Starting phenix.real_space_refine
on Fri Aug 22 14:15:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ft7_50741/08_2025/9ft7_50741.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ft7_50741/08_2025/9ft7_50741.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ft7_50741/08_2025/9ft7_50741.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ft7_50741/08_2025/9ft7_50741.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ft7_50741/08_2025/9ft7_50741.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ft7_50741/08_2025/9ft7_50741.cif"
  }
  resolution = 3.16
  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=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     S      22      5.16       5
     C    2656      2.51       5
     N     652      2.21       5
     O     684      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4016
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1987
          Classifications: {'peptide': 258}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 253}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 61
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 22
          Unusual residues: {'  K': 2, 'EIC': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.36, per 1000 atoms: 0.34
  Number of scatterers: 4016
  At special positions: 0
  Unit cell: (80.704, 69.056, 93.184, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       2     19.00
     S      22     16.00
     O     684      8.00
     N     652      7.00
     C    2656      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: 0.28
  Conformation dependent library (CDL) restraints added in 135.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  960

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      82.4% 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 14 through 64
      removed outlier: 3.746A  pdb=" N   ALA A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A  43 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   ALA A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   HIS A  45 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 84
    Processing helix  chain 'A' and resid 96 through 109
    Processing helix  chain 'A' and resid 120 through 164
      removed outlier: 3.519A  pdb=" N   ILE A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE A 129 " --> pdb=" O   ILE A 125 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU A 132 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 221
      Proline residue:  A 218  - end of helix
    Processing helix  chain 'A' and resid 223 through 236
    Processing helix  chain 'A' and resid 253 through 294
    Processing helix  chain 'B' and resid 15 through 64
      removed outlier: 3.746A  pdb=" N   ALA B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU B  43 " --> pdb=" O   SER B  39 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   ALA B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   HIS B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 84
    Processing helix  chain 'B' and resid 96 through 109
    Processing helix  chain 'B' and resid 120 through 164
      removed outlier: 3.519A  pdb=" N   ILE B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   PHE B 129 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 221
      Proline residue:  B 218  - end of helix
    Processing helix  chain 'B' and resid 223 through 236
    Processing helix  chain 'B' and resid 253 through 294

    347 hydrogen bonds defined for protein.
    1041 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: 0.64

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1234
        1.34 -     1.46: 709
        1.46 -     1.57: 2137
        1.57 -     1.69: 0
        1.69 -     1.80: 30
  Bond restraints: 4110
  Sorted by residual:
  bond pdb=" CB  THR A 116 "
       pdb=" CG2 THR A 116 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.44e+00
  bond pdb=" CB  THR B 116 "
       pdb=" CG2 THR B 116 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.44e+00
  bond pdb=" CB  THR B 138 "
       pdb=" CG2 THR B 138 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.38e+00
  bond pdb=" CB  THR A 138 "
       pdb=" CG2 THR A 138 "
    ideal  model  delta    sigma   weight residual
    1.521  1.482  0.039 3.30e-02 9.18e+02 1.36e+00
  bond pdb=" C1  EIC B 401 "
       pdb=" C2  EIC B 401 "
    ideal  model  delta    sigma   weight residual
    1.539  1.516  0.023 2.00e-02 2.50e+03 1.28e+00
  ... (remaining 4105 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 4990
        1.01 -     2.02: 480
        2.02 -     3.02: 78
        3.02 -     4.03: 22
        4.03 -     5.04: 2
  Bond angle restraints: 5572
  Sorted by residual:
  angle pdb=" N   GLU B  42 "
        pdb=" CA  GLU B  42 "
        pdb=" C   GLU B  42 "
      ideal   model   delta    sigma   weight residual
     112.54  115.62   -3.08 1.51e+00 4.39e-01 4.15e+00
  angle pdb=" N   GLU A  42 "
        pdb=" CA  GLU A  42 "
        pdb=" C   GLU A  42 "
      ideal   model   delta    sigma   weight residual
     112.54  115.62   -3.08 1.51e+00 4.39e-01 4.15e+00
  angle pdb=" C   PHE A 142 "
        pdb=" N   ASN A 143 "
        pdb=" CA  ASN A 143 "
      ideal   model   delta    sigma   weight residual
     120.68  117.29    3.39 1.70e+00 3.46e-01 3.97e+00
  angle pdb=" C   PHE B 142 "
        pdb=" N   ASN B 143 "
        pdb=" CA  ASN B 143 "
      ideal   model   delta    sigma   weight residual
     120.68  117.31    3.37 1.70e+00 3.46e-01 3.92e+00
  angle pdb=" N   THR A 138 "
        pdb=" CA  THR A 138 "
        pdb=" C   THR A 138 "
      ideal   model   delta    sigma   weight residual
     111.36  113.48   -2.12 1.09e+00 8.42e-01 3.80e+00
  ... (remaining 5567 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    16.36: 2182
       16.36 -    32.72: 128
       32.72 -    49.08: 24
       49.08 -    65.44: 6
       65.44 -    81.80: 2
  Dihedral angle restraints: 2342
    sinusoidal: 844
      harmonic: 1498
  Sorted by residual:
  dihedral pdb=" CA  TRP A  95 "
           pdb=" C   TRP A  95 "
           pdb=" N   ASP A  96 "
           pdb=" CA  ASP A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.35   23.65     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  TRP B  95 "
           pdb=" C   TRP B  95 "
           pdb=" N   ASP B  96 "
           pdb=" CA  ASP B  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.39   23.61     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  GLU B  42 "
           pdb=" C   GLU B  42 "
           pdb=" N   LEU B  43 "
           pdb=" CA  LEU B  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.61   21.39     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 2339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 323
       0.032 -    0.064: 231
       0.064 -    0.096: 64
       0.096 -    0.128: 14
       0.128 -    0.160: 6
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" CA  THR A 217 "
            pdb=" N   THR A 217 "
            pdb=" C   THR A 217 "
            pdb=" CB  THR A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  THR B 217 "
            pdb=" N   THR B 217 "
            pdb=" C   THR B 217 "
            pdb=" CB  THR B 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  THR A 110 "
            pdb=" N   THR A 110 "
            pdb=" C   THR A 110 "
            pdb=" CB  THR A 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.96e-01
  ... (remaining 635 not shown)

  Planarity restraints: 690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 139 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.45e+00
        pdb=" C   ILE A 139 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A 139 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A 140 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 139 "   -0.012 2.00e-02 2.50e+03   2.34e-02 5.45e+00
        pdb=" C   ILE B 139 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ILE B 139 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU B 140 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 270 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.16e+00
        pdb=" C   CYS B 270 "    0.039 2.00e-02 2.50e+03
        pdb=" O   CYS B 270 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   CYS B 271 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 687 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.88: 1539
        2.88 -     3.45: 4651
        3.45 -     4.01: 7541
        4.01 -     4.58: 11069
        4.58 -     5.14: 15538
  Nonbonded interactions: 40338
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  78 "
            pdb=" OE2 GLU B  79 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OE2 GLU A  79 "
            pdb=" OH  TYR B  78 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OH  TYR A 216 "
            pdb=" OD1 ASN A 261 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" OH  TYR B 216 "
            pdb=" OD1 ASN B 261 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" NH1 ARG A  94 "
            pdb=" OE1 GLN A 247 "
     model   vdw
     2.384 3.120
  ... (remaining 40333 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 14 through 401)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.830
  Find NCS groups from input model:        0.060
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
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      :  0.006   0.040   4110  Z= 0.261
  Angle     :  0.666   5.041   5572  Z= 0.415
  Chirality :  0.045   0.160    638
  Planarity :  0.006   0.029    690
  Dihedral  : 11.556  81.805   1382
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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:  1.52 (0.34), residues: 508
  helix:  1.31 (0.23), residues: 416
  sheet:  None (None), residues: 0
  loop : -0.10 (0.63), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  87 
 TYR   0.019   0.004   TYR B 251 
 PHE   0.020   0.002   PHE B  38 
 TRP   0.029   0.004   TRP A  53 
 HIS   0.004   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 4110)
  covalent geometry    : angle       0.66575 ( 5572)
  hydrogen bonds       : bond        0.12492 (  347)
  hydrogen bonds       : angle       5.03666 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  198 MET cc_start: 0.7665 (ttp) cc_final: 0.7320 (ttt)
REVERT: B  198 MET cc_start: 0.7675 (ttp) cc_final: 0.7329 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0739
  time to fit residues: 2.8784
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
B 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.159043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.119490 restraints weight = 4353.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.29
r_work: 0.3288 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4110  Z= 0.146
  Angle     :  0.463   5.739   5572  Z= 0.261
  Chirality :  0.035   0.154    638
  Planarity :  0.003   0.024    690
  Dihedral  :  6.733  55.552    592
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 0.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  3.54 %
    Favored  : 95.96 %
  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:  4.16 (0.35), residues: 508
  helix:  3.16 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.51 (0.69), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.011   0.001   TYR B 251 
 PHE   0.008   0.001   PHE A 232 
 TRP   0.010   0.001   TRP B  53 
 HIS   0.003   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4110)
  covalent geometry    : angle       0.46262 ( 5572)
  hydrogen bonds       : bond        0.04673 (  347)
  hydrogen bonds       : angle       3.21369 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.7084 (tt0) cc_final: 0.6726 (mt-10)
REVERT: A  198 MET cc_start: 0.7034 (ttp) cc_final: 0.6690 (ttt)
REVERT: B   80 GLU cc_start: 0.7086 (tt0) cc_final: 0.6739 (mt-10)
REVERT: B  198 MET cc_start: 0.7044 (ttp) cc_final: 0.6700 (ttt)
  outliers start: 2
  outliers final: 2
  residues processed: 25
  average time/residue: 0.0595
  time to fit residues: 2.0600
Evaluate side-chains
  21 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 31 optimal weight:    0.1980
   chunk 26 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 247 GLN
A 250 HIS
B 247 GLN
B 250 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.159831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.119132 restraints weight = 4203.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.36
r_work: 0.3258 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4110  Z= 0.120
  Angle     :  0.410   5.040   5572  Z= 0.229
  Chirality :  0.034   0.150    638
  Planarity :  0.003   0.027    690
  Dihedral  :  6.608  55.641    592
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  3.28 %
    Favored  : 95.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.86 (0.36), residues: 508
  helix:  3.60 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  1.02 (0.71), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  94 
 TYR   0.009   0.001   TYR A 229 
 PHE   0.007   0.001   PHE B 232 
 TRP   0.005   0.001   TRP A  53 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4110)
  covalent geometry    : angle       0.40974 ( 5572)
  hydrogen bonds       : bond        0.04124 (  347)
  hydrogen bonds       : angle       2.92446 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.6883 (tt0) cc_final: 0.6602 (mt-10)
REVERT: A  198 MET cc_start: 0.6857 (ttp) cc_final: 0.6520 (ttt)
REVERT: B   80 GLU cc_start: 0.6874 (tt0) cc_final: 0.6596 (mt-10)
REVERT: B  198 MET cc_start: 0.6865 (ttp) cc_final: 0.6527 (ttt)
  outliers start: 6
  outliers final: 4
  residues processed: 28
  average time/residue: 0.0446
  time to fit residues: 1.9405
Evaluate side-chains
  28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   chunk 43 optimal weight:    0.0970
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
B 250 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.160331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.119330 restraints weight = 4157.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.35
r_work: 0.3263 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4110  Z= 0.115
  Angle     :  0.391   4.954   5572  Z= 0.221
  Chirality :  0.033   0.141    638
  Planarity :  0.002   0.027    690
  Dihedral  :  6.598  55.779    592
  Min Nonbonded Distance : 2.668

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  4.80 %
    Favored  : 93.94 %
  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:  4.97 (0.36), residues: 508
  helix:  3.72 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.86 (0.69), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  94 
 TYR   0.008   0.001   TYR A 229 
 PHE   0.007   0.001   PHE B 232 
 TRP   0.003   0.001   TRP A 289 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4110)
  covalent geometry    : angle       0.39147 ( 5572)
  hydrogen bonds       : bond        0.03963 (  347)
  hydrogen bonds       : angle       2.83474 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.6855 (tt0) cc_final: 0.6573 (mt-10)
REVERT: A  198 MET cc_start: 0.6913 (ttp) cc_final: 0.6571 (ttt)
REVERT: B   80 GLU cc_start: 0.6837 (tt0) cc_final: 0.6566 (mt-10)
REVERT: B  198 MET cc_start: 0.6921 (ttp) cc_final: 0.6579 (ttt)
  outliers start: 5
  outliers final: 4
  residues processed: 25
  average time/residue: 0.0818
  time to fit residues: 2.7439
Evaluate side-chains
  26 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 49 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 247 GLN
B 247 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.159123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.118010 restraints weight = 4214.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.35
r_work: 0.3244 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4110  Z= 0.124
  Angle     :  0.398   4.846   5572  Z= 0.222
  Chirality :  0.033   0.147    638
  Planarity :  0.002   0.027    690
  Dihedral  :  6.647  55.731    592
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 1.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  4.55 %
    Favored  : 92.93 %
  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:  4.98 (0.36), residues: 508
  helix:  3.73 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.78 (0.70), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.009   0.001   TYR A 229 
 PHE   0.008   0.001   PHE A 232 
 TRP   0.003   0.001   TRP A 289 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4110)
  covalent geometry    : angle       0.39772 ( 5572)
  hydrogen bonds       : bond        0.04051 (  347)
  hydrogen bonds       : angle       2.84258 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.6823 (tt0) cc_final: 0.6536 (mt-10)
REVERT: A  198 MET cc_start: 0.6879 (ttp) cc_final: 0.6556 (ttt)
REVERT: B   80 GLU cc_start: 0.6819 (tt0) cc_final: 0.6534 (mt-10)
REVERT: B  198 MET cc_start: 0.6897 (ttp) cc_final: 0.6574 (ttt)
  outliers start: 10
  outliers final: 8
  residues processed: 30
  average time/residue: 0.0783
  time to fit residues: 3.1022
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.158806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.117479 restraints weight = 4276.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.36
r_work: 0.3247 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4110  Z= 0.132
  Angle     :  0.404   4.884   5572  Z= 0.225
  Chirality :  0.034   0.151    638
  Planarity :  0.003   0.026    690
  Dihedral  :  6.708  56.234    592
  Min Nonbonded Distance : 2.666

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  4.55 %
    Favored  : 92.93 %
  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:  4.97 (0.36), residues: 508
  helix:  3.74 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.68 (0.69), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  62 
 TYR   0.009   0.001   TYR A 229 
 PHE   0.008   0.001   PHE A 232 
 TRP   0.003   0.001   TRP A 289 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4110)
  covalent geometry    : angle       0.40418 ( 5572)
  hydrogen bonds       : bond        0.04121 (  347)
  hydrogen bonds       : angle       2.85481 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.6908 (tt0) cc_final: 0.6578 (mt-10)
REVERT: A  198 MET cc_start: 0.6977 (ttp) cc_final: 0.6644 (ttt)
REVERT: B   80 GLU cc_start: 0.6891 (tt0) cc_final: 0.6568 (mt-10)
REVERT: B  198 MET cc_start: 0.6978 (ttp) cc_final: 0.6646 (ttt)
  outliers start: 10
  outliers final: 8
  residues processed: 30
  average time/residue: 0.0703
  time to fit residues: 2.7028
Evaluate side-chains
  29 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 247 GLN
B 247 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.158759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.117394 restraints weight = 4272.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.35
r_work: 0.3238 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4110  Z= 0.134
  Angle     :  0.402   4.904   5572  Z= 0.224
  Chirality :  0.034   0.152    638
  Planarity :  0.002   0.026    690
  Dihedral  :  6.737  56.472    592
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  5.05 %
    Favored  : 92.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.95 (0.36), residues: 508
  helix:  3.73 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.65 (0.69), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  94 
 TYR   0.008   0.001   TYR A 229 
 PHE   0.008   0.001   PHE A 232 
 TRP   0.003   0.001   TRP A 289 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4110)
  covalent geometry    : angle       0.40249 ( 5572)
  hydrogen bonds       : bond        0.04132 (  347)
  hydrogen bonds       : angle       2.85335 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 21
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.6903 (tt0) cc_final: 0.6560 (mt-10)
REVERT: B   80 GLU cc_start: 0.6888 (tt0) cc_final: 0.6550 (mt-10)
  outliers start: 10
  outliers final: 8
  residues processed: 29
  average time/residue: 0.0750
  time to fit residues: 2.8591
Evaluate side-chains
  29 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0570
   chunk 43 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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 = 0.3913 r_free = 0.3913 target = 0.160635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.119256 restraints weight = 4210.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.35
r_work: 0.3269 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4110  Z= 0.110
  Angle     :  0.376   4.828   5572  Z= 0.211
  Chirality :  0.033   0.143    638
  Planarity :  0.002   0.026    690
  Dihedral  :  6.658  56.367    592
  Min Nonbonded Distance : 2.670

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  5.56 %
    Favored  : 91.92 %
  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:  5.01 (0.36), residues: 508
  helix:  3.78 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.63 (0.67), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  94 
 TYR   0.008   0.001   TYR B 229 
 PHE   0.007   0.001   PHE B 232 
 TRP   0.004   0.001   TRP A 289 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4110)
  covalent geometry    : angle       0.37639 ( 5572)
  hydrogen bonds       : bond        0.03846 (  347)
  hydrogen bonds       : angle       2.75928 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.6896 (tt0) cc_final: 0.6559 (mt-10)
REVERT: B   80 GLU cc_start: 0.6892 (tt0) cc_final: 0.6559 (mt-10)
  outliers start: 10
  outliers final: 8
  residues processed: 30
  average time/residue: 0.0787
  time to fit residues: 3.0889
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 46 optimal weight:    0.2980
   chunk 29 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.159110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.117625 restraints weight = 4269.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.37
r_work: 0.3248 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4110  Z= 0.127
  Angle     :  0.394   4.823   5572  Z= 0.220
  Chirality :  0.033   0.148    638
  Planarity :  0.002   0.025    690
  Dihedral  :  6.696  56.716    592
  Min Nonbonded Distance : 2.667

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  5.30 %
    Favored  : 92.68 %
  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:  4.98 (0.36), residues: 508
  helix:  3.77 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.57 (0.67), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.008   0.001   TYR B 229 
 PHE   0.008   0.001   PHE B 232 
 TRP   0.003   0.001   TRP B 289 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4110)
  covalent geometry    : angle       0.39380 ( 5572)
  hydrogen bonds       : bond        0.04008 (  347)
  hydrogen bonds       : angle       2.80659 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.6912 (tt0) cc_final: 0.6560 (mt-10)
REVERT: B   80 GLU cc_start: 0.6907 (tt0) cc_final: 0.6559 (mt-10)
  outliers start: 8
  outliers final: 8
  residues processed: 30
  average time/residue: 0.0659
  time to fit residues: 2.5987
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0870
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3906 r_free = 0.3906 target = 0.159868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.118552 restraints weight = 4208.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.33
r_work: 0.3261 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4110  Z= 0.118
  Angle     :  0.384   4.818   5572  Z= 0.215
  Chirality :  0.033   0.145    638
  Planarity :  0.002   0.025    690
  Dihedral  :  6.675  56.877    592
  Min Nonbonded Distance : 2.669

Molprobity Statistics.
  All-atom Clashscore : 2.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  5.05 %
    Favored  : 92.93 %
  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:  5.01 (0.36), residues: 508
  helix:  3.79 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.58 (0.67), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.008   0.001   TYR A 229 
 PHE   0.008   0.001   PHE B 232 
 TRP   0.004   0.001   TRP A 289 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 4110)
  covalent geometry    : angle       0.38420 ( 5572)
  hydrogen bonds       : bond        0.03901 (  347)
  hydrogen bonds       : angle       2.77488 ( 1041)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   80 GLU cc_start: 0.6902 (tt0) cc_final: 0.6549 (mt-10)
REVERT: B   80 GLU cc_start: 0.6895 (tt0) cc_final: 0.6546 (mt-10)
  outliers start: 8
  outliers final: 8
  residues processed: 30
  average time/residue: 0.0751
  time to fit residues: 2.9904
Evaluate side-chains
  30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 22
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain B residue   42 GLU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  272 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.159139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.117649 restraints weight = 4225.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.34
r_work: 0.3250 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4110  Z= 0.127
  Angle     :  0.394   4.829   5572  Z= 0.220
  Chirality :  0.033   0.148    638
  Planarity :  0.002   0.025    690
  Dihedral  :  6.714  56.976    592
  Min Nonbonded Distance : 2.667

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  4.80 %
    Favored  : 93.18 %
  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:  4.99 (0.36), residues: 508
  helix:  3.78 (0.23), residues: 420
  sheet:  None (None), residues: 0
  loop :  0.56 (0.67), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.008   0.001   TYR A 229 
 PHE   0.008   0.001   PHE A 232 
 TRP   0.003   0.001   TRP A 289 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4110)
  covalent geometry    : angle       0.39438 ( 5572)
  hydrogen bonds       : bond        0.04016 (  347)
  hydrogen bonds       : angle       2.80475 ( 1041)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1004.97 seconds
wall clock time: 17 minutes 57.10 seconds (1077.10 seconds total)