Starting phenix.real_space_refine
on Wed Aug  5 13:21:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ziv_74285/08_2026/9ziv_74285.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ziv_74285/08_2026/9ziv_74285.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ziv_74285/08_2026/9ziv_74285.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ziv_74285/08_2026/9ziv_74285.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ziv_74285/08_2026/9ziv_74285.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ziv_74285/08_2026/9ziv_74285.cif"
  }
  resolution = 3.5
  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=   0.007
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: 6
    Type Number    sf(0)   Gaussians
     P     417      5.49       5
     Mg     38      5.21       5
     S       3      5.16       5
     C    4604      2.51       5
     N    1834      2.21       5
     O    3051      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9947
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 8962
          Classifications: {'RNA': 417}
          Modifications used: {'rna2p_pur': 40, 'rna2p_pyr': 22, 'rna3p_pur': 203, 'rna3p_pyr': 152}
          Link IDs: {'rna2p': 62, 'rna3p': 354}
    Chain: "B"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 947
          Classifications: {'peptide': 116}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 38
          Unusual residues: {' MG': 38}
          Classifications: {'undetermined': 38}
          Link IDs: {None: 37}
  Time building chain proxies: 2.66, per 1000 atoms: 0.27
  Number of scatterers: 9947
  At special positions: 0
  Unit cell: (94.428, 170.556, 141.276, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       3     16.00
     P     417     15.00
     Mg     38     11.99
     O    3051      8.00
     N    1834      7.00
     C    4604      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: 0.82
  Conformation dependent library (CDL) restraints added in 78.0 milliseconds
  

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  216

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 1 sheets defined
      50.0% alpha, 14.7% beta
      143 base pairs and 199 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 6
      removed outlier: 3.562A  pdb=" N   ARG B   6 " --> pdb=" O   LYS B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 20
    Processing helix  chain 'B' and resid 48 through 52
      removed outlier: 3.727A  pdb=" N   LEU B  51 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLY B  52 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 48 through 52'
    Processing helix  chain 'B' and resid 53 through 71
      removed outlier: 3.658A  pdb=" N   ARG B  57 " --> pdb=" O   LYS B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 90
      removed outlier: 3.852A  pdb=" N   ALA B  90 " --> pdb=" O   GLN B  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 87 through 90'
    Processing helix  chain 'B' and resid 93 through 106
    Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24

    44 hydrogen bonds defined for protein.
    126 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      366 hydrogen bonds
      632 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      199 stacking parallelities
  Total time for adding SS restraints: 2.66

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1391
        1.33 -     1.45: 5288
        1.45 -     1.58: 3483
        1.58 -     1.70: 833
        1.70 -     1.82: 5
  Bond restraints: 11000
  Sorted by residual:
  bond pdb=" N9    G A 230 "
       pdb=" C4    G A 230 "
    ideal  model  delta    sigma   weight residual
    1.375  1.390 -0.015 8.00e-03 1.56e+04 3.43e+00
  bond pdb=" N9    A A 216 "
       pdb=" C4    A A 216 "
    ideal  model  delta    sigma   weight residual
    1.374  1.384 -0.010 6.00e-03 2.78e+04 3.03e+00
  bond pdb=" C2    G A 227 "
       pdb=" N3    G A 227 "
    ideal  model  delta    sigma   weight residual
    1.323  1.310  0.013 8.00e-03 1.56e+04 2.46e+00
  bond pdb=" C8    G A 383 "
       pdb=" N7    G A 383 "
    ideal  model  delta    sigma   weight residual
    1.305  1.296  0.009 6.00e-03 2.78e+04 2.04e+00
  bond pdb=" N7    A A 218 "
       pdb=" C5    A A 218 "
    ideal  model  delta    sigma   weight residual
    1.388  1.380  0.008 6.00e-03 2.78e+04 1.99e+00
  ... (remaining 10995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.25: 16929
        5.25 -    10.51: 12
       10.51 -    15.76: 1
       15.76 -    21.01: 0
       21.01 -    26.26: 2
  Bond angle restraints: 16944
  Sorted by residual:
  angle pdb=" O3'   A A 332 "
        pdb=" P     U A 333 "
        pdb=" OP1   U A 333 "
      ideal   model   delta    sigma   weight residual
     108.00   81.74   26.26 3.00e+00 1.11e-01 7.66e+01
  angle pdb=" O3'   A A 332 "
        pdb=" P     U A 333 "
        pdb=" OP2   U A 333 "
      ideal   model   delta    sigma   weight residual
     108.00   82.12   25.88 3.00e+00 1.11e-01 7.44e+01
  angle pdb=" O2    C A  36 "
        pdb=" C2    C A  36 "
        pdb=" N3    C A  36 "
      ideal   model   delta    sigma   weight residual
     121.90  116.97    4.93 7.00e-01 2.04e+00 4.97e+01
  angle pdb=" O2    C A 386 "
        pdb=" C2    C A 386 "
        pdb=" N3    C A 386 "
      ideal   model   delta    sigma   weight residual
     121.90  117.61    4.29 7.00e-01 2.04e+00 3.76e+01
  angle pdb=" C1'   C A 344 "
        pdb=" N1    C A 344 "
        pdb=" C2    C A 344 "
      ideal   model   delta    sigma   weight residual
     118.80  124.44   -5.64 1.10e+00 8.26e-01 2.63e+01
  ... (remaining 16939 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.65: 5916
       34.65 -    69.29: 1047
       69.29 -   103.94: 138
      103.94 -   138.59: 9
      138.59 -   173.23: 6
  Dihedral angle restraints: 7116
    sinusoidal: 6779
      harmonic: 337
  Sorted by residual:
  dihedral pdb=" O4'   C A 347 "
           pdb=" C1'   C A 347 "
           pdb=" N1    C A 347 "
           pdb=" C2    C A 347 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   26.77  173.23     1      1.50e+01 4.44e-03 8.50e+01
  dihedral pdb=" O4'   U A 180 "
           pdb=" C1'   U A 180 "
           pdb=" N1    U A 180 "
           pdb=" C2    U A 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   46.43  153.57     1      1.50e+01 4.44e-03 8.09e+01
  dihedral pdb=" O4'   U A 370 "
           pdb=" C1'   U A 370 "
           pdb=" N1    U A 370 "
           pdb=" C2    U A 370 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -75.24  -84.76     1      1.50e+01 4.44e-03 3.88e+01
  ... (remaining 7113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.382: 2220
       0.382 -    0.764: 0
       0.764 -    1.146: 0
       1.146 -    1.529: 0
       1.529 -    1.911: 1
  Chirality restraints: 2221
  Sorted by residual:
  chirality pdb=" P     U A 333 "
            pdb=" OP1   U A 333 "
            pdb=" OP2   U A 333 "
            pdb=" O5'   U A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.50    1.91 2.00e-01 2.50e+01 9.13e+01
  chirality pdb=" C1'   C A 347 "
            pdb=" O4'   C A 347 "
            pdb=" C2'   C A 347 "
            pdb=" N1    C A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.24    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" C3'   A A 241 "
            pdb=" C4'   A A 241 "
            pdb=" O3'   A A 241 "
            pdb=" C2'   A A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.25   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 2218 not shown)

  Planarity restraints: 581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  46 "   -0.032 2.00e-02 2.50e+03   1.45e-02 6.27e+00
        pdb=" N9    G A  46 "    0.034 2.00e-02 2.50e+03
        pdb=" C8    G A  46 "    0.005 2.00e-02 2.50e+03
        pdb=" N7    G A  46 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G A  46 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G A  46 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G A  46 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    G A  46 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G A  46 "   -0.008 2.00e-02 2.50e+03
        pdb=" N2    G A  46 "    0.010 2.00e-02 2.50e+03
        pdb=" N3    G A  46 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    G A  46 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 347 "    0.031 2.00e-02 2.50e+03   1.55e-02 5.41e+00
        pdb=" N1    C A 347 "   -0.028 2.00e-02 2.50e+03
        pdb=" C2    C A 347 "    0.000 2.00e-02 2.50e+03
        pdb=" O2    C A 347 "   -0.011 2.00e-02 2.50e+03
        pdb=" N3    C A 347 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    C A 347 "    0.007 2.00e-02 2.50e+03
        pdb=" N4    C A 347 "    0.008 2.00e-02 2.50e+03
        pdb=" C5    C A 347 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    C A 347 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 187 "   -0.028 2.00e-02 2.50e+03   1.29e-02 4.57e+00
        pdb=" N9    A A 187 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    A A 187 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A A 187 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A A 187 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A A 187 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A A 187 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A A 187 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A A 187 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A A 187 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A A 187 "    0.002 2.00e-02 2.50e+03
  ... (remaining 578 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 57
        2.57 -     3.15: 7477
        3.15 -     3.73: 21602
        3.73 -     4.32: 27440
        4.32 -     4.90: 34369
  Nonbonded interactions: 90945
  Sorted by model distance:
  nonbonded pdb=" O4    U A 393 "
            pdb="MG    MG A 531 "
     model   vdw
     1.981 2.170
  nonbonded pdb=" O2'   A A 277 "
            pdb="MG    MG A 511 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OP2   C A 103 "
            pdb="MG    MG A 510 "
     model   vdw
     2.000 2.170
  nonbonded pdb=" OP1   G A 275 "
            pdb="MG    MG A 512 "
     model   vdw
     2.009 2.170
  nonbonded pdb=" OP2   C A 386 "
            pdb="MG    MG A 501 "
     model   vdw
     2.014 2.170
  ... (remaining 90940 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.220
  Find NCS groups from input model:        0.030
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11000  Z= 0.259
  Angle     :  0.903  26.264  16944  Z= 0.736
  Chirality :  0.076   1.911   2221
  Planarity :  0.004   0.020    581
  Dihedral  : 26.013 173.232   6900
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 40.40 %
    Favored  : 55.56 %
  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 are not related in a simple way.
  whole: -1.06 (0.79), residues: 114
  helix: -0.39 (0.74), residues: 52
  sheet:  0.41 (0.95), residues: 25
  loop : -1.79 (1.08), residues: 37

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  86 
 TYR   0.007   0.001   TYR B  94 
 PHE   0.008   0.001   PHE B  13 
 HIS   0.005   0.003   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.26 (11000)
  covalent geometry    : angle       0.90301 /  0.74 (16944)
  hydrogen bonds       : bond        0.07705 /  8.62 (  410)
  hydrogen bonds       : angle       2.69345 /  3.70 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 ASN cc_start: 0.8646 (p0) cc_final: 0.7932 (m-40)
REVERT: B   92 MET cc_start: 0.8022 (tpt) cc_final: 0.7590 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 26
  average time/residue: 0.0915
  time to fit residues: 3.5719
Evaluate side-chains
  21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   43 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:   30.0000
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:    9.9990
   overall best weight:    7.7790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.059437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.035185 restraints weight = 66477.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.036254 restraints weight = 27008.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.036754 restraints weight = 20963.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.036931 restraints weight = 19158.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 13)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.036931 restraints weight = 18602.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11000  Z= 0.473
  Angle     :  1.087  28.388  16944  Z= 0.524
  Chirality :  0.082   1.678   2221
  Planarity :  0.007   0.035    581
  Dihedral  : 26.311 174.926   6652
  Min Nonbonded Distance : 1.668

Molprobity Statistics.
  All-atom Clashscore : 33.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers : 10.10 %
    Allowed  : 35.35 %
    Favored  : 54.55 %
  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 are not related in a simple way.
  whole: -1.77 (0.78), residues: 114
  helix: -0.75 (0.74), residues: 50
  sheet:  0.01 (1.00), residues: 26
  loop : -2.48 (0.97), residues: 38

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  62 
 TYR   0.010   0.002   TYR B  81 
 PHE   0.017   0.003   PHE B  13 
 HIS   0.003   0.002   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00643 /  0.47 (11000)
  covalent geometry    : angle       1.08721 /  0.52 (16944)
  hydrogen bonds       : bond        0.13523 / 14.68 (  410)
  hydrogen bonds       : angle       3.30598 /  4.51 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 16
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: B   10 ASN cc_start: 0.8743 (p0) cc_final: 0.7969 (m-40)
REVERT: B   17 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7767 (m-80)
REVERT: B   92 MET cc_start: 0.8047 (tpt) cc_final: 0.7584 (mmt)
  outliers start: 10
  outliers final: 7
  residues processed: 23
  average time/residue: 0.1032
  time to fit residues: 3.5131
Evaluate side-chains
  24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 16
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue  113 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 16 optimal weight:   30.0000
   overall best weight:    6.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.059371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.034845 restraints weight = 67899.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.036120 restraints weight = 27765.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.036606 restraints weight = 21399.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.036804 restraints weight = 19553.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.036804 restraints weight = 18944.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  11000  Z= 0.379
  Angle     :  0.927  27.972  16944  Z= 0.464
  Chirality :  0.070   1.734   2221
  Planarity :  0.006   0.028    581
  Dihedral  : 26.593 175.427   6651
  Min Nonbonded Distance : 1.713

Molprobity Statistics.
  All-atom Clashscore : 27.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 36.36 %
    Favored  : 52.53 %
  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 are not related in a simple way.
  whole: -2.00 (0.75), residues: 114
  helix: -0.93 (0.73), residues: 50
  sheet:  0.07 (1.00), residues: 25
  loop : -2.71 (0.87), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 106 
 TYR   0.009   0.001   TYR B  81 
 PHE   0.016   0.003   PHE B  13 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00532 /  0.38 (11000)
  covalent geometry    : angle       0.92694 /  0.46 (16944)
  hydrogen bonds       : bond        0.11769 / 12.91 (  410)
  hydrogen bonds       : angle       3.24366 /  4.45 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 16
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 ASN cc_start: 0.8754 (p0) cc_final: 0.8065 (m-40)
REVERT: B   12 GLU cc_start: 0.9280 (pm20) cc_final: 0.8981 (pm20)
REVERT: B   17 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7747 (m-80)
REVERT: B   19 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7373 (mp10)
REVERT: B   92 MET cc_start: 0.7982 (tpt) cc_final: 0.7569 (mmm)
REVERT: B  113 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7400 (mmtm)
  outliers start: 11
  outliers final: 5
  residues processed: 24
  average time/residue: 0.1177
  time to fit residues: 3.9322
Evaluate side-chains
  24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 16
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue  113 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:   40.0000
   chunk 40 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 22 optimal weight:   30.0000
   chunk 48 optimal weight:    0.0770
   chunk 17 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 36 optimal weight:   50.0000
   chunk 12 optimal weight:   40.0000
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    4.8148

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.059499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.034994 restraints weight = 67522.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.036260 restraints weight = 27530.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.036784 restraints weight = 21198.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.036976 restraints weight = 19385.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 12)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.036977 restraints weight = 18799.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11000  Z= 0.303
  Angle     :  0.835  27.092  16944  Z= 0.425
  Chirality :  0.066   1.746   2221
  Planarity :  0.006   0.073    581
  Dihedral  : 26.630 175.394   6651
  Min Nonbonded Distance : 1.730

Molprobity Statistics.
  All-atom Clashscore : 26.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers : 12.12 %
    Allowed  : 35.35 %
    Favored  : 52.53 %
  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 are not related in a simple way.
  whole: -1.75 (0.77), residues: 114
  helix: -0.56 (0.76), residues: 50
  sheet:  0.13 (1.01), residues: 25
  loop : -2.77 (0.88), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 106 
 TYR   0.008   0.001   TYR B  81 
 PHE   0.016   0.003   PHE B  13 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.30 (11000)
  covalent geometry    : angle       0.83505 /  0.43 (16944)
  hydrogen bonds       : bond        0.11531 / 12.76 (  410)
  hydrogen bonds       : angle       3.16375 /  4.34 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 16
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 ASN cc_start: 0.8747 (p0) cc_final: 0.8432 (m-40)
REVERT: B   17 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7787 (m-80)
REVERT: B   19 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7334 (mp10)
REVERT: B   92 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7619 (mmm)
  outliers start: 12
  outliers final: 7
  residues processed: 25
  average time/residue: 0.0880
  time to fit residues: 3.3557
Evaluate side-chains
  26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 16
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  104 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 22 optimal weight:   30.0000
   chunk 41 optimal weight:    0.0370
   chunk 14 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0030
   chunk 5 optimal weight:    9.9990
   chunk 23 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   overall best weight:    4.4074

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.059556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.035051 restraints weight = 66996.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.036247 restraints weight = 27363.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.036775 restraints weight = 21091.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.036983 restraints weight = 19309.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.037009 restraints weight = 18678.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11000  Z= 0.287
  Angle     :  0.810  26.795  16944  Z= 0.417
  Chirality :  0.065   1.776   2221
  Planarity :  0.005   0.026    581
  Dihedral  : 26.684 175.527   6651
  Min Nonbonded Distance : 1.748

Molprobity Statistics.
  All-atom Clashscore : 25.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  8.08 %
    Allowed  : 37.37 %
    Favored  : 54.55 %
  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 are not related in a simple way.
  whole: -1.72 (0.77), residues: 114
  helix: -0.47 (0.77), residues: 50
  sheet: -0.00 (0.98), residues: 25
  loop : -2.74 (0.88), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 106 
 TYR   0.008   0.001   TYR B  40 
 PHE   0.015   0.003   PHE B  13 
 HIS   0.001   0.000   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.29 (11000)
  covalent geometry    : angle       0.81014 /  0.42 (16944)
  hydrogen bonds       : bond        0.11139 / 12.34 (  410)
  hydrogen bonds       : angle       3.15814 /  4.37 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 17
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 ASN cc_start: 0.8909 (p0) cc_final: 0.8353 (t0)
REVERT: B   17 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7759 (m-80)
REVERT: B   19 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7379 (mp10)
REVERT: B   92 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7631 (mmm)
  outliers start: 8
  outliers final: 5
  residues processed: 22
  average time/residue: 0.1017
  time to fit residues: 3.3438
Evaluate side-chains
  25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 17
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   92 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9990
   chunk 38 optimal weight:   10.0000
   chunk 36 optimal weight:   50.0000
   chunk 49 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:   30.0000
   overall best weight:    6.9992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.058829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.034074 restraints weight = 67661.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.035212 restraints weight = 27785.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.035716 restraints weight = 21721.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.035853 restraints weight = 19965.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.035853 restraints weight = 19495.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11000  Z= 0.439
  Angle     :  1.042  27.317  16944  Z= 0.508
  Chirality :  0.078   1.728   2221
  Planarity :  0.006   0.031    581
  Dihedral  : 26.779 178.024   6651
  Min Nonbonded Distance : 1.665

Molprobity Statistics.
  All-atom Clashscore : 35.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.04 %
    Favored  : 85.96 %
  Rotamer:
    Outliers : 10.10 %
    Allowed  : 37.37 %
    Favored  : 52.53 %
  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 are not related in a simple way.
  whole: -2.20 (0.75), residues: 114
  helix: -0.74 (0.75), residues: 50
  sheet: -0.41 (0.99), residues: 25
  loop : -3.07 (0.84), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 106 
 TYR   0.010   0.002   TYR B  81 
 PHE   0.016   0.003   PHE B  13 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00606 /  0.44 (11000)
  covalent geometry    : angle       1.04212 /  0.51 (16944)
  hydrogen bonds       : bond        0.13345 / 14.66 (  410)
  hydrogen bonds       : angle       3.41523 /  4.67 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 17
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 ASN cc_start: 0.8918 (p0) cc_final: 0.8254 (t0)
REVERT: B   17 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7766 (m-80)
REVERT: B   19 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7302 (mp10)
REVERT: B   92 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7596 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 24
  average time/residue: 0.0907
  time to fit residues: 3.3121
Evaluate side-chains
  26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 16
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  104 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 12 optimal weight:   40.0000
   chunk 27 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 34 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 21 optimal weight:   30.0000
   chunk 47 optimal weight:    0.8980
   overall best weight:    4.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.059386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.034924 restraints weight = 66982.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.036094 restraints weight = 27437.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.036628 restraints weight = 20996.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.036833 restraints weight = 19232.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.036840 restraints weight = 18579.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11000  Z= 0.292
  Angle     :  0.835  27.040  16944  Z= 0.428
  Chirality :  0.066   1.733   2221
  Planarity :  0.005   0.027    581
  Dihedral  : 26.817 177.408   6651
  Min Nonbonded Distance : 1.741

Molprobity Statistics.
  All-atom Clashscore : 27.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.40 %
    Favored  : 88.60 %
  Rotamer:
    Outliers : 10.10 %
    Allowed  : 39.39 %
    Favored  : 50.51 %
  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 are not related in a simple way.
  whole: -1.99 (0.76), residues: 114
  helix: -0.55 (0.77), residues: 50
  sheet: -0.28 (0.98), residues: 25
  loop : -3.00 (0.84), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 106 
 TYR   0.009   0.001   TYR B  81 
 PHE   0.016   0.003   PHE B  13 
 HIS   0.001   0.000   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.29 (11000)
  covalent geometry    : angle       0.83479 /  0.43 (16944)
  hydrogen bonds       : bond        0.11474 / 12.69 (  410)
  hydrogen bonds       : angle       3.19069 /  4.36 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 16
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 ASN cc_start: 0.8849 (p0) cc_final: 0.8197 (t0)
REVERT: B   17 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7761 (m-80)
REVERT: B   19 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7383 (mp10)
REVERT: B   92 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7627 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 23
  average time/residue: 0.0849
  time to fit residues: 2.9572
Evaluate side-chains
  26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 16
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  104 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:   30.0000
   chunk 29 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 41 optimal weight:    0.6980
   chunk 32 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 16 optimal weight:   30.0000
   chunk 15 optimal weight:   30.0000
   overall best weight:    7.9394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.058524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.033920 restraints weight = 65909.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.034958 restraints weight = 27697.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.035430 restraints weight = 21430.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.035627 restraints weight = 19721.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.035627 restraints weight = 19092.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  11000  Z= 0.486
  Angle     :  1.135  27.504  16944  Z= 0.549
  Chirality :  0.083   1.726   2221
  Planarity :  0.007   0.036    581
  Dihedral  : 26.941 179.870   6651
  Min Nonbonded Distance : 1.655

Molprobity Statistics.
  All-atom Clashscore : 41.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.04 %
    Favored  : 85.96 %
  Rotamer:
    Outliers : 12.12 %
    Allowed  : 35.35 %
    Favored  : 52.53 %
  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 are not related in a simple way.
  whole: -2.64 (0.73), residues: 114
  helix: -1.10 (0.72), residues: 50
  sheet: -0.72 (1.01), residues: 25
  loop : -3.21 (0.82), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 106 
 TYR   0.011   0.002   TYR B  81 
 PHE   0.017   0.004   PHE B  41 
 HIS   0.001   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00667 /  0.49 (11000)
  covalent geometry    : angle       1.13497 /  0.55 (16944)
  hydrogen bonds       : bond        0.14670 / 16.08 (  410)
  hydrogen bonds       : angle       3.58674 /  4.89 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 17
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7778 (m-80)
REVERT: B   19 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7306 (mp10)
REVERT: B   65 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7427 (mtt180)
REVERT: B   92 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7570 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 24
  average time/residue: 0.1018
  time to fit residues: 3.5272
Evaluate side-chains
  28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 17
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   92 MET
Chi-restraints excluded: chain B residue  104 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   chunk 36 optimal weight:   40.0000
   chunk 0 optimal weight:   30.0000
   chunk 48 optimal weight:    0.0670
   chunk 2 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   overall best weight:    7.4128

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.058665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.034004 restraints weight = 66909.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.035116 restraints weight = 28149.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.035591 restraints weight = 21819.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.035793 restraints weight = 20054.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.035871 restraints weight = 19365.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  11000  Z= 0.442
  Angle     :  1.067  27.452  16944  Z= 0.525
  Chirality :  0.078   1.687   2221
  Planarity :  0.007   0.032    581
  Dihedral  : 27.106 179.927   6651
  Min Nonbonded Distance : 1.676

Molprobity Statistics.
  All-atom Clashscore : 37.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.91 %
    Favored  : 85.09 %
  Rotamer:
    Outliers : 10.10 %
    Allowed  : 39.39 %
    Favored  : 50.51 %
  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 are not related in a simple way.
  whole: -2.71 (0.73), residues: 114
  helix: -1.08 (0.72), residues: 50
  sheet: -0.78 (0.99), residues: 25
  loop : -3.35 (0.81), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   6 
 TYR   0.011   0.002   TYR B  81 
 PHE   0.014   0.003   PHE B  41 
 HIS   0.002   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00615 /  0.44 (11000)
  covalent geometry    : angle       1.06727 /  0.52 (16944)
  hydrogen bonds       : bond        0.13561 / 14.92 (  410)
  hydrogen bonds       : angle       3.56560 /  4.83 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 17
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7777 (m-80)
REVERT: B   19 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7391 (mp10)
REVERT: B   65 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7291 (mtt180)
REVERT: B   92 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7532 (mmt)
  outliers start: 10
  outliers final: 6
  residues processed: 24
  average time/residue: 0.0841
  time to fit residues: 2.9167
Evaluate side-chains
  25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 16
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   92 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 15 optimal weight:   30.0000
   chunk 46 optimal weight:    0.9980
   chunk 25 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 12 optimal weight:   40.0000
   chunk 16 optimal weight:   30.0000
   overall best weight:    7.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.058500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.033865 restraints weight = 65865.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.034953 restraints weight = 27653.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.035446 restraints weight = 21434.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.035647 restraints weight = 19657.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.035647 restraints weight = 19016.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11000  Z= 0.461
  Angle     :  1.093  27.246  16944  Z= 0.537
  Chirality :  0.081   1.724   2221
  Planarity :  0.007   0.032    581
  Dihedral  : 27.165 178.916   6649
  Min Nonbonded Distance : 1.679

Molprobity Statistics.
  All-atom Clashscore : 39.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.79 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  9.09 %
    Allowed  : 42.42 %
    Favored  : 48.48 %
  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 are not related in a simple way.
  whole: -2.87 (0.72), residues: 114
  helix: -1.30 (0.70), residues: 50
  sheet: -0.75 (1.00), residues: 25
  loop : -3.39 (0.81), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B   6 
 TYR   0.011   0.002   TYR B  81 
 PHE   0.017   0.004   PHE B  41 
 HIS   0.002   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00638 /  0.46 (11000)
  covalent geometry    : angle       1.09314 /  0.54 (16944)
  hydrogen bonds       : bond        0.14292 / 15.68 (  410)
  hydrogen bonds       : angle       3.61904 /  4.95 (  758)

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

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

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  228 Ramachandran restraints generated.
    114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 15
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7816 (m-10)
REVERT: B   19 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7399 (mp10)
REVERT: B   92 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7513 (mmt)
  outliers start: 9
  outliers final: 6
  residues processed: 21
  average time/residue: 0.0913
  time to fit residues: 2.7942
Evaluate side-chains
  24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 15
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   19 GLN
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain B residue   92 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 39 optimal weight:    8.9990
   chunk 21 optimal weight:   30.0000
   chunk 5 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   overall best weight:    6.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.058794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.034554 restraints weight = 67073.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.035671 restraints weight = 27293.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.036168 restraints weight = 21074.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 15)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.036170 restraints weight = 19289.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.036170 restraints weight = 19278.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11000  Z= 0.386
  Angle     :  0.978  27.304  16944  Z= 0.491
  Chirality :  0.074   1.703   2221
  Planarity :  0.006   0.030    581
  Dihedral  : 27.152 179.494   6649
  Min Nonbonded Distance : 1.704

Molprobity Statistics.
  All-atom Clashscore : 33.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.91 %
    Favored  : 85.09 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 40.40 %
    Favored  : 48.48 %
  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 are not related in a simple way.
  whole: -2.98 (0.72), residues: 114
  helix: -1.46 (0.69), residues: 50
  sheet: -0.65 (1.01), residues: 25
  loop : -3.45 (0.81), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  65 
 TYR   0.010   0.002   TYR B  81 
 PHE   0.013   0.003   PHE B  13 
 HIS   0.002   0.001   HIS B 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.39 (11000)
  covalent geometry    : angle       0.97821 /  0.49 (16944)
  hydrogen bonds       : bond        0.12931 / 14.28 (  410)
  hydrogen bonds       : angle       3.46924 /  4.73 (  758)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2427.78 seconds
wall clock time: 42 minutes 32.98 seconds (2552.98 seconds total)