Starting phenix.real_space_refine
on Fri Aug 22 13:47:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eqj_28538/08_2025/8eqj_28538_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eqj_28538/08_2025/8eqj_28538.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eqj_28538/08_2025/8eqj_28538.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eqj_28538/08_2025/8eqj_28538.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eqj_28538/08_2025/8eqj_28538_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eqj_28538/08_2025/8eqj_28538_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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
     P       4      5.49       5
     S      16      5.16       5
     C    2140      2.51       5
     N     492      2.21       5
     O     580      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: 3232
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1571
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 4, 'TRANS': 187}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'PEE': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 57
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.21, per 1000 atoms: 0.37
  Number of scatterers: 3232
  At special positions: 0
  Unit cell: (64.988, 61.612, 91.152, 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)
     S      16     16.00
     P       4     15.00
     O     580      8.00
     N     492      7.00
     C    2140      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 114.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  732

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 4 sheets defined
      49.5% alpha, 21.9% 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 43 through 61
      removed outlier: 3.592A  pdb=" N   LYS A  61 " --> pdb=" O   GLN A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 100
    Processing helix  chain 'A' and resid 105 through 134
    Processing helix  chain 'A' and resid 136 through 141
      removed outlier: 3.598A  pdb=" N   LEU A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 224
    Processing helix  chain 'B' and resid 43 through 61
      removed outlier: 3.591A  pdb=" N   LYS B  61 " --> pdb=" O   GLN B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 100
    Processing helix  chain 'B' and resid 105 through 134
    Processing helix  chain 'B' and resid 136 through 141
      removed outlier: 3.598A  pdb=" N   LEU B 140 " --> pdb=" O   LYS B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160
      removed outlier: 5.922A  pdb=" N   HIS A 150 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   CYS A 200 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   LEU A 214 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ASN A 234 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A 216 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   THR A 229 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 186
    Processing sheet with id=AA3, first strand: chain 'B' and resid 155 through 160
      removed outlier: 5.922A  pdb=" N   HIS B 150 " --> pdb=" O   CYS B 200 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   CYS B 200 " --> pdb=" O   HIS B 150 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   LEU B 214 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ASN B 234 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER B 216 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   THR B 229 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 186

    198 hydrogen bonds defined for protein.
    582 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: 0.44

  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:
        1.18 -     1.31: 470
        1.31 -     1.43: 1028
        1.43 -     1.56: 1798
        1.56 -     1.68: 8
        1.68 -     1.81: 18
  Bond restraints: 3322
  Sorted by residual:
  bond pdb=" C30 PEE A 401 "
       pdb=" O3  PEE A 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.398 -0.071 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" C30 PEE B 401 "
       pdb=" O3  PEE B 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.398 -0.071 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" C30 PEE B 402 "
       pdb=" O3  PEE B 402 "
    ideal  model  delta    sigma   weight residual
    1.327  1.398 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C30 PEE A 402 "
       pdb=" O3  PEE A 402 "
    ideal  model  delta    sigma   weight residual
    1.327  1.398 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C10 PEE B 402 "
       pdb=" O2  PEE B 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.403 -0.071 2.00e-02 2.50e+03 1.24e+01
  ... (remaining 3317 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.38: 4468
        3.38 -     6.75: 34
        6.75 -    10.13: 11
       10.13 -    13.50: 3
       13.50 -    16.88: 4
  Bond angle restraints: 4520
  Sorted by residual:
  angle pdb=" O3P PEE B 402 "
        pdb=" P   PEE B 402 "
        pdb=" O4P PEE B 402 "
      ideal   model   delta    sigma   weight residual
      92.91  109.79  -16.88 3.00e+00 1.11e-01 3.16e+01
  angle pdb=" O3P PEE A 402 "
        pdb=" P   PEE A 402 "
        pdb=" O4P PEE A 402 "
      ideal   model   delta    sigma   weight residual
      92.91  109.79  -16.88 3.00e+00 1.11e-01 3.16e+01
  angle pdb=" O3P PEE A 401 "
        pdb=" P   PEE A 401 "
        pdb=" O4P PEE A 401 "
      ideal   model   delta    sigma   weight residual
      92.91  109.75  -16.84 3.00e+00 1.11e-01 3.15e+01
  angle pdb=" O3P PEE B 401 "
        pdb=" P   PEE B 401 "
        pdb=" O4P PEE B 401 "
      ideal   model   delta    sigma   weight residual
      92.91  109.74  -16.83 3.00e+00 1.11e-01 3.15e+01
  angle pdb=" O1P PEE A 402 "
        pdb=" P   PEE A 402 "
        pdb=" O2P PEE A 402 "
      ideal   model   delta    sigma   weight residual
     119.43  109.11   10.32 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 4515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.91: 1826
       34.91 -    69.82: 36
       69.82 -   104.73: 16
      104.73 -   139.64: 10
      139.64 -   174.54: 10
  Dihedral angle restraints: 1898
    sinusoidal: 754
      harmonic: 1144
  Sorted by residual:
  dihedral pdb=" C3  PEE A 401 "
           pdb=" C1  PEE A 401 "
           pdb=" C2  PEE A 401 "
           pdb=" O3P PEE A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73 -111.81  174.54     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C3  PEE B 401 "
           pdb=" C1  PEE B 401 "
           pdb=" C2  PEE B 401 "
           pdb=" O3P PEE B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73 -111.79  174.52     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O2  PEE B 401 "
           pdb=" C1  PEE B 401 "
           pdb=" C2  PEE B 401 "
           pdb=" O3P PEE B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.04  129.14  170.90     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 1895 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 362
       0.037 -    0.073: 100
       0.073 -    0.110: 36
       0.110 -    0.146: 2
       0.146 -    0.183: 6
  Chirality restraints: 506
  Sorted by residual:
  chirality pdb=" C2  PEE A 401 "
            pdb=" C1  PEE A 401 "
            pdb=" C3  PEE A 401 "
            pdb=" O2  PEE A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.51    0.18 2.00e-01 2.50e+01 8.36e-01
  chirality pdb=" C2  PEE B 401 "
            pdb=" C1  PEE B 401 "
            pdb=" C3  PEE B 401 "
            pdb=" O2  PEE B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.51    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" C2  PEE B 402 "
            pdb=" C1  PEE B 402 "
            pdb=" C3  PEE B 402 "
            pdb=" O2  PEE B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.50    0.17 2.00e-01 2.50e+01 7.16e-01
  ... (remaining 503 not shown)

  Planarity restraints: 534
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  87 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.47e+00
        pdb=" C   PHE A  87 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   PHE A  87 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A  88 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  87 "   -0.009 2.00e-02 2.50e+03   1.86e-02 3.47e+00
        pdb=" C   PHE B  87 "    0.032 2.00e-02 2.50e+03
        pdb=" O   PHE B  87 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL B  88 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  84 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.38e+00
        pdb=" C   LEU B  84 "    0.027 2.00e-02 2.50e+03
        pdb=" O   LEU B  84 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU B  85 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 531 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 433
        2.75 -     3.29: 3209
        3.29 -     3.83: 5428
        3.83 -     4.36: 6101
        4.36 -     4.90: 10714
  Nonbonded interactions: 25885
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 151 "
            pdb=" O   TYR A 154 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG1 THR B 151 "
            pdb=" O   TYR B 154 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG  SER A 205 "
            pdb=" O   THR A 208 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OG  SER B 205 "
            pdb=" O   THR B 208 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" ND2 ASN B 137 "
            pdb=" O   CYS B 157 "
     model   vdw
     2.309 3.120
  ... (remaining 25880 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.640
  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:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.620
  Find NCS groups from input model:        0.010
  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:8.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
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      :  0.005   0.071   3322  Z= 0.255
  Angle     :  0.940  16.875   4520  Z= 0.385
  Chirality :  0.043   0.183    506
  Planarity :  0.005   0.029    534
  Dihedral  : 24.650 174.544   1166
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.19 (0.41), residues: 376
  helix:  0.56 (0.38), residues: 174
  sheet:  0.33 (0.51), residues: 88
  loop : -1.44 (0.51), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 122 
 TYR   0.016   0.001   TYR B 107 
 PHE   0.006   0.001   PHE A 146 
 TRP   0.024   0.002   TRP B 193 
 HIS   0.001   0.000   HIS B  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 3322)
  covalent geometry    : angle       0.93972 ( 4520)
  hydrogen bonds       : bond        0.13998 (  198)
  hydrogen bonds       : angle       7.18371 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  131 TRP cc_start: 0.7835 (t60) cc_final: 0.7447 (t60)
REVERT: A  147 LEU cc_start: 0.7854 (tp) cc_final: 0.7291 (tm)
REVERT: A  154 TYR cc_start: 0.7156 (t80) cc_final: 0.6951 (t80)
REVERT: A  185 GLN cc_start: 0.8176 (pp30) cc_final: 0.7914 (pp30)
REVERT: A  192 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7848 (mtpp)
REVERT: A  198 LYS cc_start: 0.7426 (mmmm) cc_final: 0.6927 (mtpt)
REVERT: A  202 VAL cc_start: 0.7707 (m) cc_final: 0.7404 (p)
REVERT: A  210 ASP cc_start: 0.7522 (m-30) cc_final: 0.7186 (m-30)
REVERT: A  222 ASP cc_start: 0.7900 (t0) cc_final: 0.7699 (t0)
REVERT: B  131 TRP cc_start: 0.7837 (t60) cc_final: 0.7447 (t60)
REVERT: B  147 LEU cc_start: 0.7845 (tp) cc_final: 0.7282 (tm)
REVERT: B  154 TYR cc_start: 0.7138 (t80) cc_final: 0.6934 (t80)
REVERT: B  185 GLN cc_start: 0.8186 (pp30) cc_final: 0.7928 (pp30)
REVERT: B  192 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7853 (mtpp)
REVERT: B  198 LYS cc_start: 0.7415 (mmmm) cc_final: 0.6911 (mtpt)
REVERT: B  202 VAL cc_start: 0.7705 (m) cc_final: 0.7402 (p)
REVERT: B  210 ASP cc_start: 0.7518 (m-30) cc_final: 0.7182 (m-30)
REVERT: B  222 ASP cc_start: 0.7899 (t0) cc_final: 0.7698 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.2853
  time to fit residues: 29.9765
Evaluate side-chains
  60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0470
   chunk 30 optimal weight:    0.3980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
B  70 GLN
B 116 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.153316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119933 restraints weight = 3626.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.52
r_work: 0.2979 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3322  Z= 0.134
  Angle     :  0.508   5.475   4520  Z= 0.264
  Chirality :  0.041   0.132    506
  Planarity :  0.004   0.033    534
  Dihedral  : 26.176 143.012    490
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 14.37 %
    Favored  : 85.34 %
  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:  1.38 (0.41), residues: 376
  helix:  2.42 (0.37), residues: 178
  sheet:  0.67 (0.58), residues: 68
  loop : -1.14 (0.48), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  68 
 TYR   0.013   0.001   TYR A 215 
 PHE   0.008   0.001   PHE A 146 
 TRP   0.012   0.001   TRP A 193 
 HIS   0.001   0.000   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3322)
  covalent geometry    : angle       0.50779 ( 4520)
  hydrogen bonds       : bond        0.03047 (  198)
  hydrogen bonds       : angle       4.65221 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   68 ARG cc_start: 0.7637 (ttt-90) cc_final: 0.6775 (ttp-170)
REVERT: A  131 TRP cc_start: 0.8263 (t60) cc_final: 0.8012 (t60)
REVERT: A  198 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7851 (mtpt)
REVERT: B   68 ARG cc_start: 0.7624 (ttt-90) cc_final: 0.6765 (ttp-170)
REVERT: B  131 TRP cc_start: 0.8251 (t60) cc_final: 0.8001 (t60)
REVERT: B  198 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7860 (mtpt)
  outliers start: 1
  outliers final: 0
  residues processed: 64
  average time/residue: 0.4039
  time to fit residues: 26.7571
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0060
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.134039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.099669 restraints weight = 3729.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.62
r_work: 0.2868 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3322  Z= 0.154
  Angle     :  0.524   4.678   4520  Z= 0.268
  Chirality :  0.040   0.131    506
  Planarity :  0.004   0.035    534
  Dihedral  : 20.016 126.340    490
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.66 %
    Favored  : 82.47 %
  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:  1.59 (0.43), residues: 376
  helix:  2.74 (0.37), residues: 178
  sheet:  0.27 (0.58), residues: 72
  loop : -1.02 (0.50), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 134 
 TYR   0.013   0.001   TYR A 211 
 PHE   0.008   0.001   PHE B 146 
 TRP   0.011   0.001   TRP A 131 
 HIS   0.002   0.000   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3322)
  covalent geometry    : angle       0.52386 ( 4520)
  hydrogen bonds       : bond        0.02910 (  198)
  hydrogen bonds       : angle       4.62027 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   68 ARG cc_start: 0.7710 (ttt-90) cc_final: 0.6914 (ttp-170)
REVERT: B   68 ARG cc_start: 0.7706 (ttt-90) cc_final: 0.6912 (ttp-170)
  outliers start: 10
  outliers final: 4
  residues processed: 54
  average time/residue: 0.3716
  time to fit residues: 20.9098
Evaluate side-chains
  50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  197 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.130951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.096657 restraints weight = 3639.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.61
r_work: 0.2838 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3322  Z= 0.157
  Angle     :  0.485   5.306   4520  Z= 0.252
  Chirality :  0.039   0.129    506
  Planarity :  0.004   0.037    534
  Dihedral  : 18.540 133.830    490
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.82 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.42), residues: 376
  helix:  2.73 (0.37), residues: 178
  sheet: -0.01 (0.56), residues: 72
  loop : -1.10 (0.49), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  68 
 TYR   0.013   0.001   TYR A 215 
 PHE   0.006   0.001   PHE B 230 
 TRP   0.012   0.001   TRP A 149 
 HIS   0.001   0.000   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3322)
  covalent geometry    : angle       0.48511 ( 4520)
  hydrogen bonds       : bond        0.02929 (  198)
  hydrogen bonds       : angle       4.54559 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.121 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 48
  average time/residue: 0.2846
  time to fit residues: 14.4625
Evaluate side-chains
  57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  155 ASP
Chi-restraints excluded: chain B residue  197 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   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 = 0.3468 r_free = 0.3468 target = 0.131171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.099866 restraints weight = 3568.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 2.39
r_work: 0.2826 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3322  Z= 0.173
  Angle     :  0.490   5.848   4520  Z= 0.257
  Chirality :  0.040   0.131    506
  Planarity :  0.004   0.038    534
  Dihedral  : 17.962 152.113    490
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.11 %
    Favored  : 77.59 %
  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:  1.38 (0.43), residues: 376
  helix:  2.73 (0.38), residues: 178
  sheet: -0.20 (0.56), residues: 72
  loop : -1.11 (0.50), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.012   0.001   TYR B 215 
 PHE   0.011   0.001   PHE A  43 
 TRP   0.010   0.001   TRP B 149 
 HIS   0.001   0.000   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 3322)
  covalent geometry    : angle       0.48999 ( 4520)
  hydrogen bonds       : bond        0.03097 (  198)
  hydrogen bonds       : angle       4.63100 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   68 ARG cc_start: 0.7808 (ttt-90) cc_final: 0.6900 (ttp-170)
REVERT: B   68 ARG cc_start: 0.7760 (ttt-90) cc_final: 0.6881 (ttp-170)
  outliers start: 8
  outliers final: 6
  residues processed: 60
  average time/residue: 0.3662
  time to fit residues: 22.8796
Evaluate side-chains
  49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  202 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0370
   chunk 4 optimal weight:    0.4980
   chunk 25 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A 150 HIS
B 150 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.129539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.096374 restraints weight = 3652.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.52
r_work: 0.2851 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3322  Z= 0.119
  Angle     :  0.449   4.822   4520  Z= 0.238
  Chirality :  0.039   0.117    506
  Planarity :  0.004   0.037    534
  Dihedral  : 17.413 152.571    490
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.98 %
    Favored  : 75.86 %
  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:  1.57 (0.42), residues: 376
  helix:  2.89 (0.37), residues: 178
  sheet:  0.19 (0.57), residues: 68
  loop : -1.20 (0.49), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  68 
 TYR   0.008   0.001   TYR A 109 
 PHE   0.011   0.001   PHE A  43 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.001   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3322)
  covalent geometry    : angle       0.44892 ( 4520)
  hydrogen bonds       : bond        0.02849 (  198)
  hydrogen bonds       : angle       4.45396 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   68 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.6812 (ttp-170)
REVERT: B   68 ARG cc_start: 0.7617 (ttt-90) cc_final: 0.6806 (ttp-170)
  outliers start: 11
  outliers final: 5
  residues processed: 55
  average time/residue: 0.3459
  time to fit residues: 19.7709
Evaluate side-chains
  50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  197 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    0.0030
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0770
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.3748

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.129737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.096340 restraints weight = 3695.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.53
r_work: 0.2847 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3322  Z= 0.112
  Angle     :  0.450   4.828   4520  Z= 0.238
  Chirality :  0.039   0.121    506
  Planarity :  0.004   0.037    534
  Dihedral  : 17.152 155.797    490
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 22.99 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.43), residues: 376
  helix:  2.98 (0.37), residues: 178
  sheet:  0.13 (0.58), residues: 68
  loop : -1.16 (0.48), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  68 
 TYR   0.010   0.001   TYR A 215 
 PHE   0.011   0.001   PHE A  43 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.001   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3322)
  covalent geometry    : angle       0.45037 ( 4520)
  hydrogen bonds       : bond        0.02746 (  198)
  hydrogen bonds       : angle       4.41490 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.071 
Fit side-chains
REVERT: A   68 ARG cc_start: 0.7567 (ttt-90) cc_final: 0.6700 (ttp-170)
REVERT: B   68 ARG cc_start: 0.7550 (ttt-90) cc_final: 0.6690 (ttp-170)
  outliers start: 5
  outliers final: 4
  residues processed: 53
  average time/residue: 0.3690
  time to fit residues: 20.3087
Evaluate side-chains
  52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  216 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3414 r_free = 0.3414 target = 0.127624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.094327 restraints weight = 3682.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.50
r_work: 0.2813 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3322  Z= 0.163
  Angle     :  0.511   5.870   4520  Z= 0.262
  Chirality :  0.041   0.128    506
  Planarity :  0.004   0.038    534
  Dihedral  : 17.280 157.632    490
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 23.85 %
    Favored  : 75.29 %
  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:  1.58 (0.43), residues: 376
  helix:  2.91 (0.38), residues: 178
  sheet: -0.17 (0.61), residues: 68
  loop : -0.99 (0.48), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  68 
 TYR   0.015   0.001   TYR A 215 
 PHE   0.011   0.001   PHE A  43 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.001   0.000   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 3322)
  covalent geometry    : angle       0.51117 ( 4520)
  hydrogen bonds       : bond        0.02935 (  198)
  hydrogen bonds       : angle       4.54504 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A   68 ARG cc_start: 0.7636 (ttt-90) cc_final: 0.6802 (ttp-170)
REVERT: B   68 ARG cc_start: 0.7610 (ttt-90) cc_final: 0.6788 (ttp-170)
  outliers start: 3
  outliers final: 3
  residues processed: 46
  average time/residue: 0.3984
  time to fit residues: 18.9778
Evaluate side-chains
  43 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  197 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    0.2980
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.131722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.100470 restraints weight = 3629.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.40
r_work: 0.2846 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2671 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.4568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3322  Z= 0.140
  Angle     :  0.497   7.736   4520  Z= 0.253
  Chirality :  0.040   0.128    506
  Planarity :  0.004   0.038    534
  Dihedral  : 17.238 160.337    490
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 25.29 %
    Favored  : 73.85 %
  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:  1.70 (0.43), residues: 376
  helix:  3.31 (0.37), residues: 166
  sheet: -0.20 (0.62), residues: 68
  loop : -0.92 (0.48), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  68 
 TYR   0.009   0.001   TYR A 109 
 PHE   0.010   0.001   PHE A  43 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.001   0.000   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3322)
  covalent geometry    : angle       0.49699 ( 4520)
  hydrogen bonds       : bond        0.02890 (  198)
  hydrogen bonds       : angle       4.49836 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 43
  average time/residue: 0.3271
  time to fit residues: 14.7096
Evaluate side-chains
  42 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  197 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
B 218 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.131492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.100239 restraints weight = 3588.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.40
r_work: 0.2839 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2666 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3322  Z= 0.143
  Angle     :  0.498   7.297   4520  Z= 0.254
  Chirality :  0.040   0.121    506
  Planarity :  0.004   0.038    534
  Dihedral  : 17.238 162.062    490
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 24.71 %
    Favored  : 74.14 %
  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:  1.47 (0.43), residues: 376
  helix:  2.92 (0.38), residues: 178
  sheet: -0.25 (0.59), residues: 72
  loop : -1.20 (0.48), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  68 
 TYR   0.009   0.001   TYR A 109 
 PHE   0.009   0.001   PHE A  43 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.001   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3322)
  covalent geometry    : angle       0.49834 ( 4520)
  hydrogen bonds       : bond        0.02886 (  198)
  hydrogen bonds       : angle       4.48925 (  582)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.118 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 43
  average time/residue: 0.2839
  time to fit residues: 12.9067
Evaluate side-chains
  42 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  202 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0040
   chunk 12 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.3440 r_free = 0.3440 target = 0.129697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.097180 restraints weight = 3750.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.47
r_work: 0.2840 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.4682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3322  Z= 0.124
  Angle     :  0.485   7.297   4520  Z= 0.247
  Chirality :  0.039   0.120    506
  Planarity :  0.004   0.037    534
  Dihedral  : 17.191 163.202    490
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 25.57 %
    Favored  : 73.85 %
  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:  1.71 (0.43), residues: 376
  helix:  3.32 (0.37), residues: 166
  sheet: -0.12 (0.61), residues: 72
  loop : -1.00 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.008   0.001   TYR A 109 
 PHE   0.009   0.001   PHE A  43 
 TRP   0.011   0.001   TRP A 149 
 HIS   0.001   0.000   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3322)
  covalent geometry    : angle       0.48453 ( 4520)
  hydrogen bonds       : bond        0.02836 (  198)
  hydrogen bonds       : angle       4.43468 (  582)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1104.95 seconds
wall clock time: 19 minutes 40.82 seconds (1180.82 seconds total)