** C 141 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 = 0.4184 r_free = 0.4184 target = 0.064779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.040578 restraints weight = 36273.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 7.44
r_work: 0.3018 rms_B_bonded: 5.80 restraints_weight: 2.0000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4761  Z= 0.099
  Angle     :  0.487   6.050   6516  Z= 0.248
  Chirality :  0.043   0.150    756
  Planarity :  0.005   0.078    855
  Dihedral  :  3.926  27.266    660
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 13.50 %
    Favored  : 85.28 %
  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: -0.91 (0.34), residues: 636
  helix:  1.10 (0.56), residues: 93
  sheet: -2.70 (0.45), residues: 108
  loop : -0.36 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 150 
 TYR   0.013   0.001   TYR B  64 
 PHE   0.006   0.001   PHE A 210 
 TRP   0.009   0.001   TRP B  73 
 HIS   0.003   0.001   HIS B 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 4761)
  covalent geometry    : angle       0.48750 ( 6516)
  hydrogen bonds       : bond        0.04484 (   61)
  hydrogen bonds       : angle       4.85860 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 10
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  198 MET cc_start: 0.3215 (ppp) cc_final: 0.1213 (tpt)
REVERT: B  198 MET cc_start: 0.5625 (tpp) cc_final: 0.4827 (tpp)
REVERT: C   69 MET cc_start: 0.8973 (mtt) cc_final: 0.8681 (mtt)
  outliers start: 6
  outliers final: 1
  residues processed: 16
  average time/residue: 0.6034
  time to fit residues: 10.1448
Evaluate side-chains
  11 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 10
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 3 optimal weight:    5.9990
   chunk 58 optimal weight:   50.0000
   chunk 7 optimal weight:    9.9990
   chunk 40 optimal weight:   30.0000
   chunk 53 optimal weight:    0.0970
   chunk 25 optimal weight:    8.9990
   chunk 38 optimal weight:   50.0000
   chunk 57 optimal weight:   30.0000
   chunk 6 optimal weight:    5.9990
   overall best weight:    6.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 141 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 = 0.4162 r_free = 0.4162 target = 0.064036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.039230 restraints weight = 36026.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 6.74
r_work: 0.2947 rms_B_bonded: 5.88 restraints_weight: 2.0000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4761  Z= 0.135
  Angle     :  0.495   5.845   6516  Z= 0.246
  Chirality :  0.043   0.145    756
  Planarity :  0.004   0.076    855
  Dihedral  :  3.804  24.550    660
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 15.75 %
    Favored  : 83.44 %
  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: -0.80 (0.34), residues: 636
  helix:  1.71 (0.60), residues: 93
  sheet: -2.67 (0.45), residues: 108
  loop : -0.42 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 152 
 TYR   0.012   0.001   TYR B  64 
 PHE   0.007   0.001   PHE B 206 
 TRP   0.005   0.001   TRP B  73 
 HIS   0.003   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4761)
  covalent geometry    : angle       0.49466 ( 6516)
  hydrogen bonds       : bond        0.05593 (   61)
  hydrogen bonds       : angle       4.45910 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.3085 (ppp) cc_final: 0.1363 (tpt)
REVERT: B  198 MET cc_start: 0.5553 (tpp) cc_final: 0.4758 (tpt)
REVERT: C   69 MET cc_start: 0.9057 (mtt) cc_final: 0.8461 (mtt)
  outliers start: 4
  outliers final: 1
  residues processed: 14
  average time/residue: 0.6876
  time to fit residues: 10.1347
Evaluate side-chains
  11 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 10
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 52 optimal weight:   30.0000
   chunk 24 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 35 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 34 optimal weight:   50.0000
   chunk 37 optimal weight:    5.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 GLN
** C 141 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 = 0.4149 r_free = 0.4149 target = 0.063669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.039602 restraints weight = 35431.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 7.18
r_work: 0.2938 rms_B_bonded: 5.49 restraints_weight: 2.0000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4761  Z= 0.145
  Angle     :  0.496   5.875   6516  Z= 0.247
  Chirality :  0.043   0.152    756
  Planarity :  0.004   0.074    855
  Dihedral  :  3.821  23.741    660
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.54 %
    Favored  : 82.82 %
  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: -0.68 (0.34), residues: 636
  helix:  2.02 (0.58), residues: 90
  sheet: -2.11 (0.47), residues: 120
  loop : -0.45 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 150 
 TYR   0.013   0.001   TYR B  64 
 PHE   0.008   0.001   PHE B 206 
 TRP   0.008   0.001   TRP B  73 
 HIS   0.003   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4761)
  covalent geometry    : angle       0.49586 ( 6516)
  hydrogen bonds       : bond        0.05211 (   61)
  hydrogen bonds       : angle       4.20385 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 10
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  198 MET cc_start: 0.3094 (ppp) cc_final: 0.1484 (tpt)
REVERT: B  127 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7832 (m)
REVERT: B  198 MET cc_start: 0.5766 (tpp) cc_final: 0.4988 (tpt)
REVERT: C   69 MET cc_start: 0.9125 (mtt) cc_final: 0.8497 (mtt)
  outliers start: 8
  outliers final: 2
  residues processed: 17
  average time/residue: 0.6156
  time to fit residues: 11.0691
Evaluate side-chains
  13 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 10
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  156 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 15 optimal weight:   30.0000
   chunk 41 optimal weight:   30.0000
   chunk 18 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0970
   chunk 55 optimal weight:   50.0000
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    3.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 GLN
** C 141 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 = 0.4163 r_free = 0.4163 target = 0.064174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.039729 restraints weight = 35432.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 6.46
r_work: 0.2974 rms_B_bonded: 5.29 restraints_weight: 2.0000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4761  Z= 0.100
  Angle     :  0.461   5.457   6516  Z= 0.229
  Chirality :  0.042   0.145    756
  Planarity :  0.004   0.068    855
  Dihedral  :  3.684  25.543    660
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.34 %
    Favored  : 83.23 %
  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: -0.61 (0.34), residues: 636
  helix:  2.37 (0.59), residues: 90
  sheet: -2.08 (0.47), residues: 120
  loop : -0.48 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 150 
 TYR   0.010   0.001   TYR B  64 
 PHE   0.005   0.001   PHE B 206 
 TRP   0.009   0.001   TRP B  73 
 HIS   0.003   0.001   HIS B 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 4761)
  covalent geometry    : angle       0.46075 ( 6516)
  hydrogen bonds       : bond        0.04059 (   61)
  hydrogen bonds       : angle       3.81076 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 11
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8298 (pmm)
REVERT: A  198 MET cc_start: 0.3034 (ppp) cc_final: 0.1582 (tpt)
REVERT: B  127 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7847 (m)
REVERT: B  198 MET cc_start: 0.5519 (tpp) cc_final: 0.4795 (tpt)
REVERT: C   69 MET cc_start: 0.9036 (mtt) cc_final: 0.8396 (mtt)
  outliers start: 7
  outliers final: 2
  residues processed: 17
  average time/residue: 0.6120
  time to fit residues: 10.9749
Evaluate side-chains
  15 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 11
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 28 optimal weight:    0.0170
   chunk 32 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 59 optimal weight:   50.0000
   chunk 21 optimal weight:   20.0000
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 37 optimal weight:   40.0000
   chunk 3 optimal weight:    5.9990
   chunk 39 optimal weight:   40.0000
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.8222

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 GLN
** C 141 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 = 0.4183 r_free = 0.4183 target = 0.064827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.040588 restraints weight = 37180.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 7.03
r_work: 0.2998 rms_B_bonded: 5.71 restraints_weight: 2.0000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4761  Z= 0.084
  Angle     :  0.451   5.346   6516  Z= 0.223
  Chirality :  0.042   0.168    756
  Planarity :  0.004   0.063    855
  Dihedral  :  3.599  26.466    660
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.54 %
    Favored  : 83.23 %
  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: -0.68 (0.34), residues: 636
  helix:  2.39 (0.59), residues: 93
  sheet: -2.43 (0.46), residues: 114
  loop : -0.50 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 150 
 TYR   0.008   0.001   TYR B  64 
 PHE   0.003   0.001   PHE B 206 
 TRP   0.009   0.001   TRP B  73 
 HIS   0.003   0.001   HIS B 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 4761)
  covalent geometry    : angle       0.45140 ( 6516)
  hydrogen bonds       : bond        0.03424 (   61)
  hydrogen bonds       : angle       3.48132 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 11
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  198 MET cc_start: 0.2922 (OUTLIER) cc_final: 0.1440 (tpt)
REVERT: B   64 TYR cc_start: 0.7384 (m-80) cc_final: 0.7059 (m-80)
REVERT: B  127 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7978 (m)
REVERT: B  198 MET cc_start: 0.5343 (tpp) cc_final: 0.4567 (tpt)
REVERT: C   69 MET cc_start: 0.9029 (mtt) cc_final: 0.8389 (mtt)
  outliers start: 6
  outliers final: 1
  residues processed: 15
  average time/residue: 0.8038
  time to fit residues: 12.6171
Evaluate side-chains
  14 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 11
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 58 optimal weight:   50.0000
   chunk 13 optimal weight:   40.0000
   chunk 40 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 46 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 14 optimal weight:   30.0000
   overall best weight:    8.3992

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 GLN
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 141 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 = 0.4139 r_free = 0.4139 target = 0.063295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.038685 restraints weight = 36231.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 7.16
r_work: 0.2926 rms_B_bonded: 5.58 restraints_weight: 2.0000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4761  Z= 0.175
  Angle     :  0.521   6.343   6516  Z= 0.263
  Chirality :  0.044   0.147    756
  Planarity :  0.004   0.065    855
  Dihedral  :  3.872  22.489    660
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.34 %
    Favored  : 82.82 %
  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: -0.64 (0.35), residues: 636
  helix:  2.59 (0.58), residues: 90
  sheet: -2.06 (0.48), residues: 120
  loop : -0.57 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 150 
 TYR   0.014   0.001   TYR B  64 
 PHE   0.009   0.001   PHE B 206 
 TRP   0.004   0.001   TRP B 108 
 HIS   0.004   0.001   HIS C 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 4761)
  covalent geometry    : angle       0.52147 ( 6516)
  hydrogen bonds       : bond        0.05949 (   61)
  hydrogen bonds       : angle       4.03377 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 12
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8906 (ptp) cc_final: 0.8577 (pmm)
REVERT: A  198 MET cc_start: 0.2693 (OUTLIER) cc_final: 0.1402 (tpt)
REVERT: B  127 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7927 (m)
REVERT: B  198 MET cc_start: 0.5303 (tpp) cc_final: 0.4580 (tpt)
REVERT: C   69 MET cc_start: 0.9074 (mtt) cc_final: 0.8423 (mtt)
  outliers start: 9
  outliers final: 3
  residues processed: 20
  average time/residue: 0.5941
  time to fit residues: 12.5174
Evaluate side-chains
  17 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  156 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 36 optimal weight:   50.0000
   chunk 55 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 57 optimal weight:   50.0000
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:   50.0000
   chunk 33 optimal weight:    0.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 GLN
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 HIS ** 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 = 0.4147 r_free = 0.4147 target = 0.063752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.039409 restraints weight = 37158.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 6.91
r_work: 0.2952 rms_B_bonded: 5.52 restraints_weight: 2.0000
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4761  Z= 0.126
  Angle     :  0.495   5.599   6516  Z= 0.248
  Chirality :  0.043   0.143    756
  Planarity :  0.004   0.065    855
  Dihedral  :  3.789  24.139    660
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.95 %
    Favored  : 82.82 %
  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: -0.64 (0.34), residues: 636
  helix:  2.66 (0.58), residues: 90
  sheet: -2.00 (0.48), residues: 120
  loop : -0.61 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 150 
 TYR   0.011   0.001   TYR C  64 
 PHE   0.007   0.001   PHE B 206 
 TRP   0.008   0.001   TRP C  73 
 HIS   0.003   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4761)
  covalent geometry    : angle       0.49458 ( 6516)
  hydrogen bonds       : bond        0.04691 (   61)
  hydrogen bonds       : angle       3.81665 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 12
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8935 (ptp) cc_final: 0.8712 (pmm)
REVERT: A  198 MET cc_start: 0.3083 (OUTLIER) cc_final: 0.1619 (tpt)
REVERT: B   64 TYR cc_start: 0.7715 (m-80) cc_final: 0.7228 (m-80)
REVERT: B  127 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7923 (m)
REVERT: B  198 MET cc_start: 0.5481 (tpp) cc_final: 0.4767 (tpt)
REVERT: C   69 MET cc_start: 0.9063 (mtt) cc_final: 0.8447 (mtt)
  outliers start: 6
  outliers final: 3
  residues processed: 17
  average time/residue: 0.6129
  time to fit residues: 10.9812
Evaluate side-chains
  17 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  156 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 41 optimal weight:   40.0000
   chunk 33 optimal weight:    9.9990
   chunk 35 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   chunk 37 optimal weight:   50.0000
   chunk 15 optimal weight:    8.9990
   chunk 55 optimal weight:   20.0000
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 40 optimal weight:   40.0000
   chunk 39 optimal weight:   40.0000
   overall best weight:    8.5992

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 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 = 0.4118 r_free = 0.4118 target = 0.063028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.038549 restraints weight = 36235.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 6.93
r_work: 0.2920 rms_B_bonded: 5.71 restraints_weight: 2.0000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4761  Z= 0.180
  Angle     :  0.544   6.363   6516  Z= 0.275
  Chirality :  0.044   0.152    756
  Planarity :  0.004   0.067    855
  Dihedral  :  4.013  23.512    660
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.16 %
    Favored  : 82.62 %
  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: -0.71 (0.34), residues: 636
  helix:  2.61 (0.57), residues: 90
  sheet: -2.07 (0.48), residues: 120
  loop : -0.66 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 150 
 TYR   0.015   0.002   TYR C  64 
 PHE   0.012   0.001   PHE B 206 
 TRP   0.007   0.001   TRP B  73 
 HIS   0.004   0.001   HIS C 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 4761)
  covalent geometry    : angle       0.54365 ( 6516)
  hydrogen bonds       : bond        0.05932 (   61)
  hydrogen bonds       : angle       4.07314 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.3529 (OUTLIER) cc_final: 0.1745 (tpt)
REVERT: B  127 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7854 (m)
REVERT: B  198 MET cc_start: 0.5333 (tpp) cc_final: 0.4645 (tpt)
REVERT: C   69 MET cc_start: 0.9101 (mtt) cc_final: 0.8397 (mtt)
  outliers start: 6
  outliers final: 3
  residues processed: 19
  average time/residue: 0.5455
  time to fit residues: 11.0049
Evaluate side-chains
  18 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 13
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  156 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 53 optimal weight:    9.9990
   chunk 11 optimal weight:    0.3980
   chunk 36 optimal weight:   50.0000
   chunk 14 optimal weight:   50.0000
   chunk 26 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 17 optimal weight:   40.0000
   chunk 39 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   overall best weight:    2.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.065483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.042383 restraints weight = 37849.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 5.05
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4761  Z= 0.096
  Angle     :  0.515  10.369   6516  Z= 0.251
  Chirality :  0.043   0.146    756
  Planarity :  0.004   0.063    855
  Dihedral  :  3.801  27.423    660
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 16.56 %
    Favored  : 82.41 %
  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: -0.59 (0.34), residues: 636
  helix:  2.89 (0.58), residues: 90
  sheet: -1.94 (0.48), residues: 120
  loop : -0.64 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 150 
 TYR   0.009   0.001   TYR C  64 
 PHE   0.004   0.001   PHE B 206 
 TRP   0.014   0.001   TRP C  73 
 HIS   0.003   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4761)
  covalent geometry    : angle       0.51473 ( 6516)
  hydrogen bonds       : bond        0.03812 (   61)
  hydrogen bonds       : angle       3.54853 (  159)

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

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

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1272 Ramachandran restraints generated.
    636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 MET cc_start: 0.3457 (OUTLIER) cc_final: 0.1859 (tpt)
REVERT: B   64 TYR cc_start: 0.7679 (m-80) cc_final: 0.7349 (m-80)
REVERT: B  127 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7860 (m)
REVERT: B  198 MET cc_start: 0.5516 (tpp) cc_final: 0.4619 (tpt)
REVERT: C   69 MET cc_start: 0.8906 (mtt) cc_final: 0.8352 (mtt)
  outliers start: 5
  outliers final: 1
  residues processed: 16
  average time/residue: 0.6621
  time to fit residues: 11.1819
Evaluate side-chains
  15 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  156 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 44 optimal weight:   20.0000
   chunk 45 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 58 optimal weight:   50.0000
   chunk 34 optimal weight:   30.0000
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:   40.0000
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 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 = 0.4124 r_free = 0.4124 target = 0.063187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.039289 restraints weight = 37054.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 6.41
r_work: 0.2958 rms_B_bonded: 5.33 restraints_weight: 2.0000
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8758
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4761  Z= 0.150
  Angle     :  0.527  10.249   6516  Z= 0.260
  Chirality :  0.043   0.145    756
  Planarity :  0.004   0.063    855
  Dihedral  :  3.872  25.688    660
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 16.97 %
    Favored  : 82.41 %
  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: -0.66 (0.34), residues: 636
  helix:  2.82 (0.57), residues: 90
  sheet: -2.52 (0.53), residues: 90
  loop : -0.68 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 150 
 TYR   0.013   0.001   TYR C  64 
 PHE   0.008   0.001   PHE B 206 
 TRP   0.008   0.001   TRP C  73 
 HIS   0.003   0.001   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4761)
  covalent geometry    : angle       0.52737 ( 6516)
  hydrogen bonds       : bond        0.05147 (   61)
  hydrogen bonds       : angle       3.73497 (  159)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3375.31 seconds
wall clock time: 58 minutes 19.57 seconds (3499.57 seconds total)