Starting phenix.real_space_refine
on Wed Sep 17 04:11:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g2w_50986/09_2025/9g2w_50986.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g2w_50986/09_2025/9g2w_50986.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g2w_50986/09_2025/9g2w_50986.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g2w_50986/09_2025/9g2w_50986.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g2w_50986/09_2025/9g2w_50986.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g2w_50986/09_2025/9g2w_50986.map"
  }
  resolution = 3.6
  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    2404      2.51       5
     N     677      2.21       5
     O     741      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  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: 3838
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1939
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
    Chain: "B"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1899
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 1
  Time building chain proxies: 1.24, per 1000 atoms: 0.32
  Number of scatterers: 3838
  At special positions: 0
  Unit cell: (114.208, 83.664, 115.536, 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     741      8.00
     N     677      7.00
     C    2404      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 164.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  914

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      93.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 30
      removed outlier: 3.654A  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 84
      removed outlier: 3.578A  pdb=" N   ARG A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    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 181
      removed outlier: 4.107A  pdb=" N   TYR A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   LYS A 156 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 215
      removed outlier: 3.972A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 252
      removed outlier: 3.884A  pdb=" N   THR A 219 " --> pdb=" O   GLY A 215 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   HIS A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ALA A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 30
    Processing helix  chain 'B' and resid 39 through 68
    Processing helix  chain 'B' and resid 70 through 84
      removed outlier: 3.520A  pdb=" N   ARG B  74 " --> pdb=" O   ASN B  70 " (cutoff:3.500A)
    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
      removed outlier: 3.529A  pdb=" N   LEU B 147 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 181
      removed outlier: 3.541A  pdb=" N   THR B 157 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 215
    Processing helix  chain 'B' and resid 215 through 252

    367 hydrogen bonds defined for protein.
    1101 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: 0.59

  Time building geometry restraints manager: 0.38 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: 859
        1.33 -     1.45: 760
        1.45 -     1.57: 2248
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 3891
  Sorted by residual:
  bond pdb=" N   ILE A  91 "
       pdb=" CA  ILE A  91 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.20e-02 6.94e+03 8.44e+00
  bond pdb=" N   ILE A 216 "
       pdb=" CA  ILE A 216 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.26e-02 6.30e+03 7.96e+00
  bond pdb=" N   ASN A  93 "
       pdb=" CA  ASN A  93 "
    ideal  model  delta    sigma   weight residual
    1.462  1.488 -0.026 9.50e-03 1.11e+04 7.61e+00
  bond pdb=" N   ILE A  75 "
       pdb=" CA  ILE A  75 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.59e+00
  bond pdb=" N   ILE B 151 "
       pdb=" CA  ILE B 151 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.26e-02 6.30e+03 7.58e+00
  ... (remaining 3886 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 3763
        1.04 -     2.09: 775
        2.09 -     3.13: 652
        3.13 -     4.18: 36
        4.18 -     5.22: 9
  Bond angle restraints: 5235
  Sorted by residual:
  angle pdb=" N   LEU A  30 "
        pdb=" CA  LEU A  30 "
        pdb=" C   LEU A  30 "
      ideal   model   delta    sigma   weight residual
     112.87  108.08    4.79 1.20e+00 6.94e-01 1.59e+01
  angle pdb=" N   GLY A  31 "
        pdb=" CA  GLY A  31 "
        pdb=" C   GLY A  31 "
      ideal   model   delta    sigma   weight residual
     115.40  110.27    5.13 1.32e+00 5.74e-01 1.51e+01
  angle pdb=" N   GLU B 214 "
        pdb=" CA  GLU B 214 "
        pdb=" C   GLU B 214 "
      ideal   model   delta    sigma   weight residual
     113.23  108.50    4.73 1.24e+00 6.50e-01 1.45e+01
  angle pdb=" CA  ALA B 182 "
        pdb=" C   ALA B 182 "
        pdb=" O   ALA B 182 "
      ideal   model   delta    sigma   weight residual
     122.64  118.13    4.51 1.25e+00 6.40e-01 1.30e+01
  angle pdb=" N   LEU A  83 "
        pdb=" CA  LEU A  83 "
        pdb=" C   LEU A  83 "
      ideal   model   delta    sigma   weight residual
     113.01  108.81    4.20 1.20e+00 6.94e-01 1.23e+01
  ... (remaining 5230 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.50: 2167
       15.50 -    31.00: 169
       31.00 -    46.50: 47
       46.50 -    62.00: 30
       62.00 -    77.50: 6
  Dihedral angle restraints: 2419
    sinusoidal: 1014
      harmonic: 1405
  Sorted by residual:
  dihedral pdb=" CD  ARG B 210 "
           pdb=" NE  ARG B 210 "
           pdb=" CZ  ARG B 210 "
           pdb=" NH1 ARG B 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.61  -32.61     1      1.00e+01 1.00e-02 1.51e+01
  dihedral pdb=" CD  ARG B 169 "
           pdb=" NE  ARG B 169 "
           pdb=" CZ  ARG B 169 "
           pdb=" NH1 ARG B 169 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -27.47   27.47     1      1.00e+01 1.00e-02 1.08e+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  -26.98   26.98     1      1.00e+01 1.00e-02 1.05e+01
  ... (remaining 2416 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 271
       0.043 -    0.085: 105
       0.085 -    0.127: 124
       0.127 -    0.169: 62
       0.169 -    0.211: 28
  Chirality restraints: 590
  Sorted by residual:
  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    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ASP B 203 "
            pdb=" N   ASP B 203 "
            pdb=" C   ASP B 203 "
            pdb=" CB  ASP B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  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    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 587 not shown)

  Planarity restraints: 681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 210 "   -0.574 9.50e-02 1.11e+02   2.57e-01 4.04e+01
        pdb=" NE  ARG B 210 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 210 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 210 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 210 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 169 "   -0.493 9.50e-02 1.11e+02   2.21e-01 2.99e+01
        pdb=" NE  ARG B 169 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 169 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 169 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 169 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 225 "    0.487 9.50e-02 1.11e+02   2.18e-01 2.92e+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
  ... (remaining 678 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1456
        2.86 -     3.37: 4479
        3.37 -     3.88: 6652
        3.88 -     4.39: 7661
        4.39 -     4.90: 11287
  Nonbonded interactions: 31535
  Sorted by model distance:
  nonbonded pdb=" O   SER B 200 "
            pdb=" OD1 ASP B 203 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   LEU B 195 "
            pdb=" OG1 THR B 198 "
     model   vdw
     2.399 3.040
  nonbonded pdb=" NE2 GLN A 243 "
            pdb=" OD1 ASP A 247 "
     model   vdw
     2.399 3.120
  nonbonded pdb=" O   ASP A  14 "
            pdb=" OG1 THR A  17 "
     model   vdw
     2.414 3.040
  nonbonded pdb=" N   GLU A 186 "
            pdb=" OE1 GLU A 186 "
     model   vdw
     2.419 3.120
  ... (remaining 31530 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' and (resid 13 through 30 or resid 35 through 252))
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.500
  Find NCS groups from input model:        0.040
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
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      :  0.009   0.044   3891  Z= 0.679
  Angle     :  1.167   5.221   5235  Z= 0.968
  Chirality :  0.084   0.211    590
  Planarity :  0.024   0.257    681
  Dihedral  : 14.466  77.496   1505
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  5.11 %
    Favored  : 94.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.34), residues: 472
  helix: -0.00 (0.22), residues: 430
  sheet:  None (None), residues: 0
  loop : -1.86 (0.79), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.036   0.004   ARG A 127 
 TYR   0.023   0.002   TYR A 244 
 PHE   0.028   0.002   PHE B  78 
 TRP   0.006   0.001   TRP A  55 
 HIS   0.007   0.002   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00876 ( 3891)
  covalent geometry    : angle       1.16673 ( 5235)
  hydrogen bonds       : bond        0.15286 (  367)
  hydrogen bonds       : angle       6.46360 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8484 (tm-30)
REVERT: B  235 MET cc_start: 0.8855 (tmm) cc_final: 0.8616 (tmm)
  outliers start: 3
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0673
  time to fit residues: 6.5570
Evaluate side-chains
  43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 228 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.060791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.047475 restraints weight = 18568.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.049046 restraints weight = 8354.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.050034 restraints weight = 5009.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.050556 restraints weight = 3654.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.050706 restraints weight = 3100.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3891  Z= 0.158
  Angle     :  0.535  10.207   5235  Z= 0.292
  Chirality :  0.033   0.124    590
  Planarity :  0.004   0.032    681
  Dihedral  :  2.991  12.231    521
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  9.49 %
    Favored  : 88.81 %
  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:  4.53 (0.34), residues: 472
  helix:  3.20 (0.22), residues: 435
  sheet:  None (None), residues: 0
  loop : -0.22 (0.88), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 188 
 TYR   0.016   0.001   TYR B 238 
 PHE   0.021   0.002   PHE B  78 
 TRP   0.007   0.001   TRP A  55 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3891)
  covalent geometry    : angle       0.53520 ( 5235)
  hydrogen bonds       : bond        0.06932 (  367)
  hydrogen bonds       : angle       3.97657 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7454 (mt-10)
REVERT: A  121 CYS cc_start: 0.8383 (t) cc_final: 0.8040 (t)
REVERT: B   64 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8455 (tm-30)
REVERT: B  125 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8570 (mp10)
REVERT: B  235 MET cc_start: 0.8995 (tmm) cc_final: 0.8631 (tmm)
REVERT: B  245 MET cc_start: 0.9290 (tpp) cc_final: 0.8974 (tpp)
  outliers start: 7
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0746
  time to fit residues: 4.9754
Evaluate side-chains
  46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  234 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 39 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 193 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.061133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.047974 restraints weight = 19064.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.049548 restraints weight = 8595.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.050577 restraints weight = 5150.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.051205 restraints weight = 3736.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.051467 restraints weight = 3107.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3891  Z= 0.141
  Angle     :  0.540   9.082   5235  Z= 0.279
  Chirality :  0.032   0.114    590
  Planarity :  0.004   0.034    681
  Dihedral  :  3.021  12.872    521
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.22 %
    Favored  : 88.08 %
  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:  5.91 (0.35), residues: 472
  helix:  4.10 (0.22), residues: 435
  sheet:  None (None), residues: 0
  loop :  0.11 (0.92), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 178 
 TYR   0.014   0.001   TYR B 238 
 PHE   0.021   0.002   PHE B  78 
 TRP   0.005   0.001   TRP B  55 
 HIS   0.009   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3891)
  covalent geometry    : angle       0.54021 ( 5235)
  hydrogen bonds       : bond        0.06105 (  367)
  hydrogen bonds       : angle       3.50583 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 CYS cc_start: 0.8324 (t) cc_final: 0.7931 (t)
REVERT: B  103 ASP cc_start: 0.8662 (t0) cc_final: 0.8176 (t0)
REVERT: B  125 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8568 (mp10)
REVERT: B  235 MET cc_start: 0.8988 (tmm) cc_final: 0.8709 (tmm)
REVERT: B  245 MET cc_start: 0.9225 (tpp) cc_final: 0.8894 (tpp)
  outliers start: 7
  outliers final: 4
  residues processed: 49
  average time/residue: 0.0631
  time to fit residues: 4.0731
Evaluate side-chains
  44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.061131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.047926 restraints weight = 19221.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.049484 restraints weight = 8773.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.050467 restraints weight = 5324.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.051012 restraints weight = 3897.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.051390 restraints weight = 3301.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3891  Z= 0.132
  Angle     :  0.510   7.499   5235  Z= 0.268
  Chirality :  0.032   0.117    590
  Planarity :  0.003   0.031    681
  Dihedral  :  3.017  12.285    521
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.68 %
    Favored  : 86.37 %
  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:  6.23 (0.35), residues: 472
  helix:  4.30 (0.22), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.34 (0.90), residues: 38

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 225 
 TYR   0.012   0.001   TYR B 242 
 PHE   0.024   0.002   PHE A  25 
 TRP   0.005   0.001   TRP B  55 
 HIS   0.009   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3891)
  covalent geometry    : angle       0.51048 ( 5235)
  hydrogen bonds       : bond        0.05692 (  367)
  hydrogen bonds       : angle       3.29697 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 CYS cc_start: 0.8446 (t) cc_final: 0.8046 (t)
REVERT: A  179 LEU cc_start: 0.9338 (tt) cc_final: 0.8980 (pp)
REVERT: B  125 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8592 (mp10)
REVERT: B  235 MET cc_start: 0.8915 (tmm) cc_final: 0.8645 (tmm)
REVERT: B  245 MET cc_start: 0.9223 (tpp) cc_final: 0.8902 (tpp)
  outliers start: 8
  outliers final: 7
  residues processed: 45
  average time/residue: 0.0662
  time to fit residues: 3.9097
Evaluate side-chains
  44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.060975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.047854 restraints weight = 19226.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.049385 restraints weight = 8778.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.050375 restraints weight = 5339.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.050909 restraints weight = 3897.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.051303 restraints weight = 3308.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3891  Z= 0.135
  Angle     :  0.508   6.956   5235  Z= 0.265
  Chirality :  0.033   0.117    590
  Planarity :  0.003   0.030    681
  Dihedral  :  3.089  15.359    521
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 10.95 %
    Favored  : 86.62 %
  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:  6.17 (0.35), residues: 472
  helix:  4.27 (0.22), residues: 435
  sheet:  None (None), residues: 0
  loop :  0.14 (0.91), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 225 
 TYR   0.023   0.001   TYR B 242 
 PHE   0.021   0.002   PHE A  25 
 TRP   0.005   0.001   TRP B  55 
 HIS   0.017   0.002   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3891)
  covalent geometry    : angle       0.50813 ( 5235)
  hydrogen bonds       : bond        0.05704 (  367)
  hydrogen bonds       : angle       3.29642 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 CYS cc_start: 0.8512 (t) cc_final: 0.8069 (t)
REVERT: A  179 LEU cc_start: 0.9417 (tt) cc_final: 0.9120 (pp)
REVERT: A  235 MET cc_start: 0.9025 (tpp) cc_final: 0.8531 (tmm)
REVERT: B  103 ASP cc_start: 0.8710 (t0) cc_final: 0.8116 (t0)
REVERT: B  125 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8582 (mp10)
REVERT: B  235 MET cc_start: 0.8963 (tmm) cc_final: 0.8675 (tmm)
REVERT: B  245 MET cc_start: 0.9216 (tpp) cc_final: 0.8814 (tpp)
  outliers start: 10
  outliers final: 6
  residues processed: 43
  average time/residue: 0.0678
  time to fit residues: 3.8322
Evaluate side-chains
  43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.061245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.048077 restraints weight = 19413.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.049585 restraints weight = 8878.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.050576 restraints weight = 5419.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.051202 restraints weight = 3970.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.051338 restraints weight = 3304.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3891  Z= 0.129
  Angle     :  0.506   8.148   5235  Z= 0.263
  Chirality :  0.032   0.116    590
  Planarity :  0.003   0.029    681
  Dihedral  :  3.112  17.122    521
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.44 %
    Favored  : 86.13 %
  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:  6.23 (0.35), residues: 472
  helix:  4.30 (0.22), residues: 435
  sheet:  None (None), residues: 0
  loop :  0.29 (0.93), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 225 
 TYR   0.020   0.001   TYR B 242 
 PHE   0.014   0.002   PHE A  25 
 TRP   0.006   0.001   TRP B  55 
 HIS   0.007   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 3891)
  covalent geometry    : angle       0.50587 ( 5235)
  hydrogen bonds       : bond        0.05470 (  367)
  hydrogen bonds       : angle       3.23405 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 CYS cc_start: 0.8492 (t) cc_final: 0.8049 (t)
REVERT: A  179 LEU cc_start: 0.9399 (tt) cc_final: 0.9124 (pp)
REVERT: A  235 MET cc_start: 0.9039 (tpp) cc_final: 0.8452 (tmm)
REVERT: B  125 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8643 (mp10)
REVERT: B  235 MET cc_start: 0.8911 (tmm) cc_final: 0.8659 (tmm)
REVERT: B  245 MET cc_start: 0.9191 (tpp) cc_final: 0.8795 (tpp)
  outliers start: 10
  outliers final: 5
  residues processed: 46
  average time/residue: 0.0666
  time to fit residues: 4.0268
Evaluate side-chains
  44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.061044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.047592 restraints weight = 19883.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.049207 restraints weight = 9124.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.050235 restraints weight = 5552.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.050831 restraints weight = 4064.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.051077 restraints weight = 3390.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3891  Z= 0.129
  Angle     :  0.524   7.637   5235  Z= 0.267
  Chirality :  0.033   0.152    590
  Planarity :  0.003   0.028    681
  Dihedral  :  3.114  17.188    521
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.90 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  6.23 (0.35), residues: 472
  helix:  4.30 (0.22), residues: 435
  sheet:  None (None), residues: 0
  loop :  0.34 (0.95), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 225 
 TYR   0.018   0.001   TYR B 242 
 PHE   0.013   0.002   PHE A  25 
 TRP   0.006   0.001   TRP B  55 
 HIS   0.003   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 3891)
  covalent geometry    : angle       0.52422 ( 5235)
  hydrogen bonds       : bond        0.05373 (  367)
  hydrogen bonds       : angle       3.23088 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 CYS cc_start: 0.8406 (t) cc_final: 0.8155 (t)
REVERT: A  235 MET cc_start: 0.9081 (tpp) cc_final: 0.8438 (tmm)
REVERT: B   58 LYS cc_start: 0.9457 (mttt) cc_final: 0.9244 (mtmt)
REVERT: B  103 ASP cc_start: 0.8833 (t0) cc_final: 0.8173 (t0)
REVERT: B  125 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8602 (mp10)
REVERT: B  235 MET cc_start: 0.8889 (tmm) cc_final: 0.8633 (tmm)
REVERT: B  245 MET cc_start: 0.9221 (tpp) cc_final: 0.8821 (tpp)
  outliers start: 8
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0658
  time to fit residues: 4.1926
Evaluate side-chains
  44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.060761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.047393 restraints weight = 19965.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.048975 restraints weight = 9120.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.049965 restraints weight = 5596.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.050589 restraints weight = 4141.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.050785 restraints weight = 3456.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3891  Z= 0.135
  Angle     :  0.558   9.382   5235  Z= 0.279
  Chirality :  0.034   0.145    590
  Planarity :  0.003   0.027    681
  Dihedral  :  3.161  17.690    521
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.60 %
    Favored  : 83.94 %
  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:  6.19 (0.35), residues: 472
  helix:  4.27 (0.22), residues: 435
  sheet:  None (None), residues: 0
  loop :  0.38 (0.95), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 225 
 TYR   0.018   0.001   TYR B 242 
 PHE   0.015   0.002   PHE A  25 
 TRP   0.006   0.001   TRP B  55 
 HIS   0.003   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3891)
  covalent geometry    : angle       0.55827 ( 5235)
  hydrogen bonds       : bond        0.05442 (  367)
  hydrogen bonds       : angle       3.27018 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 CYS cc_start: 0.8417 (t) cc_final: 0.8177 (t)
REVERT: A  179 LEU cc_start: 0.9379 (tt) cc_final: 0.9023 (pp)
REVERT: A  235 MET cc_start: 0.9068 (tpp) cc_final: 0.8462 (tmm)
REVERT: B  125 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8574 (mp10)
  outliers start: 6
  outliers final: 5
  residues processed: 44
  average time/residue: 0.0670
  time to fit residues: 3.8610
Evaluate side-chains
  43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.2386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.059797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.046736 restraints weight = 19780.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.048183 restraints weight = 9246.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.049096 restraints weight = 5705.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 15)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.049524 restraints weight = 4234.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.049742 restraints weight = 3647.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3891  Z= 0.159
  Angle     :  0.602   9.839   5235  Z= 0.304
  Chirality :  0.034   0.130    590
  Planarity :  0.003   0.027    681
  Dihedral  :  3.204  17.811    521
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.87 %
    Favored  : 84.43 %
  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:  6.02 (0.35), residues: 472
  helix:  4.16 (0.22), residues: 435
  sheet:  None (None), residues: 0
  loop :  0.32 (0.96), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 225 
 TYR   0.018   0.002   TYR B 242 
 PHE   0.014   0.002   PHE B 150 
 TRP   0.004   0.001   TRP A  55 
 HIS   0.010   0.002   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3891)
  covalent geometry    : angle       0.60241 ( 5235)
  hydrogen bonds       : bond        0.05836 (  367)
  hydrogen bonds       : angle       3.41127 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 CYS cc_start: 0.8592 (t) cc_final: 0.8337 (t)
REVERT: A  179 LEU cc_start: 0.9370 (tt) cc_final: 0.8955 (pp)
REVERT: A  235 MET cc_start: 0.9014 (tpp) cc_final: 0.8418 (tmm)
REVERT: B  103 ASP cc_start: 0.8803 (t0) cc_final: 0.8252 (t0)
REVERT: B  125 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8687 (mp10)
REVERT: B  245 MET cc_start: 0.9144 (tpp) cc_final: 0.8844 (tpp)
REVERT: B  248 LEU cc_start: 0.8712 (tt) cc_final: 0.8417 (tt)
  outliers start: 7
  outliers final: 6
  residues processed: 43
  average time/residue: 0.0600
  time to fit residues: 3.5013
Evaluate side-chains
  44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue   41 HIS
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  190 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0570
   chunk 11 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0870
   overall best weight:    0.4276

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.061924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.048540 restraints weight = 20059.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.050141 restraints weight = 9194.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.051192 restraints weight = 5597.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.051741 restraints weight = 4088.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.052068 restraints weight = 3452.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.4788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   3891  Z= 0.131
  Angle     :  0.596   9.729   5235  Z= 0.293
  Chirality :  0.033   0.159    590
  Planarity :  0.003   0.028    681
  Dihedral  :  3.173  17.898    521
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 14.36 %
    Favored  : 84.67 %
  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:  6.26 (0.35), residues: 472
  helix:  4.33 (0.22), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.27 (0.91), residues: 38

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.020   0.002   TYR A 244 
 PHE   0.017   0.001   PHE A  25 
 TRP   0.006   0.001   TRP A  55 
 HIS   0.013   0.001   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 3891)
  covalent geometry    : angle       0.59594 ( 5235)
  hydrogen bonds       : bond        0.05128 (  367)
  hydrogen bonds       : angle       3.17262 ( 1101)

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

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

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  944 Ramachandran restraints generated.
    472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 CYS cc_start: 0.8306 (t) cc_final: 0.8106 (t)
REVERT: A  235 MET cc_start: 0.9063 (tpp) cc_final: 0.8398 (tmm)
REVERT: B  125 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8673 (mp10)
REVERT: B  245 MET cc_start: 0.9158 (tpp) cc_final: 0.8918 (tpp)
  outliers start: 4
  outliers final: 3
  residues processed: 45
  average time/residue: 0.0730
  time to fit residues: 4.2529
Evaluate side-chains
  45 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain B residue   41 HIS
Chi-restraints excluded: chain B residue  125 GLN
Chi-restraints excluded: chain B residue  165 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   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  41 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 = 0.3569 r_free = 0.3569 target = 0.061256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.048065 restraints weight = 20057.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.049629 restraints weight = 9178.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.050645 restraints weight = 5649.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.051221 restraints weight = 4162.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.051460 restraints weight = 3486.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.4853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3891  Z= 0.137
  Angle     :  0.615   9.311   5235  Z= 0.308
  Chirality :  0.034   0.182    590
  Planarity :  0.003   0.028    681
  Dihedral  :  3.170  18.014    521
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 14.11 %
    Favored  : 84.67 %
  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:  6.07 (0.35), residues: 472
  helix:  4.20 (0.22), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.28 (0.92), residues: 38

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.043   0.002   TYR A 244 
 PHE   0.016   0.001   PHE A  25 
 TRP   0.005   0.001   TRP A  55 
 HIS   0.013   0.002   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3891)
  covalent geometry    : angle       0.61509 ( 5235)
  hydrogen bonds       : bond        0.05218 (  367)
  hydrogen bonds       : angle       3.26713 ( 1101)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 901.39 seconds
wall clock time: 16 minutes 15.73 seconds (975.73 seconds total)