Starting phenix.real_space_refine
on Tue Mar  3 18:23:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xss_22305/03_2026/6xss_22305.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xss_22305/03_2026/6xss_22305.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xss_22305/03_2026/6xss_22305.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xss_22305/03_2026/6xss_22305.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xss_22305/03_2026/6xss_22305.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xss_22305/03_2026/6xss_22305.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       8      5.16       5
     C    4956      2.51       5
     N    1464      2.21       5
     O    1620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8048
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 260, 2012
          Classifications: {'peptide': 260}
          Link IDs: {'PTRANS': 8, 'TRANS': 251}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.11, per 1000 atoms: 0.14
  Number of scatterers: 8048
  At special positions: 0
  Unit cell: (121.119, 121.119, 77.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       8     16.00
     O    1620      8.00
     N    1464      7.00
     C    4956      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 306.6 milliseconds
  

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2024

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      95.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 14
      removed outlier: 3.811A  pdb=" N   VAL A   5 " --> pdb=" O   ALA A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 31
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 3.839A  pdb=" N   LEU A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU A  48 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 65
    Processing helix  chain 'A' and resid 68 through 99
      removed outlier: 3.600A  pdb=" N   ARG A  72 " --> pdb=" O   MET A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 124
    Processing helix  chain 'A' and resid 127 through 155
    Processing helix  chain 'A' and resid 156 through 180
    Processing helix  chain 'A' and resid 183 through 211
    Processing helix  chain 'A' and resid 212 through 236
    Processing helix  chain 'A' and resid 239 through 260
    Processing helix  chain 'B' and resid 2 through 14
    Processing helix  chain 'B' and resid 16 through 31
    Processing helix  chain 'B' and resid 34 through 49
      removed outlier: 3.839A  pdb=" N   LEU B  47 " --> pdb=" O   SER B  43 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B  48 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 65
    Processing helix  chain 'B' and resid 68 through 99
      removed outlier: 3.600A  pdb=" N   ARG B  72 " --> pdb=" O   MET B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 124
    Processing helix  chain 'B' and resid 127 through 155
    Processing helix  chain 'B' and resid 156 through 180
    Processing helix  chain 'B' and resid 183 through 211
    Processing helix  chain 'B' and resid 212 through 236
    Processing helix  chain 'B' and resid 239 through 260
    Processing helix  chain 'C' and resid 2 through 14
    Processing helix  chain 'C' and resid 16 through 31
    Processing helix  chain 'C' and resid 34 through 49
      removed outlier: 3.839A  pdb=" N   LEU C  47 " --> pdb=" O   SER C  43 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU C  48 " --> pdb=" O   VAL C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 65
    Processing helix  chain 'C' and resid 68 through 99
      removed outlier: 3.600A  pdb=" N   ARG C  72 " --> pdb=" O   MET C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 124
    Processing helix  chain 'C' and resid 127 through 155
    Processing helix  chain 'C' and resid 156 through 180
    Processing helix  chain 'C' and resid 183 through 211
    Processing helix  chain 'C' and resid 212 through 236
    Processing helix  chain 'C' and resid 239 through 260
    Processing helix  chain 'D' and resid 2 through 14
    Processing helix  chain 'D' and resid 16 through 31
    Processing helix  chain 'D' and resid 34 through 49
      removed outlier: 3.839A  pdb=" N   LEU D  47 " --> pdb=" O   SER D  43 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 65
    Processing helix  chain 'D' and resid 68 through 99
      removed outlier: 3.600A  pdb=" N   ARG D  72 " --> pdb=" O   MET D  68 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 124
    Processing helix  chain 'D' and resid 127 through 155
    Processing helix  chain 'D' and resid 156 through 180
    Processing helix  chain 'D' and resid 183 through 211
    Processing helix  chain 'D' and resid 212 through 236
    Processing helix  chain 'D' and resid 239 through 260

    804 hydrogen bonds defined for protein.
    2412 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: 1.37

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2960
        1.34 -     1.46: 365
        1.46 -     1.57: 4755
        1.57 -     1.69: 0
        1.69 -     1.80: 16
  Bond restraints: 8096
  Sorted by residual:
  bond pdb=" N   ASN A  15 "
       pdb=" CA  ASN A  15 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.32e-02 5.74e+03 9.92e-01
  bond pdb=" N   ASN B  15 "
       pdb=" CA  ASN B  15 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.32e-02 5.74e+03 9.81e-01
  bond pdb=" N   ASN C  15 "
       pdb=" CA  ASN C  15 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.32e-02 5.74e+03 9.63e-01
  bond pdb=" N   ASN D  15 "
       pdb=" CA  ASN D  15 "
    ideal  model  delta    sigma   weight residual
    1.459  1.471 -0.013 1.32e-02 5.74e+03 9.34e-01
  bond pdb=" C   GLY D  49 "
       pdb=" O   GLY D  49 "
    ideal  model  delta    sigma   weight residual
    1.240  1.229  0.012 1.29e-02 6.01e+03 7.97e-01
  ... (remaining 8091 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 10856
        2.72 -     5.44: 65
        5.44 -     8.16: 7
        8.16 -    10.88: 0
       10.88 -    13.60: 4
  Bond angle restraints: 10932
  Sorted by residual:
  angle pdb=" CA  LEU A 222 "
        pdb=" CB  LEU A 222 "
        pdb=" CG  LEU A 222 "
      ideal   model   delta    sigma   weight residual
     116.30  129.90  -13.60 3.50e+00 8.16e-02 1.51e+01
  angle pdb=" CA  LEU D 222 "
        pdb=" CB  LEU D 222 "
        pdb=" CG  LEU D 222 "
      ideal   model   delta    sigma   weight residual
     116.30  129.89  -13.59 3.50e+00 8.16e-02 1.51e+01
  angle pdb=" CA  LEU C 222 "
        pdb=" CB  LEU C 222 "
        pdb=" CG  LEU C 222 "
      ideal   model   delta    sigma   weight residual
     116.30  129.89  -13.59 3.50e+00 8.16e-02 1.51e+01
  angle pdb=" CA  LEU B 222 "
        pdb=" CB  LEU B 222 "
        pdb=" CG  LEU B 222 "
      ideal   model   delta    sigma   weight residual
     116.30  129.84  -13.54 3.50e+00 8.16e-02 1.50e+01
  angle pdb=" N   GLY C  49 "
        pdb=" CA  GLY C  49 "
        pdb=" C   GLY C  49 "
      ideal   model   delta    sigma   weight residual
     114.85  110.60    4.25 1.35e+00 5.49e-01 9.90e+00
  ... (remaining 10927 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 4804
       17.34 -    34.68: 360
       34.68 -    52.02: 40
       52.02 -    69.37: 4
       69.37 -    86.71: 12
  Dihedral angle restraints: 5220
    sinusoidal: 2156
      harmonic: 3064
  Sorted by residual:
  dihedral pdb=" N   ASN C  15 "
           pdb=" C   ASN C  15 "
           pdb=" CA  ASN C  15 "
           pdb=" CB  ASN C  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.00   -9.20     0      2.50e+00 1.60e-01 1.35e+01
  dihedral pdb=" N   ASN A  15 "
           pdb=" C   ASN A  15 "
           pdb=" CA  ASN A  15 "
           pdb=" CB  ASN A  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.99   -9.19     0      2.50e+00 1.60e-01 1.35e+01
  dihedral pdb=" N   ASN B  15 "
           pdb=" C   ASN B  15 "
           pdb=" CA  ASN B  15 "
           pdb=" CB  ASN B  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.96   -9.16     0      2.50e+00 1.60e-01 1.34e+01
  ... (remaining 5217 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1198
       0.066 -    0.131: 94
       0.131 -    0.197: 4
       0.197 -    0.263: 0
       0.263 -    0.328: 4
  Chirality restraints: 1300
  Sorted by residual:
  chirality pdb=" CA  ASN C  15 "
            pdb=" N   ASN C  15 "
            pdb=" C   ASN C  15 "
            pdb=" CB  ASN C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" CA  ASN A  15 "
            pdb=" N   ASN A  15 "
            pdb=" C   ASN A  15 "
            pdb=" CB  ASN A  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.68e+00
  chirality pdb=" CA  ASN B  15 "
            pdb=" N   ASN B  15 "
            pdb=" C   ASN B  15 "
            pdb=" CB  ASN B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.63e+00
  ... (remaining 1297 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D  14 "    0.006 2.00e-02 2.50e+03   1.31e-02 1.72e+00
        pdb=" C   LEU D  14 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   LEU D  14 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASN D  15 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  14 "    0.006 2.00e-02 2.50e+03   1.30e-02 1.70e+00
        pdb=" C   LEU C  14 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   LEU C  14 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASN C  15 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  14 "    0.006 2.00e-02 2.50e+03   1.29e-02 1.66e+00
        pdb=" C   LEU A  14 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   LEU A  14 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASN A  15 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 49
        2.45 -     3.07: 5477
        3.07 -     3.68: 12994
        3.68 -     4.29: 17762
        4.29 -     4.90: 28573
  Nonbonded interactions: 64855
  Sorted by model distance:
  nonbonded pdb=" CB  ALA D  94 "
            pdb=" CD2 LEU D 148 "
     model   vdw
     1.843 3.880
  nonbonded pdb=" CB  ALA A  94 "
            pdb=" CD2 LEU A 148 "
     model   vdw
     1.843 3.880
  nonbonded pdb=" CB  ALA C  94 "
            pdb=" CD2 LEU C 148 "
     model   vdw
     1.843 3.880
  nonbonded pdb=" CB  ALA B  94 "
            pdb=" CD2 LEU B 148 "
     model   vdw
     1.844 3.880
  nonbonded pdb=" NH2 ARG A  83 "
            pdb=" OE1 GLU A 142 "
     model   vdw
     1.982 3.120
  ... (remaining 64850 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8096  Z= 0.141
  Angle     :  0.628  13.605  10932  Z= 0.356
  Chirality :  0.038   0.328   1300
  Planarity :  0.003   0.024   1468
  Dihedral  : 12.310  86.708   3196
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 28.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.23), residues: 1032
  helix:  0.08 (0.14), residues: 976
  sheet:  None (None), residues: 0
  loop : -3.14 (1.01), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 123 
 TYR   0.002   0.001   TYR D  24 
 TRP   0.006   0.001   TRP C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8096)
  covalent geometry    : angle       0.62805 (10932)
  hydrogen bonds       : bond        0.06974 (  804)
  hydrogen bonds       : angle       3.27178 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 0.235 
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: A   15 ASN cc_start: 0.8100 (m-40) cc_final: 0.7624 (t0)
REVERT: A   60 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8225 (mmtm)
REVERT: A  119 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: A  168 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7436 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7917 (m-40) cc_final: 0.7506 (p0)
REVERT: A  191 LYS cc_start: 0.9054 (mttt) cc_final: 0.8101 (mmmt)
REVERT: A  195 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8075 (mm-30)
REVERT: A  201 VAL cc_start: 0.9397 (m) cc_final: 0.9173 (m)
REVERT: A  209 LYS cc_start: 0.8246 (mttt) cc_final: 0.7892 (tmmt)
REVERT: A  210 THR cc_start: 0.6614 (m) cc_final: 0.6301 (p)
REVERT: B   31 ASP cc_start: 0.8454 (t0) cc_final: 0.8217 (t0)
REVERT: B   60 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8171 (mmtm)
REVERT: B  154 THR cc_start: 0.6909 (p) cc_final: 0.6668 (t)
REVERT: B  168 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7466 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7866 (m-40) cc_final: 0.7459 (p0)
REVERT: B  191 LYS cc_start: 0.9054 (mttt) cc_final: 0.8037 (mmmt)
REVERT: B  195 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8048 (mm-30)
REVERT: B  210 THR cc_start: 0.6841 (m) cc_final: 0.6596 (p)
REVERT: B  224 ARG cc_start: 0.8521 (mtt90) cc_final: 0.7812 (mtp-110)
REVERT: C   60 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8135 (mmmt)
REVERT: C  168 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7152 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7347 (m-40) cc_final: 0.7106 (p0)
REVERT: C  195 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8081 (mm-30)
REVERT: C  201 VAL cc_start: 0.9295 (m) cc_final: 0.8097 (t)
REVERT: C  224 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7877 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8079 (m-40) cc_final: 0.7650 (t0)
REVERT: D  119 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7599 (tm-30)
REVERT: D  168 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7321 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7872 (m-40) cc_final: 0.7483 (p0)
REVERT: D  191 LYS cc_start: 0.9031 (mttt) cc_final: 0.8042 (mmmt)
REVERT: D  195 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8097 (mm-30)
REVERT: D  201 VAL cc_start: 0.9307 (m) cc_final: 0.9080 (m)
REVERT: D  224 ARG cc_start: 0.8439 (mtt90) cc_final: 0.7783 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 307
  average time/residue: 0.1417
  time to fit residues: 52.7286
Evaluate side-chains
  155 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
C 131 ASN
C 234 GLN
D 131 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.106816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.074421 restraints weight = 27449.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.076468 restraints weight = 16467.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.077789 restraints weight = 12221.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.078556 restraints weight = 10176.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.078975 restraints weight = 9116.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8096  Z= 0.168
  Angle     :  0.696  11.159  10932  Z= 0.336
  Chirality :  0.038   0.172   1300
  Planarity :  0.004   0.041   1468
  Dihedral  :  3.465  11.926   1148
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.71 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.25), residues: 1032
  helix:  1.18 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -4.18 (1.03), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 179 
 TYR   0.011   0.003   TYR A  24 
 TRP   0.009   0.001   TRP B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 8096)
  covalent geometry    : angle       0.69603 (10932)
  hydrogen bonds       : bond        0.03314 (  804)
  hydrogen bonds       : angle       3.39081 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8473 (m-40) cc_final: 0.7820 (t0)
REVERT: A   77 ILE cc_start: 0.9130 (mt) cc_final: 0.8926 (tp)
REVERT: A  131 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8063 (t0)
REVERT: A  168 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7319 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7986 (m-40) cc_final: 0.7691 (p0)
REVERT: A  186 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7606 (m)
REVERT: A  195 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8159 (mm-30)
REVERT: A  224 ARG cc_start: 0.8581 (mtt90) cc_final: 0.7873 (mtp-110)
REVERT: B  154 THR cc_start: 0.6861 (p) cc_final: 0.6616 (t)
REVERT: B  168 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7268 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7879 (m-40) cc_final: 0.7438 (p0)
REVERT: B  195 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8142 (mm-30)
REVERT: B  210 THR cc_start: 0.6845 (m) cc_final: 0.6630 (p)
REVERT: B  224 ARG cc_start: 0.8579 (mtt90) cc_final: 0.7869 (mtp-110)
REVERT: C   69 ASP cc_start: 0.8441 (p0) cc_final: 0.8160 (p0)
REVERT: C  124 ASP cc_start: 0.8454 (t0) cc_final: 0.8195 (t70)
REVERT: C  168 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7066 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7474 (m-40) cc_final: 0.7153 (p0)
REVERT: C  195 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8229 (mm-30)
REVERT: C  224 ARG cc_start: 0.8387 (mtt90) cc_final: 0.7891 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8466 (m-40) cc_final: 0.7790 (t0)
REVERT: D  168 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7187 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7851 (m-40) cc_final: 0.7422 (p0)
REVERT: D  195 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8187 (mm-30)
REVERT: D  201 VAL cc_start: 0.9254 (m) cc_final: 0.9037 (m)
REVERT: D  224 ARG cc_start: 0.8474 (mtt90) cc_final: 0.7858 (mtp-110)
  outliers start: 16
  outliers final: 10
  residues processed: 189
  average time/residue: 0.1202
  time to fit residues: 28.7881
Evaluate side-chains
  149 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  204 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  154 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 47 optimal weight:   30.0000
   chunk 67 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
C 187 ASN
D 131 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.107448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.075409 restraints weight = 27125.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.077550 restraints weight = 16235.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.078888 restraints weight = 11919.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.079641 restraints weight = 9877.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.080165 restraints weight = 8832.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8096  Z= 0.127
  Angle     :  0.651  11.326  10932  Z= 0.308
  Chirality :  0.035   0.145   1300
  Planarity :  0.004   0.043   1468
  Dihedral  :  3.393  11.996   1148
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.05 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.25), residues: 1032
  helix:  1.76 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -4.06 (0.85), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 102 
 TYR   0.008   0.002   TYR D  24 
 TRP   0.007   0.001   TRP B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8096)
  covalent geometry    : angle       0.65142 (10932)
  hydrogen bonds       : bond        0.03125 (  804)
  hydrogen bonds       : angle       3.20728 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8459 (m-40) cc_final: 0.7903 (t0)
REVERT: A  168 ARG cc_start: 0.7832 (mtt180) cc_final: 0.7339 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7896 (m-40) cc_final: 0.7693 (p0)
REVERT: A  195 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8117 (mm-30)
REVERT: A  224 ARG cc_start: 0.8554 (mtt90) cc_final: 0.7812 (mtp-110)
REVERT: B  154 THR cc_start: 0.6805 (p) cc_final: 0.6573 (t)
REVERT: B  168 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7212 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7875 (m-40) cc_final: 0.7397 (p0)
REVERT: B  195 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8120 (mm-30)
REVERT: B  210 THR cc_start: 0.6761 (m) cc_final: 0.6552 (p)
REVERT: B  224 ARG cc_start: 0.8634 (mtt90) cc_final: 0.7905 (mtp-110)
REVERT: C   69 ASP cc_start: 0.8420 (p0) cc_final: 0.8152 (p0)
REVERT: C  124 ASP cc_start: 0.8487 (t0) cc_final: 0.8261 (t70)
REVERT: C  149 GLU cc_start: 0.8195 (pt0) cc_final: 0.7749 (tm-30)
REVERT: C  154 THR cc_start: 0.6221 (p) cc_final: 0.5938 (t)
REVERT: C  165 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8516 (pt0)
REVERT: C  168 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7108 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7460 (m-40) cc_final: 0.7173 (p0)
REVERT: C  186 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7261 (m)
REVERT: C  195 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8169 (mm-30)
REVERT: C  224 ARG cc_start: 0.8364 (mtt90) cc_final: 0.7862 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8439 (m-40) cc_final: 0.7874 (t0)
REVERT: D  168 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7120 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7857 (m-40) cc_final: 0.7442 (p0)
REVERT: D  195 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: D  224 ARG cc_start: 0.8446 (mtt90) cc_final: 0.7801 (mtp-110)
  outliers start: 22
  outliers final: 10
  residues processed: 176
  average time/residue: 0.1107
  time to fit residues: 25.2252
Evaluate side-chains
  148 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  238 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 102 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.105951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.073345 restraints weight = 27744.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.075381 restraints weight = 16766.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076567 restraints weight = 12430.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.077397 restraints weight = 10401.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.077786 restraints weight = 9293.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8096  Z= 0.172
  Angle     :  0.670  10.640  10932  Z= 0.326
  Chirality :  0.035   0.144   1300
  Planarity :  0.005   0.046   1468
  Dihedral  :  3.378  12.081   1148
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 16.50 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.25), residues: 1032
  helix:  1.91 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -4.66 (0.73), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 102 
 TYR   0.015   0.003   TYR C  24 
 TRP   0.010   0.001   TRP B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8096)
  covalent geometry    : angle       0.66956 (10932)
  hydrogen bonds       : bond        0.03243 (  804)
  hydrogen bonds       : angle       3.33437 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8630 (m-40) cc_final: 0.7995 (t0)
REVERT: A   77 ILE cc_start: 0.9133 (mt) cc_final: 0.8857 (tp)
REVERT: A  168 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7211 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7918 (m-40) cc_final: 0.7629 (p0)
REVERT: A  195 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8169 (mm-30)
REVERT: A  224 ARG cc_start: 0.8602 (mtt90) cc_final: 0.7779 (mtp-110)
REVERT: B  123 ARG cc_start: 0.8023 (tpm170) cc_final: 0.7675 (mmm-85)
REVERT: B  154 THR cc_start: 0.6780 (p) cc_final: 0.6532 (t)
REVERT: B  168 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7162 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7917 (m-40) cc_final: 0.7429 (p0)
REVERT: B  195 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8162 (mm-30)
REVERT: B  210 THR cc_start: 0.6757 (m) cc_final: 0.6553 (p)
REVERT: B  224 ARG cc_start: 0.8628 (mtt90) cc_final: 0.7942 (mtp-110)
REVERT: C   69 ASP cc_start: 0.8496 (p0) cc_final: 0.8289 (p0)
REVERT: C  131 ASN cc_start: 0.7990 (m-40) cc_final: 0.7518 (m-40)
REVERT: C  149 GLU cc_start: 0.8240 (pt0) cc_final: 0.7688 (tm-30)
REVERT: C  154 THR cc_start: 0.6255 (p) cc_final: 0.5997 (t)
REVERT: C  168 ARG cc_start: 0.7845 (mtt180) cc_final: 0.6780 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7605 (m-40) cc_final: 0.7275 (p0)
REVERT: C  195 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8209 (mm-30)
REVERT: C  224 ARG cc_start: 0.8421 (mtt90) cc_final: 0.7738 (mtp-110)
REVERT: D   15 ASN cc_start: 0.8604 (m-40) cc_final: 0.7988 (t0)
REVERT: D  168 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7141 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7994 (m-40) cc_final: 0.7530 (p0)
REVERT: D  195 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8172 (mm-30)
REVERT: D  224 ARG cc_start: 0.8513 (mtt90) cc_final: 0.7883 (mtp-110)
  outliers start: 39
  outliers final: 26
  residues processed: 162
  average time/residue: 0.1083
  time to fit residues: 22.8820
Evaluate side-chains
  153 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  238 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   chunk 85 optimal weight:    0.6980
   chunk 101 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
B  92 GLN
D  92 GLN
D 187 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.106196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.074718 restraints weight = 26931.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.076814 restraints weight = 15830.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.078100 restraints weight = 11489.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.078921 restraints weight = 9444.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.079352 restraints weight = 8389.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8096  Z= 0.144
  Angle     :  0.662  11.386  10932  Z= 0.315
  Chirality :  0.035   0.154   1300
  Planarity :  0.004   0.045   1468
  Dihedral  :  3.411  12.123   1148
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.48 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.63 (0.25), residues: 1032
  helix:  2.02 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.05 (0.72), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 179 
 TYR   0.013   0.003   TYR C  24 
 TRP   0.008   0.001   TRP A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8096)
  covalent geometry    : angle       0.66192 (10932)
  hydrogen bonds       : bond        0.03193 (  804)
  hydrogen bonds       : angle       3.28388 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8707 (m-40) cc_final: 0.8143 (t0)
REVERT: A   77 ILE cc_start: 0.9116 (mt) cc_final: 0.8903 (tp)
REVERT: A  168 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7206 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7966 (m-40) cc_final: 0.7672 (p0)
REVERT: A  195 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: A  224 ARG cc_start: 0.8618 (mtt90) cc_final: 0.7730 (mtp-110)
REVERT: A  228 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8489 (pt0)
REVERT: B  154 THR cc_start: 0.6762 (p) cc_final: 0.6512 (t)
REVERT: B  168 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7126 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7955 (m-40) cc_final: 0.7435 (p0)
REVERT: B  195 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8153 (mm-30)
REVERT: B  224 ARG cc_start: 0.8636 (mtt90) cc_final: 0.7908 (mtp-110)
REVERT: C  131 ASN cc_start: 0.7928 (m-40) cc_final: 0.7493 (m-40)
REVERT: C  154 THR cc_start: 0.6281 (p) cc_final: 0.6022 (t)
REVERT: C  165 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8466 (pt0)
REVERT: C  168 ARG cc_start: 0.7773 (mtt180) cc_final: 0.6913 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7700 (m-40) cc_final: 0.7274 (p0)
REVERT: C  195 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8175 (mm-30)
REVERT: C  224 ARG cc_start: 0.8382 (mtt90) cc_final: 0.7913 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8685 (m-40) cc_final: 0.8137 (t0)
REVERT: D  168 ARG cc_start: 0.7639 (mtt180) cc_final: 0.6952 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7964 (m-40) cc_final: 0.7520 (p0)
REVERT: D  195 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8108 (mm-30)
REVERT: D  224 ARG cc_start: 0.8507 (mtt90) cc_final: 0.7910 (mtp-110)
  outliers start: 29
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1049
  time to fit residues: 20.7581
Evaluate side-chains
  149 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 35 optimal weight:   20.0000
   chunk 65 optimal weight:    0.3980
   chunk 100 optimal weight:    6.9990
   chunk 59 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 101 optimal weight:    9.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
B 187 ASN
C  15 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.106854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.074799 restraints weight = 26990.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.076964 restraints weight = 15970.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.078312 restraints weight = 11619.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.079088 restraints weight = 9592.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.079415 restraints weight = 8564.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8096  Z= 0.126
  Angle     :  0.661  12.017  10932  Z= 0.311
  Chirality :  0.034   0.140   1300
  Planarity :  0.004   0.042   1468
  Dihedral  :  3.426  12.607   1148
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 19.54 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.85 (0.25), residues: 1032
  helix:  2.17 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.05 (0.71), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 179 
 TYR   0.012   0.003   TYR C  24 
 TRP   0.006   0.001   TRP A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8096)
  covalent geometry    : angle       0.66086 (10932)
  hydrogen bonds       : bond        0.03145 (  804)
  hydrogen bonds       : angle       3.20139 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8710 (m-40) cc_final: 0.8230 (t0)
REVERT: A  168 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7142 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7951 (m-40) cc_final: 0.7616 (p0)
REVERT: A  195 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8100 (mm-30)
REVERT: A  224 ARG cc_start: 0.8542 (mtt90) cc_final: 0.7755 (mtp-110)
REVERT: B  154 THR cc_start: 0.6846 (p) cc_final: 0.6618 (t)
REVERT: B  168 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7018 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7930 (m-40) cc_final: 0.7431 (p0)
REVERT: B  195 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8095 (mm-30)
REVERT: B  224 ARG cc_start: 0.8626 (mtt90) cc_final: 0.7955 (mtp-110)
REVERT: C  131 ASN cc_start: 0.7951 (m-40) cc_final: 0.7545 (m-40)
REVERT: C  154 THR cc_start: 0.6242 (p) cc_final: 0.6017 (t)
REVERT: C  165 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8450 (pt0)
REVERT: C  168 ARG cc_start: 0.7753 (mtt180) cc_final: 0.6848 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7764 (m-40) cc_final: 0.7447 (p0)
REVERT: C  195 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8155 (mm-30)
REVERT: C  224 ARG cc_start: 0.8370 (mtt90) cc_final: 0.7904 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8671 (m-40) cc_final: 0.8194 (t0)
REVERT: D  168 ARG cc_start: 0.7601 (mtt180) cc_final: 0.6920 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7916 (m-40) cc_final: 0.7505 (p0)
REVERT: D  195 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8159 (mm-30)
REVERT: D  224 ARG cc_start: 0.8510 (mtt90) cc_final: 0.7844 (mtp-110)
  outliers start: 26
  outliers final: 19
  residues processed: 163
  average time/residue: 0.1050
  time to fit residues: 22.1088
Evaluate side-chains
  147 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0030
   chunk 91 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.5796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.106267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.074779 restraints weight = 27095.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.076873 restraints weight = 15918.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.078156 restraints weight = 11573.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.078955 restraints weight = 9544.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.079399 restraints weight = 8489.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8096  Z= 0.140
  Angle     :  0.671  12.344  10932  Z= 0.320
  Chirality :  0.035   0.139   1300
  Planarity :  0.004   0.042   1468
  Dihedral  :  3.431  12.489   1148
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 19.78 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.90 (0.25), residues: 1032
  helix:  2.20 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.16 (0.68), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 179 
 TYR   0.017   0.003   TYR C  24 
 TRP   0.008   0.001   TRP D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8096)
  covalent geometry    : angle       0.67123 (10932)
  hydrogen bonds       : bond        0.03156 (  804)
  hydrogen bonds       : angle       3.24588 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8685 (m-40) cc_final: 0.8176 (t0)
REVERT: A  168 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7084 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7959 (m-40) cc_final: 0.7628 (p0)
REVERT: A  224 ARG cc_start: 0.8512 (mtt90) cc_final: 0.7812 (mtp-110)
REVERT: B  154 THR cc_start: 0.6914 (p) cc_final: 0.6690 (t)
REVERT: B  168 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7106 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7942 (m-40) cc_final: 0.7424 (p0)
REVERT: B  195 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8128 (mm-30)
REVERT: B  224 ARG cc_start: 0.8638 (mtt90) cc_final: 0.7966 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8010 (m-40) cc_final: 0.7576 (m-40)
REVERT: C  154 THR cc_start: 0.6295 (p) cc_final: 0.6054 (t)
REVERT: C  165 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8456 (pt0)
REVERT: C  168 ARG cc_start: 0.7738 (mtt180) cc_final: 0.6845 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7712 (m-40) cc_final: 0.7381 (p0)
REVERT: C  195 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: C  224 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7886 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8707 (m-40) cc_final: 0.8172 (t0)
REVERT: D  168 ARG cc_start: 0.7648 (mtt180) cc_final: 0.6958 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7967 (m-40) cc_final: 0.7521 (p0)
REVERT: D  195 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8219 (mm-30)
REVERT: D  224 ARG cc_start: 0.8509 (mtt90) cc_final: 0.7908 (mtp-110)
  outliers start: 31
  outliers final: 23
  residues processed: 148
  average time/residue: 0.1046
  time to fit residues: 20.3937
Evaluate side-chains
  149 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 73 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.106504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.075230 restraints weight = 27057.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.077328 restraints weight = 16109.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.078609 restraints weight = 11781.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.079225 restraints weight = 9754.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.079762 restraints weight = 8806.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8096  Z= 0.133
  Angle     :  0.698  12.695  10932  Z= 0.333
  Chirality :  0.036   0.190   1300
  Planarity :  0.004   0.043   1468
  Dihedral  :  3.436  12.792   1148
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.27 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.88 (0.24), residues: 1032
  helix:  2.19 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.21 (0.67), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 202 
 TYR   0.016   0.003   TYR C  24 
 TRP   0.006   0.001   TRP B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8096)
  covalent geometry    : angle       0.69841 (10932)
  hydrogen bonds       : bond        0.03145 (  804)
  hydrogen bonds       : angle       3.25942 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8676 (m-40) cc_final: 0.8234 (t0)
REVERT: A  168 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7076 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7924 (m-40) cc_final: 0.7616 (p0)
REVERT: A  224 ARG cc_start: 0.8507 (mtt90) cc_final: 0.7750 (mtp-110)
REVERT: B  154 THR cc_start: 0.6900 (p) cc_final: 0.6668 (t)
REVERT: B  168 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7038 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7914 (m-40) cc_final: 0.7421 (p0)
REVERT: B  195 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8104 (mm-30)
REVERT: B  224 ARG cc_start: 0.8606 (mtt90) cc_final: 0.7942 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8020 (m-40) cc_final: 0.7613 (m-40)
REVERT: C  154 THR cc_start: 0.6295 (p) cc_final: 0.6048 (t)
REVERT: C  165 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8434 (pt0)
REVERT: C  168 ARG cc_start: 0.7737 (mtt180) cc_final: 0.6835 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7718 (m-40) cc_final: 0.7400 (p0)
REVERT: C  195 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8153 (mm-30)
REVERT: C  224 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7857 (tmt-80)
REVERT: C  228 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8491 (pt0)
REVERT: D   15 ASN cc_start: 0.8679 (m-40) cc_final: 0.8200 (t0)
REVERT: D  168 ARG cc_start: 0.7619 (mtt180) cc_final: 0.6949 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7913 (m-40) cc_final: 0.7450 (p0)
REVERT: D  195 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8201 (mm-30)
REVERT: D  224 ARG cc_start: 0.8530 (mtt90) cc_final: 0.7883 (mtp-110)
  outliers start: 29
  outliers final: 23
  residues processed: 144
  average time/residue: 0.1074
  time to fit residues: 20.2925
Evaluate side-chains
  148 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.106498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.074969 restraints weight = 26971.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.077059 restraints weight = 15825.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.078352 restraints weight = 11522.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.079123 restraints weight = 9490.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.079621 restraints weight = 8455.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8096  Z= 0.145
  Angle     :  0.718  13.102  10932  Z= 0.344
  Chirality :  0.037   0.181   1300
  Planarity :  0.004   0.043   1468
  Dihedral  :  3.454  12.777   1148
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.12 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.25), residues: 1032
  helix:  2.13 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.34 (0.64), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 179 
 TYR   0.019   0.003   TYR B  24 
 TRP   0.008   0.001   TRP D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8096)
  covalent geometry    : angle       0.71785 (10932)
  hydrogen bonds       : bond        0.03218 (  804)
  hydrogen bonds       : angle       3.33370 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8682 (m-40) cc_final: 0.8202 (t0)
REVERT: A  168 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7038 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7909 (m-40) cc_final: 0.7662 (p0)
REVERT: A  195 GLU cc_start: 0.8135 (mp0) cc_final: 0.7855 (mp0)
REVERT: A  224 ARG cc_start: 0.8508 (mtt90) cc_final: 0.7805 (mtp-110)
REVERT: B  154 THR cc_start: 0.6918 (p) cc_final: 0.6689 (t)
REVERT: B  168 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7051 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7969 (m-40) cc_final: 0.7438 (p0)
REVERT: B  195 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: B  224 ARG cc_start: 0.8582 (mtt90) cc_final: 0.7952 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8036 (m-40) cc_final: 0.7619 (m-40)
REVERT: C  154 THR cc_start: 0.6373 (p) cc_final: 0.6160 (t)
REVERT: C  165 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8424 (pt0)
REVERT: C  168 ARG cc_start: 0.7722 (mtt180) cc_final: 0.6845 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7695 (m-40) cc_final: 0.7328 (p0)
REVERT: C  195 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: C  224 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7923 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8702 (m-40) cc_final: 0.8207 (t0)
REVERT: D  168 ARG cc_start: 0.7580 (mtt180) cc_final: 0.6939 (ttp-110)
REVERT: D  180 ASN cc_start: 0.8038 (m-40) cc_final: 0.7518 (p0)
REVERT: D  195 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8229 (mm-30)
REVERT: D  224 ARG cc_start: 0.8544 (mtt90) cc_final: 0.7902 (mtp-110)
  outliers start: 26
  outliers final: 23
  residues processed: 141
  average time/residue: 0.0968
  time to fit residues: 18.0065
Evaluate side-chains
  146 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  238 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0980
   chunk 61 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.106005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.073673 restraints weight = 27049.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.075737 restraints weight = 16093.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.076956 restraints weight = 11800.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.077803 restraints weight = 9810.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.078223 restraints weight = 8756.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.4561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8096  Z= 0.162
  Angle     :  0.759  13.347  10932  Z= 0.363
  Chirality :  0.038   0.205   1300
  Planarity :  0.005   0.043   1468
  Dihedral  :  3.467  12.610   1148
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.12 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.25), residues: 1032
  helix:  2.02 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.45 (0.63), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 179 
 TYR   0.019   0.003   TYR B  24 
 TRP   0.008   0.001   TRP C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8096)
  covalent geometry    : angle       0.75881 (10932)
  hydrogen bonds       : bond        0.03297 (  804)
  hydrogen bonds       : angle       3.42256 ( 2412)

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8695 (m-40) cc_final: 0.8201 (t0)
REVERT: A  168 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7043 (ttp-110)
REVERT: A  180 ASN cc_start: 0.8015 (m-40) cc_final: 0.7656 (p0)
REVERT: A  224 ARG cc_start: 0.8524 (mtt90) cc_final: 0.7744 (mtp-110)
REVERT: B  154 THR cc_start: 0.6908 (p) cc_final: 0.6697 (t)
REVERT: B  168 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7098 (ttp-110)
REVERT: B  180 ASN cc_start: 0.8037 (m-40) cc_final: 0.7480 (p0)
REVERT: B  195 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8207 (mm-30)
REVERT: B  224 ARG cc_start: 0.8638 (mtt90) cc_final: 0.7993 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8052 (m-40) cc_final: 0.7640 (m-40)
REVERT: C  154 THR cc_start: 0.6426 (p) cc_final: 0.6222 (t)
REVERT: C  165 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8436 (pt0)
REVERT: C  168 ARG cc_start: 0.7719 (mtt180) cc_final: 0.6829 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7779 (m-40) cc_final: 0.7267 (p0)
REVERT: C  195 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8260 (mm-30)
REVERT: C  224 ARG cc_start: 0.8387 (mtt90) cc_final: 0.7927 (tmt-80)
REVERT: D  168 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6911 (ttp-110)
REVERT: D  180 ASN cc_start: 0.8063 (m-40) cc_final: 0.7513 (p0)
REVERT: D  195 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8265 (mm-30)
REVERT: D  224 ARG cc_start: 0.8569 (mtt90) cc_final: 0.7926 (mtp-110)
  outliers start: 26
  outliers final: 23
  residues processed: 134
  average time/residue: 0.0968
  time to fit residues: 17.1613
Evaluate side-chains
  146 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue   39 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  238 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 10 optimal weight:    0.0170
   chunk 50 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    1.0022

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

Flipped N/Q/H residues before XYZ refinement:
C 234 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.106954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.075028 restraints weight = 27000.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.077180 restraints weight = 15942.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.078509 restraints weight = 11614.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.079299 restraints weight = 9582.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.079833 restraints weight = 8531.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8096  Z= 0.135
  Angle     :  0.746  13.758  10932  Z= 0.353
  Chirality :  0.036   0.228   1300
  Planarity :  0.004   0.041   1468
  Dihedral  :  3.488  12.886   1148
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 22.57 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.25), residues: 1032
  helix:  2.05 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.18 (0.68), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 102 
 TYR   0.019   0.003   TYR B  24 
 TRP   0.006   0.001   TRP B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8096)
  covalent geometry    : angle       0.74595 (10932)
  hydrogen bonds       : bond        0.03234 (  804)
  hydrogen bonds       : angle       3.33891 ( 2412)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1486.36 seconds
wall clock time: 26 minutes 11.14 seconds (1571.14 seconds total)