Starting phenix.real_space_refine
on Mon Apr  6 08:07:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10ik_75196/04_2026/10ik_75196.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10ik_75196/04_2026/10ik_75196.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/10ik_75196/04_2026/10ik_75196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10ik_75196/04_2026/10ik_75196.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/10ik_75196/04_2026/10ik_75196.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10ik_75196/04_2026/10ik_75196.cif"
  }
  resolution = 3.2
  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=   0.001
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
     S      20      5.16       5
     C    5070      2.51       5
     N    1510      2.21       5
     O    1500      1.98       5
     H    8570      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16670
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1667
          Classifications: {'peptide': 107}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 1.80, per 1000 atoms: 0.11
  Number of scatterers: 16670
  At special positions: 0
  Unit cell: (90.906, 111.756, 71.724, 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      20     16.00
     O    1500      8.00
     N    1510      7.00
     C    5070      6.00
     H    8570      1.00
    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: 1.55
  Conformation dependent library (CDL) restraints added in 475.1 milliseconds
  

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1860

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 289
      removed outlier: 6.693A  pdb=" N   GLN A 288 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   GLN B 288 " --> pdb=" O   SER C 289 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   GLN C 288 " --> pdb=" O   SER D 289 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   GLN D 288 " --> pdb=" O   SER E 289 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   GLN E 288 " --> pdb=" O   SER F 289 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   GLN F 288 " --> pdb=" O   SER G 289 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   GLN G 288 " --> pdb=" O   SER H 289 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLN H 288 " --> pdb=" O   SER I 289 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   GLN I 288 " --> pdb=" O   SER J 289 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 293
    Processing sheet with id=AA3, first strand: chain 'A' and resid 306 through 310
    Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 339
      removed outlier: 6.205A  pdb=" N   GLY A 335 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)
      removed outlier: 8.082A  pdb=" N   GLU B 338 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   GLY B 335 " --> pdb=" O   GLN C 336 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   GLU C 338 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL B 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   GLY C 335 " --> pdb=" O   GLN D 336 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   GLU D 338 " --> pdb=" O   GLY C 335 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL C 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   GLY D 335 " --> pdb=" O   GLN E 336 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   GLU E 338 " --> pdb=" O   GLY D 335 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   VAL D 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   GLY E 335 " --> pdb=" O   GLN F 336 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   GLU F 338 " --> pdb=" O   GLY E 335 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL E 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLY F 335 " --> pdb=" O   GLN G 336 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   GLU G 338 " --> pdb=" O   GLY F 335 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL F 337 " --> pdb=" O   GLU G 338 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLY G 335 " --> pdb=" O   GLN H 336 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   GLU H 338 " --> pdb=" O   GLY G 335 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   VAL G 337 " --> pdb=" O   GLU H 338 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   GLY H 335 " --> pdb=" O   GLN I 336 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   GLU I 338 " --> pdb=" O   GLY H 335 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL H 337 " --> pdb=" O   GLU I 338 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLY I 335 " --> pdb=" O   GLN J 336 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   GLU J 338 " --> pdb=" O   GLY I 335 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   VAL I 337 " --> pdb=" O   GLU J 338 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 346
    Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 353

    108 hydrogen bonds defined for protein.
    324 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: 3.31

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8550
        1.03 -     1.23: 20
        1.23 -     1.42: 3130
        1.42 -     1.61: 5060
        1.61 -     1.81: 20
  Bond restraints: 16780
  Sorted by residual:
  bond pdb=" CB  ILE J 305 "
       pdb=" CG1 ILE J 305 "
    ideal  model  delta    sigma   weight residual
    1.530  1.411  0.119 2.00e-02 2.50e+03 3.53e+01
  bond pdb=" CB  ILE H 305 "
       pdb=" CG1 ILE H 305 "
    ideal  model  delta    sigma   weight residual
    1.530  1.412  0.118 2.00e-02 2.50e+03 3.51e+01
  bond pdb=" CB  ILE B 305 "
       pdb=" CG1 ILE B 305 "
    ideal  model  delta    sigma   weight residual
    1.530  1.412  0.118 2.00e-02 2.50e+03 3.51e+01
  bond pdb=" CB  ILE F 305 "
       pdb=" CG1 ILE F 305 "
    ideal  model  delta    sigma   weight residual
    1.530  1.412  0.118 2.00e-02 2.50e+03 3.51e+01
  bond pdb=" CB  ILE D 305 "
       pdb=" CG1 ILE D 305 "
    ideal  model  delta    sigma   weight residual
    1.530  1.412  0.118 2.00e-02 2.50e+03 3.51e+01
  ... (remaining 16775 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.07: 30530
       11.07 -    22.13: 80
       22.13 -    33.20: 20
       33.20 -    44.27: 30
       44.27 -    55.33: 10
  Bond angle restraints: 30670
  Sorted by residual:
  angle pdb=" CB  ILE E 305 "
        pdb=" CA  ILE E 305 "
        pdb=" HA  ILE E 305 "
      ideal   model   delta    sigma   weight residual
     109.00   53.67   55.33 3.00e+00 1.11e-01 3.40e+02
  angle pdb=" CB  ILE A 305 "
        pdb=" CA  ILE A 305 "
        pdb=" HA  ILE A 305 "
      ideal   model   delta    sigma   weight residual
     109.00   53.68   55.32 3.00e+00 1.11e-01 3.40e+02
  angle pdb=" CB  ILE D 305 "
        pdb=" CA  ILE D 305 "
        pdb=" HA  ILE D 305 "
      ideal   model   delta    sigma   weight residual
     109.00   53.69   55.31 3.00e+00 1.11e-01 3.40e+02
  angle pdb=" CB  ILE J 305 "
        pdb=" CA  ILE J 305 "
        pdb=" HA  ILE J 305 "
      ideal   model   delta    sigma   weight residual
     109.00   53.70   55.30 3.00e+00 1.11e-01 3.40e+02
  angle pdb=" CB  ILE F 305 "
        pdb=" CA  ILE F 305 "
        pdb=" HA  ILE F 305 "
      ideal   model   delta    sigma   weight residual
     109.00   53.70   55.30 3.00e+00 1.11e-01 3.40e+02
  ... (remaining 30665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 6576
       17.33 -    34.65: 784
       34.65 -    51.98: 200
       51.98 -    69.30: 60
       69.30 -    86.63: 40
  Dihedral angle restraints: 7660
    sinusoidal: 4440
      harmonic: 3220
  Sorted by residual:
  dihedral pdb=" CA  GLN I 276 "
           pdb=" C   GLN I 276 "
           pdb=" N   ILE I 277 "
           pdb=" CA  ILE I 277 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.19  -44.81     0      5.00e+00 4.00e-02 8.03e+01
  dihedral pdb=" CA  GLN J 276 "
           pdb=" C   GLN J 276 "
           pdb=" N   ILE J 277 "
           pdb=" CA  ILE J 277 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.21  -44.79     0      5.00e+00 4.00e-02 8.03e+01
  dihedral pdb=" CA  GLN A 276 "
           pdb=" C   GLN A 276 "
           pdb=" N   ILE A 277 "
           pdb=" CA  ILE A 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.22  -44.78     0      5.00e+00 4.00e-02 8.02e+01
  ... (remaining 7657 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.227: 1230
       0.227 -    0.454: 0
       0.454 -    0.682: 0
       0.682 -    0.909: 0
       0.909 -    1.136: 10
  Chirality restraints: 1240
  Sorted by residual:
  chirality pdb=" CB  ILE H 305 "
            pdb=" CA  ILE H 305 "
            pdb=" CG1 ILE H 305 "
            pdb=" CG2 ILE H 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.51    1.14 2.00e-01 2.50e+01 3.23e+01
  chirality pdb=" CB  ILE C 305 "
            pdb=" CA  ILE C 305 "
            pdb=" CG1 ILE C 305 "
            pdb=" CG2 ILE C 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.51    1.13 2.00e-01 2.50e+01 3.22e+01
  chirality pdb=" CB  ILE I 305 "
            pdb=" CA  ILE I 305 "
            pdb=" CG1 ILE I 305 "
            pdb=" CG2 ILE I 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.51    1.13 2.00e-01 2.50e+01 3.21e+01
  ... (remaining 1237 not shown)

  Planarity restraints: 2420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY G 304 "    0.014 2.00e-02 2.50e+03   2.22e-02 4.92e+00
        pdb=" N   ILE G 305 "   -0.038 2.00e-02 2.50e+03
        pdb=" CA  ILE G 305 "    0.009 2.00e-02 2.50e+03
        pdb=" H   ILE G 305 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 304 "    0.014 2.00e-02 2.50e+03   2.21e-02 4.90e+00
        pdb=" N   ILE A 305 "   -0.038 2.00e-02 2.50e+03
        pdb=" CA  ILE A 305 "    0.009 2.00e-02 2.50e+03
        pdb=" H   ILE A 305 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 304 "    0.014 2.00e-02 2.50e+03   2.21e-02 4.90e+00
        pdb=" N   ILE C 305 "   -0.038 2.00e-02 2.50e+03
        pdb=" CA  ILE C 305 "    0.009 2.00e-02 2.50e+03
        pdb=" H   ILE C 305 "    0.015 2.00e-02 2.50e+03
  ... (remaining 2417 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.05: 277
        2.05 -     2.69: 27681
        2.69 -     3.33: 50207
        3.33 -     3.96: 63334
        3.96 -     4.60: 100110
  Nonbonded interactions: 241609
  Sorted by model distance:
  nonbonded pdb=" HB  ILE E 305 "
            pdb="HG12 ILE E 305 "
     model   vdw
     1.416 1.952
  nonbonded pdb=" HB  ILE J 305 "
            pdb="HG12 ILE J 305 "
     model   vdw
     1.416 1.952
  nonbonded pdb=" HB  ILE A 305 "
            pdb="HG12 ILE A 305 "
     model   vdw
     1.416 1.952
  nonbonded pdb=" HB  ILE G 305 "
            pdb="HG12 ILE G 305 "
     model   vdw
     1.416 1.952
  nonbonded pdb=" HB  ILE D 305 "
            pdb="HG12 ILE D 305 "
     model   vdw
     1.416 1.952
  ... (remaining 241604 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             2.270
  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:             0.100
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.850
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.119   8210  Z= 0.285
  Angle     :  1.264  20.972  10970  Z= 0.676
  Chirality :  0.115   1.136   1240
  Planarity :  0.004   0.022   1400
  Dihedral  : 16.305  86.630   3190
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 16.10 %
    Favored  : 82.95 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.43 %
    Favored  : 75.27 %
  Cbeta Deviations :  1.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.98 %

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: -5.08 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.87 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 379 
 TYR   0.001   0.000   TYR J 310 
 PHE   0.006   0.002   PHE G 378 
 HIS   0.004   0.002   HIS F 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 ( 8210)
  covalent geometry    : angle       1.26442 (10970)
  hydrogen bonds       : bond        0.12355 (  108)
  hydrogen bonds       : angle       5.46285 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 215
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 LYS cc_start: 0.7596 (mttm) cc_final: 0.7173 (tttt)
REVERT: B  286 ASN cc_start: 0.6457 (m110) cc_final: 0.6083 (m110)
REVERT: C  280 LYS cc_start: 0.6608 (mttm) cc_final: 0.6307 (mttm)
REVERT: C  286 ASN cc_start: 0.6462 (m110) cc_final: 0.6255 (m110)
REVERT: D  289 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8102 (m)
REVERT: D  353 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7269 (mttt)
REVERT: E  343 LYS cc_start: 0.8137 (mttt) cc_final: 0.7771 (tttp)
REVERT: F  289 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8325 (m)
REVERT: F  343 LYS cc_start: 0.7980 (mttt) cc_final: 0.7703 (tttp)
REVERT: G  280 LYS cc_start: 0.7572 (mttm) cc_final: 0.7024 (mmtt)
REVERT: G  340 LYS cc_start: 0.8380 (tttt) cc_final: 0.8124 (mtpp)
REVERT: H  280 LYS cc_start: 0.6945 (mttm) cc_final: 0.6669 (mmmt)
REVERT: J  321 LYS cc_start: 0.8060 (tttt) cc_final: 0.7761 (mttm)
REVERT: J  349 ARG cc_start: 0.7625 (mtm180) cc_final: 0.6457 (mmp80)
  outliers start: 40
  outliers final: 24
  residues processed: 241
  average time/residue: 0.2544
  time to fit residues: 79.4049
Evaluate side-chains
  165 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  354 ILE
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  354 ILE
Chi-restraints excluded: chain G residue  354 ILE
Chi-restraints excluded: chain H residue  289 SER
Chi-restraints excluded: chain H residue  295 ASP
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain J residue  289 SER
Chi-restraints excluded: chain J residue  295 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0670
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
A 307 GLN
B 307 GLN
B 374 HIS
C 307 GLN
D 288 GLN
D 307 GLN
E 307 GLN
F 307 GLN
F 329 HIS
F 336 GLN
G 307 GLN
G 329 HIS
H 307 GLN
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 307 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.173455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.130389 restraints weight = 29024.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.4140 rms_B_bonded: 2.51
r_work: 0.4045 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3944 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8210  Z= 0.146
  Angle     :  0.820  14.452  10970  Z= 0.423
  Chirality :  0.135   1.572   1240
  Planarity :  0.003   0.022   1400
  Dihedral  :  8.706  43.937   1127
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 14.38 %
    Favored  : 84.67 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 19.57 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.98 %

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: -5.09 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.88 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 349 
 TYR   0.002   0.000   TYR B 310 
 PHE   0.021   0.003   PHE I 378 
 HIS   0.008   0.001   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8210)
  covalent geometry    : angle       0.82030 (10970)
  hydrogen bonds       : bond        0.04904 (  108)
  hydrogen bonds       : angle       4.37923 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 143
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 LYS cc_start: 0.7688 (mttm) cc_final: 0.7199 (tttt)
REVERT: A  305 ILE cc_start: 0.8065 (pt) cc_final: 0.7662 (mt)
REVERT: B  286 ASN cc_start: 0.6190 (m110) cc_final: 0.5820 (m110)
REVERT: B  305 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7897 (mt)
REVERT: B  338 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7395 (tm-30)
REVERT: D  289 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8009 (m)
REVERT: D  305 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7898 (mt)
REVERT: D  353 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7222 (mttp)
REVERT: E  289 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8097 (m)
REVERT: E  305 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7734 (mt)
REVERT: E  343 LYS cc_start: 0.7889 (mttt) cc_final: 0.7560 (tttp)
REVERT: F  289 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8202 (m)
REVERT: F  305 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.7831 (mt)
REVERT: F  340 LYS cc_start: 0.8252 (tttt) cc_final: 0.8037 (mttt)
REVERT: F  343 LYS cc_start: 0.7757 (mttt) cc_final: 0.7435 (tttp)
REVERT: G  276 GLN cc_start: 0.5700 (OUTLIER) cc_final: 0.4836 (pp30)
REVERT: G  280 LYS cc_start: 0.7386 (mttm) cc_final: 0.7080 (mtpp)
REVERT: G  305 ILE cc_start: 0.8228 (pt) cc_final: 0.7690 (mt)
REVERT: G  340 LYS cc_start: 0.8392 (tttt) cc_final: 0.8042 (mtpp)
REVERT: H  280 LYS cc_start: 0.6801 (mttm) cc_final: 0.6463 (tttt)
REVERT: J  321 LYS cc_start: 0.8027 (tttt) cc_final: 0.7528 (mttm)
REVERT: J  349 ARG cc_start: 0.7514 (mtm180) cc_final: 0.6256 (tpm170)
  outliers start: 52
  outliers final: 33
  residues processed: 181
  average time/residue: 0.2168
  time to fit residues: 52.9321
Evaluate side-chains
  176 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 135
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue  276 GLN
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain G residue  276 GLN
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  354 ILE
Chi-restraints excluded: chain H residue  276 GLN
Chi-restraints excluded: chain H residue  289 SER
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain H residue  376 LEU
Chi-restraints excluded: chain I residue  276 GLN
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Chi-restraints excluded: chain J residue  289 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 296 ASN
C 296 ASN
D 296 ASN
E 296 ASN
E 329 HIS
E 336 GLN
F 296 ASN
G 296 ASN
G 329 HIS
G 336 GLN
H 336 GLN
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 329 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.171512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.129358 restraints weight = 28737.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 2.42
r_work: 0.4039 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3939 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8210  Z= 0.139
  Angle     :  0.840  15.077  10970  Z= 0.417
  Chirality :  0.156   1.734   1240
  Planarity :  0.003   0.032   1400
  Dihedral  :  8.212  45.190   1116
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 15.33 %
    Favored  : 83.71 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 18.28 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.97 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.88 %

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: -5.07 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.86 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 379 
 TYR   0.003   0.000   TYR B 310 
 PHE   0.029   0.003   PHE G 378 
 HIS   0.006   0.001   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8210)
  covalent geometry    : angle       0.83970 (10970)
  hydrogen bonds       : bond        0.03497 (  108)
  hydrogen bonds       : angle       4.14834 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 148
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 LYS cc_start: 0.7704 (mttm) cc_final: 0.7245 (tttt)
REVERT: A  305 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7662 (mt)
REVERT: B  286 ASN cc_start: 0.6244 (m110) cc_final: 0.5971 (m110)
REVERT: B  338 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: C  287 VAL cc_start: 0.6096 (OUTLIER) cc_final: 0.5844 (m)
REVERT: D  289 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.7985 (m)
REVERT: D  305 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8040 (mt)
REVERT: D  329 HIS cc_start: 0.7462 (m170) cc_final: 0.7259 (m170)
REVERT: D  353 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7267 (mttp)
REVERT: E  289 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8057 (m)
REVERT: E  305 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7899 (mt)
REVERT: E  343 LYS cc_start: 0.7857 (mttt) cc_final: 0.7498 (tttp)
REVERT: E  348 ASP cc_start: 0.8454 (p0) cc_final: 0.7978 (p0)
REVERT: E  378 PHE cc_start: 0.6327 (t80) cc_final: 0.5035 (t80)
REVERT: F  289 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8119 (m)
REVERT: F  305 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8014 (mt)
REVERT: F  340 LYS cc_start: 0.8258 (tttt) cc_final: 0.7951 (mtpp)
REVERT: F  343 LYS cc_start: 0.7764 (mttt) cc_final: 0.7388 (tttp)
REVERT: F  378 PHE cc_start: 0.6824 (t80) cc_final: 0.5974 (t80)
REVERT: G  276 GLN cc_start: 0.5843 (OUTLIER) cc_final: 0.5322 (pp30)
REVERT: G  280 LYS cc_start: 0.7318 (mttm) cc_final: 0.6988 (mtpp)
REVERT: G  305 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7808 (mt)
REVERT: G  340 LYS cc_start: 0.8408 (tttt) cc_final: 0.7979 (mtpp)
REVERT: H  280 LYS cc_start: 0.6738 (mttm) cc_final: 0.6425 (tttt)
REVERT: H  287 VAL cc_start: 0.6294 (OUTLIER) cc_final: 0.5997 (m)
REVERT: H  305 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7913 (mt)
REVERT: J  321 LYS cc_start: 0.8029 (tttt) cc_final: 0.7527 (mttm)
REVERT: J  349 ARG cc_start: 0.7520 (mtm180) cc_final: 0.6178 (mmp80)
  outliers start: 63
  outliers final: 37
  residues processed: 193
  average time/residue: 0.2113
  time to fit residues: 55.8717
Evaluate side-chains
  190 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 141
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain B residue  276 GLN
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  275 VAL
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  336 GLN
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  276 GLN
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  305 ILE
Chi-restraints excluded: chain H residue  276 GLN
Chi-restraints excluded: chain H residue  287 VAL
Chi-restraints excluded: chain H residue  289 SER
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  336 GLN
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  276 GLN
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 374 HIS
E 336 GLN
G 329 HIS
H 296 ASN
I 296 ASN
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 329 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.171079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.128843 restraints weight = 28946.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 2.45
r_work: 0.4079 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3976 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8210  Z= 0.132
  Angle     :  0.819  15.301  10970  Z= 0.406
  Chirality :  0.152   1.637   1240
  Planarity :  0.003   0.022   1400
  Dihedral  :  7.849  47.102   1109
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 14.29 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 19.68 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.43 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.88 %

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: -5.06 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 349 
 TYR   0.003   0.000   TYR B 310 
 PHE   0.015   0.002   PHE G 378 
 HIS   0.005   0.001   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8210)
  covalent geometry    : angle       0.81941 (10970)
  hydrogen bonds       : bond        0.03267 (  108)
  hydrogen bonds       : angle       4.22599 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 147
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 LYS cc_start: 0.7750 (mttm) cc_final: 0.7200 (ttmt)
REVERT: A  305 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7715 (mt)
REVERT: B  286 ASN cc_start: 0.6413 (m110) cc_final: 0.6080 (m110)
REVERT: B  338 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7488 (tm-30)
REVERT: C  287 VAL cc_start: 0.6166 (OUTLIER) cc_final: 0.5912 (m)
REVERT: C  378 PHE cc_start: 0.6378 (t80) cc_final: 0.6174 (t80)
REVERT: D  289 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8077 (m)
REVERT: D  305 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8074 (mt)
REVERT: D  329 HIS cc_start: 0.7627 (m170) cc_final: 0.7415 (m170)
REVERT: D  353 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7379 (mttp)
REVERT: E  289 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8122 (m)
REVERT: E  305 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7910 (mt)
REVERT: E  343 LYS cc_start: 0.7979 (mttt) cc_final: 0.7619 (tttp)
REVERT: E  348 ASP cc_start: 0.8429 (p0) cc_final: 0.7983 (p0)
REVERT: E  374 HIS cc_start: 0.6814 (m170) cc_final: 0.6518 (m90)
REVERT: E  378 PHE cc_start: 0.6501 (t80) cc_final: 0.5333 (t80)
REVERT: F  289 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8181 (m)
REVERT: F  305 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8022 (mt)
REVERT: F  340 LYS cc_start: 0.8297 (tttt) cc_final: 0.8023 (mtpp)
REVERT: F  343 LYS cc_start: 0.7933 (mttt) cc_final: 0.7568 (tttp)
REVERT: F  378 PHE cc_start: 0.6951 (t80) cc_final: 0.6418 (t80)
REVERT: G  276 GLN cc_start: 0.5743 (OUTLIER) cc_final: 0.5202 (pp30)
REVERT: G  280 LYS cc_start: 0.7419 (mttm) cc_final: 0.7078 (mtpp)
REVERT: G  305 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7794 (mt)
REVERT: G  340 LYS cc_start: 0.8461 (tttt) cc_final: 0.8075 (mtpp)
REVERT: H  279 ASN cc_start: 0.7314 (t0) cc_final: 0.7078 (m-40)
REVERT: H  280 LYS cc_start: 0.6779 (mttm) cc_final: 0.6453 (tttt)
REVERT: H  287 VAL cc_start: 0.6470 (OUTLIER) cc_final: 0.6148 (m)
REVERT: H  305 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7986 (mt)
REVERT: J  321 LYS cc_start: 0.8101 (tttt) cc_final: 0.7604 (mttm)
REVERT: J  349 ARG cc_start: 0.7641 (mtm180) cc_final: 0.6419 (mmt-90)
  outliers start: 53
  outliers final: 37
  residues processed: 183
  average time/residue: 0.2056
  time to fit residues: 51.6431
Evaluate side-chains
  191 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 142
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  289 SER
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  289 SER
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  276 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  305 ILE
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain H residue  276 GLN
Chi-restraints excluded: chain H residue  287 VAL
Chi-restraints excluded: chain H residue  289 SER
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 40 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0980
   chunk 66 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
B 374 HIS
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.170936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.128382 restraints weight = 28384.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 2.46
r_work: 0.4037 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3937 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8210  Z= 0.170
  Angle     :  0.837  15.391  10970  Z= 0.417
  Chirality :  0.154   1.672   1240
  Planarity :  0.003   0.029   1400
  Dihedral  :  7.950  50.385   1108
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 17.05 %
    Favored  : 82.00 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 19.25 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.43 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

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: -5.10 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.88 (0.13), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I 349 
 TYR   0.005   0.001   TYR B 310 
 PHE   0.019   0.002   PHE J 378 
 HIS   0.007   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8210)
  covalent geometry    : angle       0.83671 (10970)
  hydrogen bonds       : bond        0.03165 (  108)
  hydrogen bonds       : angle       4.27578 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 150
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.6769 (t0) cc_final: 0.6513 (t0)
REVERT: A  280 LYS cc_start: 0.7780 (mttm) cc_final: 0.7235 (ttmt)
REVERT: A  305 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7764 (mt)
REVERT: B  338 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7433 (tm-30)
REVERT: C  287 VAL cc_start: 0.6136 (OUTLIER) cc_final: 0.5907 (m)
REVERT: C  378 PHE cc_start: 0.6689 (t80) cc_final: 0.6472 (t80)
REVERT: D  289 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8105 (m)
REVERT: D  305 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8027 (mt)
REVERT: D  329 HIS cc_start: 0.7794 (m170) cc_final: 0.7593 (m170)
REVERT: D  353 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7318 (mttp)
REVERT: E  289 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8167 (m)
REVERT: E  305 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7962 (mt)
REVERT: E  343 LYS cc_start: 0.7935 (mttt) cc_final: 0.7522 (tttp)
REVERT: E  348 ASP cc_start: 0.8493 (p0) cc_final: 0.8022 (p0)
REVERT: E  374 HIS cc_start: 0.6834 (m170) cc_final: 0.6516 (m90)
REVERT: E  378 PHE cc_start: 0.6733 (t80) cc_final: 0.6384 (t80)
REVERT: F  289 SER cc_start: 0.8825 (p) cc_final: 0.8204 (m)
REVERT: F  305 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8016 (mt)
REVERT: F  340 LYS cc_start: 0.8323 (tttt) cc_final: 0.8046 (mtpp)
REVERT: F  343 LYS cc_start: 0.7888 (mttt) cc_final: 0.7475 (tttp)
REVERT: G  276 GLN cc_start: 0.5983 (OUTLIER) cc_final: 0.5484 (pp30)
REVERT: G  280 LYS cc_start: 0.7372 (mttm) cc_final: 0.6998 (mtpp)
REVERT: G  305 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7661 (mt)
REVERT: G  340 LYS cc_start: 0.8453 (tttt) cc_final: 0.8050 (mtpp)
REVERT: H  280 LYS cc_start: 0.6852 (mttm) cc_final: 0.6492 (tttt)
REVERT: H  287 VAL cc_start: 0.6490 (OUTLIER) cc_final: 0.6193 (m)
REVERT: H  289 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8299 (m)
REVERT: H  305 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7936 (mt)
REVERT: I  349 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7952 (mtp-110)
REVERT: J  321 LYS cc_start: 0.8125 (tttt) cc_final: 0.7628 (mttm)
REVERT: J  349 ARG cc_start: 0.7599 (mtm180) cc_final: 0.6345 (mmt-90)
  outliers start: 57
  outliers final: 40
  residues processed: 194
  average time/residue: 0.1969
  time to fit residues: 52.3526
Evaluate side-chains
  193 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 141
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  289 SER
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  276 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  305 ILE
Chi-restraints excluded: chain H residue  276 GLN
Chi-restraints excluded: chain H residue  287 VAL
Chi-restraints excluded: chain H residue  289 SER
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  318 VAL
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  276 GLN
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
B 286 ASN
B 374 HIS
I 279 ASN
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 336 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.171774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.129430 restraints weight = 28432.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.4150 rms_B_bonded: 2.46
r_work: 0.4050 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3948 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8210  Z= 0.139
  Angle     :  0.819  15.494  10970  Z= 0.404
  Chirality :  0.153   1.652   1240
  Planarity :  0.003   0.022   1400
  Dihedral  :  7.740  50.993   1104
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 15.24 %
    Favored  : 83.81 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 20.75 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.43 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

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: -5.03 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.13), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 349 
 TYR   0.003   0.000   TYR B 310 
 PHE   0.019   0.002   PHE D 378 
 HIS   0.005   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8210)
  covalent geometry    : angle       0.81886 (10970)
  hydrogen bonds       : bond        0.02958 (  108)
  hydrogen bonds       : angle       4.31609 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 148
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.6840 (t0) cc_final: 0.6557 (t0)
REVERT: A  280 LYS cc_start: 0.7751 (mttm) cc_final: 0.7222 (ttpt)
REVERT: A  305 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7774 (mt)
REVERT: B  338 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7466 (tm-30)
REVERT: B  372 GLU cc_start: 0.4627 (OUTLIER) cc_final: 0.3949 (mm-30)
REVERT: C  287 VAL cc_start: 0.6119 (OUTLIER) cc_final: 0.5891 (m)
REVERT: D  289 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8064 (m)
REVERT: D  295 ASP cc_start: 0.8290 (p0) cc_final: 0.7858 (p0)
REVERT: D  305 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8000 (mt)
REVERT: D  353 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7338 (mttp)
REVERT: E  289 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.7941 (m)
REVERT: E  305 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7920 (mt)
REVERT: E  343 LYS cc_start: 0.7936 (mttt) cc_final: 0.7532 (tttp)
REVERT: E  348 ASP cc_start: 0.8476 (p0) cc_final: 0.8015 (p0)
REVERT: E  374 HIS cc_start: 0.6825 (m170) cc_final: 0.6455 (m90)
REVERT: E  378 PHE cc_start: 0.6608 (t80) cc_final: 0.6198 (t80)
REVERT: F  289 SER cc_start: 0.8796 (p) cc_final: 0.8126 (m)
REVERT: F  305 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7989 (mt)
REVERT: F  343 LYS cc_start: 0.7924 (mttt) cc_final: 0.7522 (tttp)
REVERT: F  374 HIS cc_start: 0.6924 (m-70) cc_final: 0.6621 (m90)
REVERT: G  276 GLN cc_start: 0.5965 (OUTLIER) cc_final: 0.5494 (pp30)
REVERT: G  280 LYS cc_start: 0.7371 (mttm) cc_final: 0.6994 (mtpp)
REVERT: G  305 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7657 (mt)
REVERT: G  340 LYS cc_start: 0.8468 (tttt) cc_final: 0.8126 (mtpp)
REVERT: H  280 LYS cc_start: 0.6868 (mttm) cc_final: 0.6470 (tttt)
REVERT: H  287 VAL cc_start: 0.6441 (OUTLIER) cc_final: 0.6119 (m)
REVERT: H  305 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7910 (mt)
REVERT: I  276 GLN cc_start: 0.6021 (OUTLIER) cc_final: 0.5766 (pp30)
REVERT: I  349 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7735 (mtp180)
REVERT: J  321 LYS cc_start: 0.8138 (tttt) cc_final: 0.7643 (mttm)
REVERT: J  349 ARG cc_start: 0.7631 (mtm180) cc_final: 0.6382 (mmt-90)
  outliers start: 51
  outliers final: 34
  residues processed: 183
  average time/residue: 0.2109
  time to fit residues: 52.1283
Evaluate side-chains
  191 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 144
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain B residue  361 THR
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  276 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  305 ILE
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain H residue  287 VAL
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  318 VAL
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  276 GLN
Chi-restraints excluded: chain I residue  279 ASN
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0470
   chunk 34 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 374 HIS
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.172797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.130312 restraints weight = 28143.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 2.47
r_work: 0.4069 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3969 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8210  Z= 0.125
  Angle     :  0.803  15.468  10970  Z= 0.395
  Chirality :  0.153   1.647   1240
  Planarity :  0.003   0.022   1400
  Dihedral  :  7.510  50.295   1100
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 15.05 %
    Favored  : 84.00 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 21.51 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.65 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

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: -4.95 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.77 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 349 
 TYR   0.002   0.000   TYR B 310 
 PHE   0.022   0.002   PHE G 378 
 HIS   0.005   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8210)
  covalent geometry    : angle       0.80288 (10970)
  hydrogen bonds       : bond        0.02819 (  108)
  hydrogen bonds       : angle       4.26170 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 147
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.6958 (t0) cc_final: 0.6418 (t0)
REVERT: A  280 LYS cc_start: 0.7735 (mttm) cc_final: 0.7199 (ttpt)
REVERT: A  281 LYS cc_start: 0.7727 (mtpt) cc_final: 0.7215 (mttt)
REVERT: A  305 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7752 (mt)
REVERT: B  286 ASN cc_start: 0.6432 (m-40) cc_final: 0.6173 (m110)
REVERT: B  338 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7372 (tm-30)
REVERT: C  287 VAL cc_start: 0.6064 (OUTLIER) cc_final: 0.5848 (m)
REVERT: D  289 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8050 (m)
REVERT: D  295 ASP cc_start: 0.8206 (p0) cc_final: 0.7771 (p0)
REVERT: D  305 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7937 (mt)
REVERT: D  353 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7331 (mttp)
REVERT: E  289 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.7931 (m)
REVERT: E  305 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7890 (mt)
REVERT: E  343 LYS cc_start: 0.7921 (mttt) cc_final: 0.7525 (tttp)
REVERT: E  348 ASP cc_start: 0.8466 (p0) cc_final: 0.8022 (p0)
REVERT: E  374 HIS cc_start: 0.6803 (m170) cc_final: 0.6368 (m90)
REVERT: E  378 PHE cc_start: 0.6721 (t80) cc_final: 0.6366 (t80)
REVERT: F  279 ASN cc_start: 0.6751 (t0) cc_final: 0.6026 (t0)
REVERT: F  289 SER cc_start: 0.8763 (p) cc_final: 0.8115 (m)
REVERT: F  305 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7954 (mt)
REVERT: F  343 LYS cc_start: 0.7912 (mttt) cc_final: 0.7517 (tttp)
REVERT: F  374 HIS cc_start: 0.6877 (m-70) cc_final: 0.6563 (m90)
REVERT: G  280 LYS cc_start: 0.7410 (mttm) cc_final: 0.6982 (mtpp)
REVERT: G  305 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7619 (mt)
REVERT: G  340 LYS cc_start: 0.8478 (tttt) cc_final: 0.8134 (mtpp)
REVERT: H  280 LYS cc_start: 0.6884 (mttm) cc_final: 0.6486 (tttt)
REVERT: H  287 VAL cc_start: 0.6391 (OUTLIER) cc_final: 0.6056 (m)
REVERT: H  305 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7915 (mt)
REVERT: I  349 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.7707 (mtp180)
REVERT: J  321 LYS cc_start: 0.8124 (tttt) cc_final: 0.7635 (mttm)
REVERT: J  349 ARG cc_start: 0.7629 (mtm180) cc_final: 0.6355 (mmt-90)
  outliers start: 47
  outliers final: 35
  residues processed: 180
  average time/residue: 0.2181
  time to fit residues: 53.2924
Evaluate side-chains
  188 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 143
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  276 GLN
Chi-restraints excluded: chain E residue  289 SER
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  305 ILE
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain H residue  276 GLN
Chi-restraints excluded: chain H residue  287 VAL
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Chi-restraints excluded: chain J residue  336 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0770
   chunk 50 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
B 374 HIS
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.173079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.130822 restraints weight = 28264.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.4166 rms_B_bonded: 2.47
r_work: 0.4065 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3964 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8210  Z= 0.125
  Angle     :  0.804  15.423  10970  Z= 0.396
  Chirality :  0.153   1.653   1240
  Planarity :  0.003   0.021   1400
  Dihedral  :  7.454  49.616   1100
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 14.86 %
    Favored  : 84.19 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 21.83 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.65 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

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: -4.95 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 379 
 TYR   0.002   0.000   TYR B 310 
 PHE   0.026   0.002   PHE J 378 
 HIS   0.004   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8210)
  covalent geometry    : angle       0.80358 (10970)
  hydrogen bonds       : bond        0.02760 (  108)
  hydrogen bonds       : angle       4.21919 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 146
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.7032 (t0) cc_final: 0.6517 (t0)
REVERT: A  280 LYS cc_start: 0.7702 (mttm) cc_final: 0.7207 (ttpt)
REVERT: A  281 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7257 (mttt)
REVERT: A  305 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7787 (mt)
REVERT: B  286 ASN cc_start: 0.6370 (m-40) cc_final: 0.6109 (m110)
REVERT: B  338 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7350 (tm-30)
REVERT: B  372 GLU cc_start: 0.4417 (OUTLIER) cc_final: 0.3904 (mm-30)
REVERT: C  287 VAL cc_start: 0.5991 (OUTLIER) cc_final: 0.5773 (m)
REVERT: D  289 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8072 (m)
REVERT: D  295 ASP cc_start: 0.8164 (p0) cc_final: 0.7757 (p0)
REVERT: D  305 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7873 (mt)
REVERT: D  353 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7280 (mttp)
REVERT: E  289 SER cc_start: 0.8605 (p) cc_final: 0.8152 (m)
REVERT: E  305 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7845 (mt)
REVERT: E  343 LYS cc_start: 0.7875 (mttt) cc_final: 0.7465 (tttp)
REVERT: E  348 ASP cc_start: 0.8491 (p0) cc_final: 0.8039 (p0)
REVERT: E  374 HIS cc_start: 0.6781 (m170) cc_final: 0.6320 (m90)
REVERT: E  378 PHE cc_start: 0.6813 (t80) cc_final: 0.6470 (t80)
REVERT: F  279 ASN cc_start: 0.6760 (t0) cc_final: 0.6064 (t0)
REVERT: F  289 SER cc_start: 0.8710 (p) cc_final: 0.8106 (m)
REVERT: F  295 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.6498 (m-30)
REVERT: F  305 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7914 (mt)
REVERT: F  343 LYS cc_start: 0.7875 (mttt) cc_final: 0.7469 (tttp)
REVERT: F  374 HIS cc_start: 0.6852 (m-70) cc_final: 0.6528 (m90)
REVERT: G  280 LYS cc_start: 0.7327 (mttm) cc_final: 0.6902 (mtpp)
REVERT: G  305 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7560 (mt)
REVERT: G  340 LYS cc_start: 0.8468 (tttt) cc_final: 0.8103 (mtpp)
REVERT: H  280 LYS cc_start: 0.6811 (mttm) cc_final: 0.6433 (tttt)
REVERT: H  287 VAL cc_start: 0.6338 (OUTLIER) cc_final: 0.6010 (m)
REVERT: H  305 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7925 (mt)
REVERT: I  349 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7680 (mtp180)
REVERT: J  321 LYS cc_start: 0.8090 (tttt) cc_final: 0.7586 (mttm)
REVERT: J  349 ARG cc_start: 0.7555 (mtm180) cc_final: 0.6279 (mmt-90)
  outliers start: 51
  outliers final: 38
  residues processed: 182
  average time/residue: 0.2063
  time to fit residues: 51.5293
Evaluate side-chains
  194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 145
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  372 GLU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  342 GLU
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  276 GLN
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  276 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  305 ILE
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain H residue  276 GLN
Chi-restraints excluded: chain H residue  287 VAL
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  318 VAL
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.171936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.129926 restraints weight = 28119.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 2.45
r_work: 0.4054 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3954 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8210  Z= 0.135
  Angle     :  0.803  15.379  10970  Z= 0.395
  Chirality :  0.153   1.665   1240
  Planarity :  0.003   0.021   1400
  Dihedral  :  7.418  49.194   1099
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 16.38 %
    Favored  : 82.67 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 22.37 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.43 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

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: -4.95 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.77 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 379 
 TYR   0.003   0.000   TYR C 310 
 PHE   0.029   0.002   PHE G 378 
 HIS   0.004   0.001   HIS D 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8210)
  covalent geometry    : angle       0.80334 (10970)
  hydrogen bonds       : bond        0.02768 (  108)
  hydrogen bonds       : angle       4.20747 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 145
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.7236 (t0) cc_final: 0.6735 (t0)
REVERT: A  280 LYS cc_start: 0.7833 (mttm) cc_final: 0.7355 (ttmt)
REVERT: A  281 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7278 (mttt)
REVERT: A  305 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7840 (mt)
REVERT: B  286 ASN cc_start: 0.6455 (m-40) cc_final: 0.6204 (m110)
REVERT: B  338 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7331 (tm-30)
REVERT: D  279 ASN cc_start: 0.7026 (t0) cc_final: 0.6674 (t0)
REVERT: D  289 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8119 (m)
REVERT: D  295 ASP cc_start: 0.8206 (p0) cc_final: 0.7012 (p0)
REVERT: D  305 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7883 (mt)
REVERT: E  289 SER cc_start: 0.8610 (p) cc_final: 0.8174 (m)
REVERT: E  295 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7580 (m-30)
REVERT: E  305 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7882 (mt)
REVERT: E  343 LYS cc_start: 0.7916 (mttt) cc_final: 0.7510 (tttp)
REVERT: E  348 ASP cc_start: 0.8505 (p0) cc_final: 0.8055 (p0)
REVERT: E  374 HIS cc_start: 0.6840 (m170) cc_final: 0.6609 (m90)
REVERT: E  378 PHE cc_start: 0.6870 (t80) cc_final: 0.6515 (t80)
REVERT: F  289 SER cc_start: 0.8734 (p) cc_final: 0.8151 (m)
REVERT: F  305 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7936 (mt)
REVERT: F  343 LYS cc_start: 0.7903 (mttt) cc_final: 0.7506 (tttp)
REVERT: F  374 HIS cc_start: 0.6929 (m-70) cc_final: 0.6589 (m90)
REVERT: G  279 ASN cc_start: 0.7099 (t0) cc_final: 0.6213 (t0)
REVERT: G  280 LYS cc_start: 0.7369 (mttm) cc_final: 0.7002 (mtpp)
REVERT: G  305 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7552 (mt)
REVERT: G  340 LYS cc_start: 0.8504 (tttt) cc_final: 0.8141 (mtpp)
REVERT: H  280 LYS cc_start: 0.6811 (mttm) cc_final: 0.6400 (tttt)
REVERT: H  287 VAL cc_start: 0.6375 (OUTLIER) cc_final: 0.6047 (m)
REVERT: H  305 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7952 (mt)
REVERT: I  349 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.7725 (mtp180)
REVERT: J  321 LYS cc_start: 0.8107 (tttt) cc_final: 0.7619 (mttm)
REVERT: J  349 ARG cc_start: 0.7561 (mtm180) cc_final: 0.6264 (mmt-90)
REVERT: J  374 HIS cc_start: 0.7267 (m170) cc_final: 0.6962 (m90)
  outliers start: 52
  outliers final: 39
  residues processed: 181
  average time/residue: 0.2032
  time to fit residues: 50.4196
Evaluate side-chains
  193 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 145
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain C residue  378 PHE
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  359 ASN
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  276 GLN
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  276 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  305 ILE
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain H residue  276 GLN
Chi-restraints excluded: chain H residue  287 VAL
Chi-restraints excluded: chain H residue  289 SER
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  318 VAL
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 374 HIS
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.169620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.128014 restraints weight = 28442.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.4127 rms_B_bonded: 2.44
r_work: 0.4026 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3923 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8210  Z= 0.162
  Angle     :  0.823  15.355  10970  Z= 0.407
  Chirality :  0.154   1.679   1240
  Planarity :  0.003   0.022   1400
  Dihedral  :  7.569  57.098   1099
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 17.52 %
    Favored  : 81.52 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 22.58 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.32 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

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: -4.95 (0.18), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 379 
 TYR   0.004   0.001   TYR B 310 
 PHE   0.026   0.002   PHE J 378 
 HIS   0.005   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8210)
  covalent geometry    : angle       0.82258 (10970)
  hydrogen bonds       : bond        0.02886 (  108)
  hydrogen bonds       : angle       4.25402 (  324)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 149
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 ASN cc_start: 0.7375 (t0) cc_final: 0.6815 (t0)
REVERT: A  280 LYS cc_start: 0.7715 (mttm) cc_final: 0.7333 (ttmt)
REVERT: A  281 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7282 (mttt)
REVERT: A  305 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7801 (mt)
REVERT: B  286 ASN cc_start: 0.6548 (m-40) cc_final: 0.6306 (m110)
REVERT: B  338 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7306 (tm-30)
REVERT: C  287 VAL cc_start: 0.6002 (OUTLIER) cc_final: 0.5795 (m)
REVERT: D  279 ASN cc_start: 0.7073 (t0) cc_final: 0.6664 (t0)
REVERT: D  289 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8113 (m)
REVERT: D  295 ASP cc_start: 0.8280 (p0) cc_final: 0.7377 (p0)
REVERT: D  305 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7841 (mt)
REVERT: E  289 SER cc_start: 0.8617 (p) cc_final: 0.8169 (m)
REVERT: E  295 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7882 (m-30)
REVERT: E  305 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7844 (mt)
REVERT: E  343 LYS cc_start: 0.7871 (mttt) cc_final: 0.7449 (tttp)
REVERT: E  348 ASP cc_start: 0.8533 (p0) cc_final: 0.8058 (p0)
REVERT: E  374 HIS cc_start: 0.6828 (m170) cc_final: 0.6582 (m90)
REVERT: E  378 PHE cc_start: 0.6937 (t80) cc_final: 0.6565 (t80)
REVERT: F  289 SER cc_start: 0.8746 (p) cc_final: 0.8153 (m)
REVERT: F  305 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7899 (mt)
REVERT: F  343 LYS cc_start: 0.7854 (mttt) cc_final: 0.7424 (tttp)
REVERT: F  374 HIS cc_start: 0.6995 (m-70) cc_final: 0.6640 (m90)
REVERT: G  279 ASN cc_start: 0.7174 (t0) cc_final: 0.6254 (t0)
REVERT: G  280 LYS cc_start: 0.7315 (mttm) cc_final: 0.7069 (mtmt)
REVERT: G  305 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7469 (mt)
REVERT: G  340 LYS cc_start: 0.8512 (tttt) cc_final: 0.8126 (mtpp)
REVERT: H  280 LYS cc_start: 0.6782 (mttm) cc_final: 0.6567 (tttt)
REVERT: H  287 VAL cc_start: 0.6357 (OUTLIER) cc_final: 0.6057 (m)
REVERT: H  289 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8246 (m)
REVERT: H  305 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7912 (mt)
REVERT: I  349 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7781 (mtp180)
REVERT: I  378 PHE cc_start: 0.6987 (m-80) cc_final: 0.6385 (m-10)
REVERT: J  321 LYS cc_start: 0.8082 (tttt) cc_final: 0.7590 (mttm)
REVERT: J  374 HIS cc_start: 0.7297 (m170) cc_final: 0.6975 (m90)
  outliers start: 53
  outliers final: 39
  residues processed: 185
  average time/residue: 0.2006
  time to fit residues: 51.7256
Evaluate side-chains
  197 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 147
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ASP
Chi-restraints excluded: chain A residue  359 ASN
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  341 SER
Chi-restraints excluded: chain B residue  359 ASN
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain C residue  341 SER
Chi-restraints excluded: chain C residue  359 ASN
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  289 SER
Chi-restraints excluded: chain D residue  305 ILE
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  341 SER
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain E residue  295 ASP
Chi-restraints excluded: chain E residue  305 ILE
Chi-restraints excluded: chain E residue  315 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  351 GLN
Chi-restraints excluded: chain E residue  359 ASN
Chi-restraints excluded: chain E residue  361 THR
Chi-restraints excluded: chain F residue  276 GLN
Chi-restraints excluded: chain F residue  295 ASP
Chi-restraints excluded: chain F residue  305 ILE
Chi-restraints excluded: chain F residue  351 GLN
Chi-restraints excluded: chain F residue  359 ASN
Chi-restraints excluded: chain F residue  361 THR
Chi-restraints excluded: chain G residue  276 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  295 ASP
Chi-restraints excluded: chain G residue  305 ILE
Chi-restraints excluded: chain G residue  315 LEU
Chi-restraints excluded: chain H residue  276 GLN
Chi-restraints excluded: chain H residue  287 VAL
Chi-restraints excluded: chain H residue  289 SER
Chi-restraints excluded: chain H residue  305 ILE
Chi-restraints excluded: chain H residue  318 VAL
Chi-restraints excluded: chain H residue  341 SER
Chi-restraints excluded: chain H residue  354 ILE
Chi-restraints excluded: chain H residue  361 THR
Chi-restraints excluded: chain I residue  289 SER
Chi-restraints excluded: chain I residue  295 ASP
Chi-restraints excluded: chain I residue  318 VAL
Chi-restraints excluded: chain I residue  341 SER
Chi-restraints excluded: chain I residue  361 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
B 374 HIS
** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.168249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.126891 restraints weight = 28502.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 2.44
r_work: 0.4017 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3913 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8210  Z= 0.169
  Angle     :  0.834  15.474  10970  Z= 0.414
  Chirality :  0.154   1.692   1240
  Planarity :  0.003   0.026   1400
  Dihedral  :  7.649  54.281   1099
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.95 %
    Allowed  : 18.00 %
    Favored  : 81.05 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 23.12 %
    Favored  : 71.40 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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: -4.92 (0.19), residues: 1050
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.14), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG G 379 
 TYR   0.004   0.001   TYR B 310 
 PHE   0.009   0.002   PHE H 378 
 HIS   0.005   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8210)
  covalent geometry    : angle       0.83365 (10970)
  hydrogen bonds       : bond        0.02947 (  108)
  hydrogen bonds       : angle       4.34903 (  324)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4904.09 seconds
wall clock time: 84 minutes 7.52 seconds (5047.52 seconds total)