Starting phenix.real_space_refine
on Wed Mar 12 13:53:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xss_22305/03_2025/6xss_22305.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xss_22305/03_2025/6xss_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xss_22305/03_2025/6xss_22305.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xss_22305/03_2025/6xss_22305.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xss_22305/03_2025/6xss_22305.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xss_22305/03_2025/6xss_22305.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:
    C, B, D
  Time building chain proxies: 3.89, per 1000 atoms: 0.48
  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: 1.96
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.62
  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: 2.32

  Time building geometry restraints manager: 2.31 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             1.240
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.060
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.890
-------------------------------------------------------------------------------
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= 0.176
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.006   0.001   TRP C   4 
 TYR   0.002   0.001   TYR D  24 
 ARG   0.006   0.000   ARG B 123 

*********************** 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  : 0.935 
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: 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: 0.7609 (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: 0.7545 (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: 0.8076 (mm-30)
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: 0.6910 (p) cc_final: 0.6669 (t)
REVERT: B  168 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7465 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7867 (m-40) cc_final: 0.7468 (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: 0.8049 (mm-30)
REVERT: B  210 THR cc_start: 0.6841 (m) cc_final: 0.6595 (p)
REVERT: B  224 ARG cc_start: 0.8521 (mtt90) cc_final: 0.7813 (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: 0.7145 (p0)
REVERT: C  195 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8081 (mm-30)
REVERT: C  224 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7877 (tmt-80)
REVERT: C  254 GLN cc_start: 0.8336 (mt0) cc_final: 0.7708 (tm-30)
REVERT: D   15 ASN cc_start: 0.8079 (m-40) cc_final: 0.7650 (t0)
REVERT: D  119 GLU cc_start: 0.8035 (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: 0.7525 (p0)
REVERT: D  191 LYS cc_start: 0.9031 (mttt) cc_final: 0.8042 (mmmt)
REVERT: D  195 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8098 (mm-30)
REVERT: D  201 VAL cc_start: 0.9307 (m) cc_final: 0.9104 (m)
REVERT: D  224 ARG cc_start: 0.8439 (mtt90) cc_final: 0.7784 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 307
  average time/residue: 0.3114
  time to fit residues: 115.9267
Evaluate side-chains
  159 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.107043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074865 restraints weight = 27285.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.076972 restraints weight = 16463.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.078266 restraints weight = 12190.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8096  Z= 0.247
  Angle     :  0.695  10.934  10932  Z= 0.334
  Chirality :  0.038   0.146   1300
  Planarity :  0.004   0.042   1468
  Dihedral  :  3.438  11.893   1148
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.71 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.25), residues: 1032
  helix:  1.16 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -4.17 (1.03), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B   4 
 TYR   0.011   0.003   TYR A  24 
 ARG   0.007   0.001   ARG B 179 

*********************** 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
  191 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 179
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8391 (m-40) cc_final: 0.7793 (t0)
REVERT: A  131 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8057 (t0)
REVERT: A  168 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7177 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7977 (m-40) cc_final: 0.7683 (p0)
REVERT: A  195 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8127 (mm-30)
REVERT: A  224 ARG cc_start: 0.8569 (mtt90) cc_final: 0.7851 (mtp-110)
REVERT: B   77 ILE cc_start: 0.9059 (mt) cc_final: 0.8856 (tp)
REVERT: B  154 THR cc_start: 0.6829 (p) cc_final: 0.6601 (t)
REVERT: B  168 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7258 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7881 (m-40) cc_final: 0.7455 (p0)
REVERT: B  195 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8120 (mm-30)
REVERT: B  210 THR cc_start: 0.6784 (m) cc_final: 0.6559 (p)
REVERT: B  224 ARG cc_start: 0.8552 (mtt90) cc_final: 0.7848 (mtp-110)
REVERT: C   69 ASP cc_start: 0.8387 (p0) cc_final: 0.8110 (p0)
REVERT: C  124 ASP cc_start: 0.8425 (t0) cc_final: 0.8224 (t70)
REVERT: C  168 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7090 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7483 (m-40) cc_final: 0.7229 (p0)
REVERT: C  195 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8146 (mm-30)
REVERT: C  224 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7889 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8444 (m-40) cc_final: 0.7798 (t0)
REVERT: D  168 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7192 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7914 (m-40) cc_final: 0.7509 (p0)
REVERT: D  195 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8179 (mm-30)
REVERT: D  224 ARG cc_start: 0.8467 (mtt90) cc_final: 0.7850 (mtp-110)
  outliers start: 12
  outliers final: 6
  residues processed: 181
  average time/residue: 0.2456
  time to fit residues: 57.2691
Evaluate side-chains
  143 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
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  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 D residue  113 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 99 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.9586

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.106529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.073680 restraints weight = 27715.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.075831 restraints weight = 16602.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.077127 restraints weight = 12211.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8096  Z= 0.242
  Angle     :  0.665  11.234  10932  Z= 0.317
  Chirality :  0.035   0.146   1300
  Planarity :  0.005   0.043   1468
  Dihedral  :  3.381  12.179   1148
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.53 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.25), residues: 1032
  helix:  1.71 (0.15), residues: 976
  sheet:  None (None), residues: 0
  loop : -2.95 (1.00), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B   4 
 TYR   0.008   0.002   TYR D  24 
 ARG   0.006   0.000   ARG B 102 

*********************** 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
  180 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8516 (m-40) cc_final: 0.7912 (t0)
REVERT: A  168 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7224 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7913 (m-40) cc_final: 0.7677 (p0)
REVERT: A  195 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: A  224 ARG cc_start: 0.8594 (mtt90) cc_final: 0.7779 (mtp-110)
REVERT: B  123 ARG cc_start: 0.8078 (tpm170) cc_final: 0.7685 (mmm-85)
REVERT: B  154 THR cc_start: 0.6853 (p) cc_final: 0.6636 (t)
REVERT: B  168 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7211 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7922 (m-40) cc_final: 0.7430 (p0)
REVERT: B  195 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8156 (mm-30)
REVERT: B  210 THR cc_start: 0.6805 (m) cc_final: 0.6591 (p)
REVERT: B  224 ARG cc_start: 0.8598 (mtt90) cc_final: 0.7903 (mtp-110)
REVERT: C   69 ASP cc_start: 0.8489 (p0) cc_final: 0.8248 (p0)
REVERT: C  124 ASP cc_start: 0.8515 (t0) cc_final: 0.8247 (t70)
REVERT: C  149 GLU cc_start: 0.8255 (pt0) cc_final: 0.7792 (tm-30)
REVERT: C  165 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8578 (pt0)
REVERT: C  168 ARG cc_start: 0.7961 (mtt180) cc_final: 0.6929 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7515 (m-40) cc_final: 0.7275 (p0)
REVERT: C  186 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7486 (m)
REVERT: C  195 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8216 (mm-30)
REVERT: C  224 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7881 (tmt-80)
REVERT: C  254 GLN cc_start: 0.8282 (mt0) cc_final: 0.7682 (tm-30)
REVERT: D   15 ASN cc_start: 0.8519 (m-40) cc_final: 0.7908 (t0)
REVERT: D  168 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7173 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7926 (m-40) cc_final: 0.7509 (p0)
REVERT: D  195 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: D  224 ARG cc_start: 0.8492 (mtt90) cc_final: 0.7856 (mtp-110)
  outliers start: 28
  outliers final: 17
  residues processed: 164
  average time/residue: 0.2376
  time to fit residues: 50.9494
Evaluate side-chains
  150 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 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  186 VAL
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 71 optimal weight:    0.9990
   chunk 101 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 89 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.107172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.075796 restraints weight = 27128.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.077939 restraints weight = 15961.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.079281 restraints weight = 11624.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3704

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= 0.186
  Angle     :  0.642  11.294  10932  Z= 0.304
  Chirality :  0.034   0.145   1300
  Planarity :  0.004   0.045   1468
  Dihedral  :  3.370  11.415   1148
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.99 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.25), residues: 1032
  helix:  1.99 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -4.17 (0.81), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B   4 
 TYR   0.007   0.002   TYR D  24 
 ARG   0.006   0.000   ARG B 102 

*********************** 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
  189 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8513 (m-40) cc_final: 0.7957 (t0)
REVERT: A  168 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7127 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7883 (m-40) cc_final: 0.7593 (p0)
REVERT: A  195 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8088 (mm-30)
REVERT: A  224 ARG cc_start: 0.8541 (mtt90) cc_final: 0.7796 (mtp-110)
REVERT: B   77 ILE cc_start: 0.9094 (mt) cc_final: 0.8860 (tp)
REVERT: B  123 ARG cc_start: 0.8128 (tpm170) cc_final: 0.7716 (mmm-85)
REVERT: B  154 THR cc_start: 0.6879 (p) cc_final: 0.6657 (t)
REVERT: B  168 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7124 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7902 (m-40) cc_final: 0.7432 (p0)
REVERT: B  195 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8064 (mm-30)
REVERT: B  224 ARG cc_start: 0.8560 (mtt90) cc_final: 0.7754 (mtp-110)
REVERT: B  228 GLU cc_start: 0.8791 (tt0) cc_final: 0.8563 (pt0)
REVERT: C   69 ASP cc_start: 0.8487 (p0) cc_final: 0.8262 (p0)
REVERT: C  124 ASP cc_start: 0.8505 (t0) cc_final: 0.8238 (t0)
REVERT: C  131 ASN cc_start: 0.7909 (m-40) cc_final: 0.7318 (m-40)
REVERT: C  149 GLU cc_start: 0.8206 (pt0) cc_final: 0.7743 (tm-30)
REVERT: C  154 THR cc_start: 0.6273 (p) cc_final: 0.6009 (t)
REVERT: C  168 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7002 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7641 (m-40) cc_final: 0.7242 (p0)
REVERT: C  195 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8140 (mm-30)
REVERT: C  224 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7869 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8490 (m-40) cc_final: 0.7938 (t0)
REVERT: D  168 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7057 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7928 (m-40) cc_final: 0.7541 (p0)
REVERT: D  195 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: D  224 ARG cc_start: 0.8439 (mtt90) cc_final: 0.7825 (mtp-110)
  outliers start: 24
  outliers final: 14
  residues processed: 174
  average time/residue: 0.2371
  time to fit residues: 53.6962
Evaluate side-chains
  152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
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  228 GLU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  148 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 101 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 91 optimal weight:    9.9990
   chunk 14 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.9788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.106549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.073830 restraints weight = 27121.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.075878 restraints weight = 16608.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.077140 restraints weight = 12359.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8096  Z= 0.245
  Angle     :  0.668  10.941  10932  Z= 0.320
  Chirality :  0.035   0.135   1300
  Planarity :  0.005   0.045   1468
  Dihedral  :  3.384  12.435   1148
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 16.87 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.25), residues: 1032
  helix:  2.02 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -4.59 (0.72), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B   4 
 TYR   0.016   0.003   TYR B  24 
 ARG   0.009   0.000   ARG D 179 

*********************** 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
  179 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 144
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8616 (m-40) cc_final: 0.8155 (t0)
REVERT: A  168 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7080 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7914 (m-40) cc_final: 0.7642 (p0)
REVERT: A  195 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8128 (mm-30)
REVERT: A  224 ARG cc_start: 0.8591 (mtt90) cc_final: 0.7847 (mtp-110)
REVERT: B  123 ARG cc_start: 0.8099 (tpm170) cc_final: 0.7726 (mmm-85)
REVERT: B  154 THR cc_start: 0.6905 (p) cc_final: 0.6684 (t)
REVERT: B  168 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7156 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7873 (m-40) cc_final: 0.7426 (p0)
REVERT: B  195 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8138 (mm-30)
REVERT: B  224 ARG cc_start: 0.8573 (mtt90) cc_final: 0.7764 (mtp-110)
REVERT: C   69 ASP cc_start: 0.8378 (p0) cc_final: 0.8167 (p0)
REVERT: C  131 ASN cc_start: 0.8030 (m-40) cc_final: 0.7537 (m-40)
REVERT: C  154 THR cc_start: 0.6245 (p) cc_final: 0.5998 (t)
REVERT: C  165 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8514 (pt0)
REVERT: C  168 ARG cc_start: 0.7842 (mtt180) cc_final: 0.6958 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7656 (m-40) cc_final: 0.7242 (p0)
REVERT: C  195 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8164 (mm-30)
REVERT: C  224 ARG cc_start: 0.8379 (mtt90) cc_final: 0.7912 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8597 (m-40) cc_final: 0.8123 (t0)
REVERT: D  168 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7064 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7895 (m-40) cc_final: 0.7501 (p0)
REVERT: D  195 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8113 (mm-30)
REVERT: D  224 ARG cc_start: 0.8505 (mtt90) cc_final: 0.7886 (mtp-110)
  outliers start: 35
  outliers final: 22
  residues processed: 158
  average time/residue: 0.2257
  time to fit residues: 46.8753
Evaluate side-chains
  148 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  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  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  186 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 31 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.105490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.072540 restraints weight = 27156.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.074559 restraints weight = 16430.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.075801 restraints weight = 12209.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.4201

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= 0.288
  Angle     :  0.687  11.655  10932  Z= 0.331
  Chirality :  0.036   0.148   1300
  Planarity :  0.005   0.046   1468
  Dihedral  :  3.428  11.973   1148
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.20 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.24), residues: 1032
  helix:  1.99 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -5.07 (0.63), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A   4 
 TYR   0.015   0.003   TYR C  24 
 ARG   0.008   0.001   ARG D 179 

*********************** 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
  170 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8698 (m-40) cc_final: 0.8205 (t0)
REVERT: A  168 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7092 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7946 (m-40) cc_final: 0.7652 (p0)
REVERT: A  195 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8184 (mm-30)
REVERT: A  224 ARG cc_start: 0.8570 (mtt90) cc_final: 0.7755 (mtp-110)
REVERT: B  154 THR cc_start: 0.6966 (p) cc_final: 0.6748 (t)
REVERT: B  168 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7147 (ttp-110)
REVERT: B  180 ASN cc_start: 0.8026 (m-40) cc_final: 0.7435 (p0)
REVERT: B  195 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8186 (mm-30)
REVERT: B  224 ARG cc_start: 0.8627 (mtt90) cc_final: 0.7981 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8083 (m-40) cc_final: 0.7586 (m-40)
REVERT: C  154 THR cc_start: 0.6370 (p) cc_final: 0.6116 (t)
REVERT: C  165 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8472 (pt0)
REVERT: C  168 ARG cc_start: 0.7771 (mtt180) cc_final: 0.6933 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7710 (m-40) cc_final: 0.7205 (p0)
REVERT: C  195 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8237 (mm-30)
REVERT: C  224 ARG cc_start: 0.8436 (mtt90) cc_final: 0.7739 (mtp-110)
REVERT: D   15 ASN cc_start: 0.8710 (m-40) cc_final: 0.8262 (t0)
REVERT: D  168 ARG cc_start: 0.7594 (mtt180) cc_final: 0.6921 (ttp-110)
REVERT: D  180 ASN cc_start: 0.8113 (m-40) cc_final: 0.7565 (p0)
REVERT: D  195 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8200 (mm-30)
REVERT: D  224 ARG cc_start: 0.8578 (mtt90) cc_final: 0.7961 (mtp-110)
  outliers start: 33
  outliers final: 25
  residues processed: 149
  average time/residue: 0.2227
  time to fit residues: 43.9211
Evaluate side-chains
  149 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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  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  192 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  154 THR
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  238 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 60 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
C  15 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.106092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.073856 restraints weight = 27210.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.075914 restraints weight = 16221.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.077206 restraints weight = 11918.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4257

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= 0.212
  Angle     :  0.686  12.684  10932  Z= 0.323
  Chirality :  0.035   0.157   1300
  Planarity :  0.004   0.044   1468
  Dihedral  :  3.437  12.437   1148
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.78 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.25), residues: 1032
  helix:  2.07 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.20 (0.71), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C   4 
 TYR   0.013   0.003   TYR C  24 
 ARG   0.007   0.000   ARG D 179 

*********************** 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
  167 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8652 (m-40) cc_final: 0.8198 (t0)
REVERT: A  168 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7040 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7988 (m-40) cc_final: 0.7638 (p0)
REVERT: A  192 LEU cc_start: 0.9232 (tp) cc_final: 0.8527 (tp)
REVERT: A  224 ARG cc_start: 0.8558 (mtt90) cc_final: 0.7508 (mtp-110)
REVERT: B  154 THR cc_start: 0.6950 (p) cc_final: 0.6726 (t)
REVERT: B  168 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7030 (ttp-110)
REVERT: B  180 ASN cc_start: 0.8004 (m-40) cc_final: 0.7440 (p0)
REVERT: B  195 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8116 (mm-30)
REVERT: B  224 ARG cc_start: 0.8699 (mtt90) cc_final: 0.8005 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8057 (m-40) cc_final: 0.7595 (m-40)
REVERT: C  154 THR cc_start: 0.6396 (p) cc_final: 0.6160 (t)
REVERT: C  165 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8449 (pt0)
REVERT: C  168 ARG cc_start: 0.7773 (mtt180) cc_final: 0.6879 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7766 (m-40) cc_final: 0.7292 (p0)
REVERT: C  195 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: C  224 ARG cc_start: 0.8375 (mtt90) cc_final: 0.7858 (tmt-80)
REVERT: C  228 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8567 (pt0)
REVERT: D   15 ASN cc_start: 0.8652 (m-40) cc_final: 0.8259 (t0)
REVERT: D  168 ARG cc_start: 0.7611 (mtt180) cc_final: 0.6928 (ttp-110)
REVERT: D  180 ASN cc_start: 0.8062 (m-40) cc_final: 0.7515 (p0)
REVERT: D  195 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8202 (mm-30)
REVERT: D  224 ARG cc_start: 0.8526 (mtt90) cc_final: 0.7913 (mtp-110)
  outliers start: 28
  outliers final: 22
  residues processed: 151
  average time/residue: 0.2193
  time to fit residues: 43.5964
Evaluate side-chains
  154 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
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  222 LEU
Chi-restraints excluded: chain B residue   74 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  192 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  186 VAL
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 67 optimal weight:    0.0170
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 73 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6818

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.107017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.074949 restraints weight = 27221.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.077062 restraints weight = 16294.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.078400 restraints weight = 11973.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.4380

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= 0.190
  Angle     :  0.699  13.502  10932  Z= 0.330
  Chirality :  0.035   0.159   1300
  Planarity :  0.004   0.044   1468
  Dihedral  :  3.456  12.454   1148
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.60 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.25), residues: 1032
  helix:  2.17 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -4.78 (0.72), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A   4 
 TYR   0.012   0.003   TYR C  24 
 ARG   0.007   0.000   ARG D 202 

*********************** 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
  175 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8631 (m-40) cc_final: 0.8295 (t0)
REVERT: A  168 ARG cc_start: 0.7549 (mtt180) cc_final: 0.6939 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7952 (m-40) cc_final: 0.7615 (p0)
REVERT: A  224 ARG cc_start: 0.8468 (mtt90) cc_final: 0.7687 (mtp-110)
REVERT: B  154 THR cc_start: 0.6955 (p) cc_final: 0.6737 (t)
REVERT: B  168 ARG cc_start: 0.7573 (mtt180) cc_final: 0.6946 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7966 (m-40) cc_final: 0.7439 (p0)
REVERT: B  195 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8149 (mm-30)
REVERT: B  224 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8000 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8049 (m-40) cc_final: 0.7628 (m-40)
REVERT: C  154 THR cc_start: 0.6361 (p) cc_final: 0.6126 (t)
REVERT: C  165 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8443 (pt0)
REVERT: C  168 ARG cc_start: 0.7744 (mtt180) cc_final: 0.6822 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7778 (m-40) cc_final: 0.7320 (p0)
REVERT: C  195 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8159 (mm-30)
REVERT: C  224 ARG cc_start: 0.8389 (mtt90) cc_final: 0.7912 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8625 (m-40) cc_final: 0.8308 (t0)
REVERT: D  168 ARG cc_start: 0.7631 (mtt180) cc_final: 0.6938 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7926 (m-40) cc_final: 0.7441 (p0)
REVERT: D  195 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8217 (mm-30)
REVERT: D  224 ARG cc_start: 0.8539 (mtt90) cc_final: 0.7890 (mtp-110)
  outliers start: 21
  outliers final: 15
  residues processed: 161
  average time/residue: 0.2169
  time to fit residues: 46.2516
Evaluate side-chains
  142 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain C residue   74 LEU
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  186 VAL
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  113 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.105893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.072923 restraints weight = 27668.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.074943 restraints weight = 16809.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.076156 restraints weight = 12523.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8096  Z= 0.243
  Angle     :  0.727  13.658  10932  Z= 0.349
  Chirality :  0.037   0.180   1300
  Planarity :  0.005   0.044   1468
  Dihedral  :  3.430  12.103   1148
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.57 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.60 (0.25), residues: 1032
  helix:  2.01 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.17 (0.73), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D   4 
 TYR   0.018   0.003   TYR B  24 
 ARG   0.007   0.000   ARG A 202 

*********************** 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
  158 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8650 (m-40) cc_final: 0.8293 (t0)
REVERT: A  168 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7003 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7988 (m-40) cc_final: 0.7621 (p0)
REVERT: A  195 GLU cc_start: 0.8264 (mp0) cc_final: 0.7963 (mp0)
REVERT: A  224 ARG cc_start: 0.8500 (mtt90) cc_final: 0.7693 (mtp-110)
REVERT: B  154 THR cc_start: 0.6957 (p) cc_final: 0.6738 (t)
REVERT: B  168 ARG cc_start: 0.7575 (mtt180) cc_final: 0.6984 (ttp-110)
REVERT: B  180 ASN cc_start: 0.8007 (m-40) cc_final: 0.7446 (p0)
REVERT: B  195 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8141 (mm-30)
REVERT: B  224 ARG cc_start: 0.8579 (mtt90) cc_final: 0.7854 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8060 (m-40) cc_final: 0.7595 (m-40)
REVERT: C  154 THR cc_start: 0.6425 (p) cc_final: 0.6223 (t)
REVERT: C  165 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8439 (pt0)
REVERT: C  168 ARG cc_start: 0.7763 (mtt180) cc_final: 0.6867 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7817 (m-40) cc_final: 0.7364 (p0)
REVERT: C  195 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8189 (mm-30)
REVERT: C  224 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7923 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8648 (m-40) cc_final: 0.8357 (t0)
REVERT: D  168 ARG cc_start: 0.7603 (mtt180) cc_final: 0.6952 (ttp-110)
REVERT: D  180 ASN cc_start: 0.8063 (m-40) cc_final: 0.7524 (p0)
REVERT: D  195 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8272 (mm-30)
REVERT: D  224 ARG cc_start: 0.8532 (mtt90) cc_final: 0.7852 (mtp-110)
  outliers start: 24
  outliers final: 19
  residues processed: 145
  average time/residue: 0.2260
  time to fit residues: 43.1157
Evaluate side-chains
  146 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
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  148 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  113 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  183 SER
Chi-restraints excluded: chain C residue  186 VAL
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  113 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 11 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:   30.0000
   chunk 59 optimal weight:    8.9990
   chunk 84 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0040
   chunk 58 optimal weight:    4.9990
   chunk 88 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    1.9398

-------------------------------------------------------------------------------
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 = 0.3924 r_free = 0.3924 target = 0.105480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.073904 restraints weight = 26803.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.075914 restraints weight = 16066.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.077105 restraints weight = 11857.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.4589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8096  Z= 0.251
  Angle     :  0.761  14.051  10932  Z= 0.361
  Chirality :  0.037   0.180   1300
  Planarity :  0.005   0.044   1468
  Dihedral  :  3.484  12.821   1148
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 17.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 22.57 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.24), residues: 1032
  helix:  1.95 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -5.06 (0.69), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B   4 
 TYR   0.018   0.003   TYR B  24 
 ARG   0.010   0.000   ARG A 202 

********************** 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
  150 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8666 (m-40) cc_final: 0.8291 (t0)
REVERT: A  168 ARG cc_start: 0.7563 (mtt180) cc_final: 0.6936 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7947 (m-40) cc_final: 0.7625 (p0)
REVERT: A  224 ARG cc_start: 0.8477 (mtt90) cc_final: 0.7674 (mtp-110)
REVERT: B  154 THR cc_start: 0.6940 (p) cc_final: 0.6713 (t)
REVERT: B  168 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7041 (ttp-110)
REVERT: B  180 ASN cc_start: 0.8068 (m-40) cc_final: 0.7477 (p0)
REVERT: B  195 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8172 (mm-30)
REVERT: B  224 ARG cc_start: 0.8565 (mtt90) cc_final: 0.7825 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8068 (m-40) cc_final: 0.7616 (m-40)
REVERT: C  154 THR cc_start: 0.6438 (p) cc_final: 0.6235 (t)
REVERT: C  165 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8435 (pt0)
REVERT: C  168 ARG cc_start: 0.7738 (mtt180) cc_final: 0.6860 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7822 (m-40) cc_final: 0.7348 (p0)
REVERT: C  195 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8195 (mm-30)
REVERT: C  224 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7921 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8674 (m-40) cc_final: 0.8350 (t0)
REVERT: D  168 ARG cc_start: 0.7587 (mtt180) cc_final: 0.6941 (ttp-110)
REVERT: D  180 ASN cc_start: 0.8046 (m-40) cc_final: 0.7500 (p0)
REVERT: D  195 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8246 (mm-30)
REVERT: D  224 ARG cc_start: 0.8532 (mtt90) cc_final: 0.7853 (mtp-110)
  outliers start: 21
  outliers final: 18
  residues processed: 138
  average time/residue: 0.2255
  time to fit residues: 41.0092
Evaluate side-chains
  142 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   80 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  113 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  183 SER
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  113 LEU
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 73 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:   20.0000
   chunk 76 optimal weight:    7.9990
   chunk 102 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.6986

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.104724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.071802 restraints weight = 27326.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.073778 restraints weight = 16443.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.075051 restraints weight = 12196.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.4684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8096  Z= 0.292
  Angle     :  0.754  13.851  10932  Z= 0.361
  Chirality :  0.038   0.177   1300
  Planarity :  0.005   0.052   1468
  Dihedral  :  3.506  13.859   1148
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.09 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.24), residues: 1032
  helix:  1.84 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -5.26 (0.66), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B   4 
 TYR   0.018   0.004   TYR C  24 
 ARG   0.013   0.001   ARG A 202 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2684.95 seconds
wall clock time: 47 minutes 6.85 seconds (2826.85 seconds total)