Starting phenix.real_space_refine
on Wed Feb 12 13:26:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xss_22305/02_2025/6xss_22305.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xss_22305/02_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_22305/02_2025/6xss_22305.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xss_22305/02_2025/6xss_22305.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xss_22305/02_2025/6xss_22305.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xss_22305/02_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-5592/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: 3.82, per 1000 atoms: 0.47
  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: 2.03
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.54
  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: 2.02

  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: 0.07
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     19.890
  Find NCS groups from input model:        0.180
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.470
-------------------------------------------------------------------------------
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  : 0.963 
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: 0.3238
  time to fit residues: 120.0757
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  : 1.102 
-------------------------------------------------------------------------------
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 = 0.074871 restraints weight = 27285.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.076925 restraints weight = 16469.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.078247 restraints weight = 12238.806|
|-----------------------------------------------------------------------------|
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  : 0.920 
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: 0.7792 (t0)
REVERT: A  131 ASN cc_start: 0.8318 (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: 0.7978 (m-40) cc_final: 0.7683 (p0)
REVERT: A  195 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8127 (mm-30)
REVERT: A  224 ARG cc_start: 0.8570 (mtt90) cc_final: 0.7853 (mtp-110)
REVERT: B   77 ILE cc_start: 0.9059 (mt) cc_final: 0.8856 (tp)
REVERT: B  154 THR cc_start: 0.6830 (p) cc_final: 0.6602 (t)
REVERT: B  168 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7258 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7882 (m-40) cc_final: 0.7456 (p0)
REVERT: B  195 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8121 (mm-30)
REVERT: B  210 THR cc_start: 0.6783 (m) cc_final: 0.6558 (p)
REVERT: B  224 ARG cc_start: 0.8553 (mtt90) cc_final: 0.7849 (mtp-110)
REVERT: C   69 ASP cc_start: 0.8387 (p0) cc_final: 0.8110 (p0)
REVERT: C  124 ASP cc_start: 0.8424 (t0) cc_final: 0.8222 (t70)
REVERT: C  168 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7090 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7485 (m-40) cc_final: 0.7230 (p0)
REVERT: C  195 GLU cc_start: 0.8618 (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: 0.7915 (m-40) cc_final: 0.7510 (p0)
REVERT: D  195 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8179 (mm-30)
REVERT: D  224 ARG cc_start: 0.8468 (mtt90) cc_final: 0.7851 (mtp-110)
  outliers start: 12
  outliers final: 6
  residues processed: 181
  average time/residue: 0.2499
  time to fit residues: 57.9077
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  : 1.130 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 70 optimal weight:    8.9990
   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:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.9384

-------------------------------------------------------------------------------
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 = 0.3940 r_free = 0.3940 target = 0.106784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074379 restraints weight = 27746.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.076428 restraints weight = 16903.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.077676 restraints weight = 12575.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8096  Z= 0.242
  Angle     :  0.664  11.141  10932  Z= 0.317
  Chirality :  0.035   0.147   1300
  Planarity :  0.005   0.043   1468
  Dihedral  :  3.377  12.041   1148
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 15.66 %
    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:  2.18 (0.25), residues: 1032
  helix:  1.70 (0.15), residues: 976
  sheet:  None (None), residues: 0
  loop : -2.97 (0.99), 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   0.008   0.001   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
  179 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8498 (m-40) cc_final: 0.7912 (t0)
REVERT: A  168 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7234 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7919 (m-40) cc_final: 0.7679 (p0)
REVERT: A  195 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8064 (mm-30)
REVERT: A  224 ARG cc_start: 0.8571 (mtt90) cc_final: 0.7756 (mtp-110)
REVERT: B  123 ARG cc_start: 0.8059 (tpm170) cc_final: 0.7675 (mmm-85)
REVERT: B  154 THR cc_start: 0.6841 (p) cc_final: 0.6620 (t)
REVERT: B  168 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7215 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7911 (m-40) cc_final: 0.7419 (p0)
REVERT: B  195 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8124 (mm-30)
REVERT: B  210 THR cc_start: 0.6854 (m) cc_final: 0.6626 (p)
REVERT: B  224 ARG cc_start: 0.8586 (mtt90) cc_final: 0.7899 (mtp-110)
REVERT: C   69 ASP cc_start: 0.8443 (p0) cc_final: 0.8185 (p0)
REVERT: C  124 ASP cc_start: 0.8522 (t0) cc_final: 0.8273 (t0)
REVERT: C  149 GLU cc_start: 0.8216 (pt0) cc_final: 0.7763 (tm-30)
REVERT: C  165 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8568 (pt0)
REVERT: C  168 ARG cc_start: 0.7957 (mtt180) cc_final: 0.6925 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7527 (m-40) cc_final: 0.7300 (p0)
REVERT: C  186 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7450 (m)
REVERT: C  195 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8197 (mm-30)
REVERT: C  224 ARG cc_start: 0.8383 (mtt90) cc_final: 0.7877 (tmt-80)
REVERT: C  254 GLN cc_start: 0.8279 (mt0) cc_final: 0.7676 (tm-30)
REVERT: D   15 ASN cc_start: 0.8515 (m-40) cc_final: 0.8012 (t0)
REVERT: D  168 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7170 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7905 (m-40) cc_final: 0.7506 (p0)
REVERT: D  195 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8118 (mm-30)
REVERT: D  224 ARG cc_start: 0.8470 (mtt90) cc_final: 0.7846 (mtp-110)
  outliers start: 27
  outliers final: 17
  residues processed: 162
  average time/residue: 0.2245
  time to fit residues: 47.4664
Evaluate side-chains
  149 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
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 A residue  228 GLU
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  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:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   chunk 80 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.107478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.075290 restraints weight = 27442.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.077427 restraints weight = 16635.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.078698 restraints weight = 12277.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3700

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= 0.189
  Angle     :  0.644  11.129  10932  Z= 0.305
  Chirality :  0.034   0.150   1300
  Planarity :  0.004   0.045   1468
  Dihedral  :  3.370  11.405   1148
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.63 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.55 (0.25), residues: 1032
  helix:  1.96 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -4.18 (0.82), 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   0.007   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
  191 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8492 (m-40) cc_final: 0.7946 (t0)
REVERT: A  168 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7145 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7895 (m-40) cc_final: 0.7594 (p0)
REVERT: A  195 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8108 (mm-30)
REVERT: A  224 ARG cc_start: 0.8561 (mtt90) cc_final: 0.7812 (mtp-110)
REVERT: B   77 ILE cc_start: 0.9081 (mt) cc_final: 0.8848 (tp)
REVERT: B  123 ARG cc_start: 0.8118 (tpm170) cc_final: 0.7710 (mmm-85)
REVERT: B  154 THR cc_start: 0.6884 (p) cc_final: 0.6663 (t)
REVERT: B  168 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7129 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7903 (m-40) cc_final: 0.7432 (p0)
REVERT: B  195 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8088 (mm-30)
REVERT: B  224 ARG cc_start: 0.8567 (mtt90) cc_final: 0.7779 (mtp-110)
REVERT: B  228 GLU cc_start: 0.8757 (tt0) cc_final: 0.8546 (pt0)
REVERT: C   69 ASP cc_start: 0.8430 (p0) cc_final: 0.8204 (p0)
REVERT: C  124 ASP cc_start: 0.8458 (t0) cc_final: 0.8189 (t0)
REVERT: C  131 ASN cc_start: 0.7905 (m-40) cc_final: 0.7311 (m-40)
REVERT: C  149 GLU cc_start: 0.8223 (pt0) cc_final: 0.7751 (tm-30)
REVERT: C  154 THR cc_start: 0.6290 (p) cc_final: 0.6031 (t)
REVERT: C  168 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7037 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7641 (m-40) cc_final: 0.7284 (p0)
REVERT: C  195 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8166 (mm-30)
REVERT: C  224 ARG cc_start: 0.8363 (mtt90) cc_final: 0.7875 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8473 (m-40) cc_final: 0.7933 (t0)
REVERT: D  168 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7037 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7930 (m-40) cc_final: 0.7571 (p0)
REVERT: D  195 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: D  224 ARG cc_start: 0.8456 (mtt90) cc_final: 0.7832 (mtp-110)
  outliers start: 25
  outliers final: 15
  residues processed: 177
  average time/residue: 0.2387
  time to fit residues: 54.8488
Evaluate side-chains
  150 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain D residue  192 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 101 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3949 r_free = 0.3949 target = 0.107094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.075610 restraints weight = 26755.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077685 restraints weight = 16137.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.078959 restraints weight = 11882.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3906

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= 0.202
  Angle     :  0.656  11.301  10932  Z= 0.311
  Chirality :  0.034   0.132   1300
  Planarity :  0.004   0.044   1468
  Dihedral  :  3.388  12.667   1148
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.11 %
    Favored  : 79.37 %
  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:  2.71 (0.25), residues: 1032
  helix:  2.07 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -4.31 (0.77), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B   4 
 TYR   0.016   0.003   TYR B  24 
 ARG   0.010   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
  180 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8584 (m-40) cc_final: 0.8132 (t0)
REVERT: A  168 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7083 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7869 (m-40) cc_final: 0.7581 (p0)
REVERT: A  195 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8091 (mm-30)
REVERT: A  224 ARG cc_start: 0.8553 (mtt90) cc_final: 0.7734 (mtp-110)
REVERT: A  228 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8489 (pt0)
REVERT: B  123 ARG cc_start: 0.8101 (tpm170) cc_final: 0.7709 (mmm-85)
REVERT: B  154 THR cc_start: 0.6885 (p) cc_final: 0.6666 (t)
REVERT: B  168 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7127 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7862 (m-40) cc_final: 0.7410 (p0)
REVERT: B  195 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8077 (mm-30)
REVERT: B  224 ARG cc_start: 0.8573 (mtt90) cc_final: 0.7797 (mtp-110)
REVERT: B  228 GLU cc_start: 0.8826 (tt0) cc_final: 0.8578 (pt0)
REVERT: C  131 ASN cc_start: 0.7968 (m-40) cc_final: 0.7331 (m-40)
REVERT: C  149 GLU cc_start: 0.8204 (pt0) cc_final: 0.7716 (tm-30)
REVERT: C  154 THR cc_start: 0.6240 (p) cc_final: 0.5978 (t)
REVERT: C  168 ARG cc_start: 0.7820 (mtt180) cc_final: 0.6935 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7747 (m-40) cc_final: 0.7349 (p0)
REVERT: C  195 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8124 (mm-30)
REVERT: C  224 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7888 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8538 (m-40) cc_final: 0.8042 (t0)
REVERT: D  168 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7011 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7942 (m-40) cc_final: 0.7590 (p0)
REVERT: D  195 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8099 (mm-30)
REVERT: D  224 ARG cc_start: 0.8452 (mtt90) cc_final: 0.7820 (mtp-110)
  outliers start: 29
  outliers final: 17
  residues processed: 161
  average time/residue: 0.2253
  time to fit residues: 47.6488
Evaluate side-chains
  152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain C residue   74 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:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0670
   chunk 78 optimal weight:    0.7980
   chunk 76 optimal weight:    9.9990
   overall best weight:    1.9724

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.106671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.074033 restraints weight = 27143.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.076096 restraints weight = 16349.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.077378 restraints weight = 12086.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8096  Z= 0.241
  Angle     :  0.670  11.881  10932  Z= 0.319
  Chirality :  0.035   0.137   1300
  Planarity :  0.004   0.044   1468
  Dihedral  :  3.381  11.517   1148
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.69 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.71 (0.25), residues: 1032
  helix:  2.09 (0.15), residues: 984
  sheet:  None (None), residues: 0
  loop : -4.71 (0.69), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B   4 
 TYR   0.014   0.003   TYR C  24 
 ARG   0.007   0.000   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
  174 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8676 (m-40) cc_final: 0.8209 (t0)
REVERT: A  168 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7137 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7942 (m-40) cc_final: 0.7665 (p0)
REVERT: A  195 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8131 (mm-30)
REVERT: A  224 ARG cc_start: 0.8567 (mtt90) cc_final: 0.7486 (mtp-110)
REVERT: B  154 THR cc_start: 0.6953 (p) cc_final: 0.6737 (t)
REVERT: B  168 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7126 (ttp-110)
REVERT: B  180 ASN cc_start: 0.8005 (m-40) cc_final: 0.7466 (p0)
REVERT: B  195 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8153 (mm-30)
REVERT: B  224 ARG cc_start: 0.8592 (mtt90) cc_final: 0.7808 (mtp-110)
REVERT: B  228 GLU cc_start: 0.8849 (tt0) cc_final: 0.8591 (pt0)
REVERT: C  131 ASN cc_start: 0.8031 (m-40) cc_final: 0.7567 (m-40)
REVERT: C  154 THR cc_start: 0.6330 (p) cc_final: 0.6085 (t)
REVERT: C  168 ARG cc_start: 0.7782 (mtt180) cc_final: 0.6883 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7814 (m-40) cc_final: 0.7344 (p0)
REVERT: C  195 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8173 (mm-30)
REVERT: C  224 ARG cc_start: 0.8392 (mtt90) cc_final: 0.7913 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8644 (m-40) cc_final: 0.8238 (t0)
REVERT: D  168 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7048 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7941 (m-40) cc_final: 0.7506 (p0)
REVERT: D  195 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8157 (mm-30)
REVERT: D  224 ARG cc_start: 0.8517 (mtt90) cc_final: 0.7882 (mtp-110)
  outliers start: 33
  outliers final: 25
  residues processed: 152
  average time/residue: 0.2353
  time to fit residues: 46.8483
Evaluate side-chains
  150 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain 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  186 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  228 GLU
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:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.106722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.075432 restraints weight = 26897.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.077535 restraints weight = 16058.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.078866 restraints weight = 11704.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8096  Z= 0.201
  Angle     :  0.670  12.711  10932  Z= 0.315
  Chirality :  0.035   0.146   1300
  Planarity :  0.004   0.042   1468
  Dihedral  :  3.409  12.681   1148
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 19.30 %
    Favored  : 76.94 %
  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:  2.15 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -4.90 (0.75), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B   4 
 TYR   0.012   0.003   TYR C  24 
 ARG   0.006   0.000   ARG D 202 

*********************** 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
  174 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8693 (m-40) cc_final: 0.8257 (t0)
REVERT: A  168 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7061 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7936 (m-40) cc_final: 0.7645 (p0)
REVERT: A  224 ARG cc_start: 0.8530 (mtt90) cc_final: 0.7720 (mtp-110)
REVERT: B  154 THR cc_start: 0.6912 (p) cc_final: 0.6699 (t)
REVERT: B  168 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7101 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7959 (m-40) cc_final: 0.7444 (p0)
REVERT: B  195 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8109 (mm-30)
REVERT: B  224 ARG cc_start: 0.8545 (mtt90) cc_final: 0.7778 (mtp-110)
REVERT: B  228 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8565 (pt0)
REVERT: C  131 ASN cc_start: 0.8034 (m-40) cc_final: 0.7568 (m-40)
REVERT: C  154 THR cc_start: 0.6263 (p) cc_final: 0.6042 (t)
REVERT: C  168 ARG cc_start: 0.7754 (mtt180) cc_final: 0.6833 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7791 (m-40) cc_final: 0.7413 (p0)
REVERT: C  195 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8141 (mm-30)
REVERT: C  224 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7898 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8648 (m-40) cc_final: 0.8287 (t0)
REVERT: D  168 ARG cc_start: 0.7609 (mtt180) cc_final: 0.6910 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7943 (m-40) cc_final: 0.7488 (p0)
REVERT: D  195 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: D  224 ARG cc_start: 0.8501 (mtt90) cc_final: 0.7865 (mtp-110)
  outliers start: 31
  outliers final: 23
  residues processed: 153
  average time/residue: 0.2359
  time to fit residues: 47.1244
Evaluate side-chains
  156 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue   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  228 GLU
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 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  228 GLU
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:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.106730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.074440 restraints weight = 27345.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.076527 restraints weight = 16274.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.077758 restraints weight = 11940.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8096  Z= 0.205
  Angle     :  0.687  13.229  10932  Z= 0.326
  Chirality :  0.036   0.149   1300
  Planarity :  0.004   0.042   1468
  Dihedral  :  3.406  12.666   1148
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.02 %
    Favored  : 76.33 %
  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 (0.24), residues: 1032
  helix:  2.06 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -4.96 (0.74), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C   4 
 TYR   0.017   0.003   TYR C  24 
 ARG   0.006   0.000   ARG D 179 

*********************** 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
  173 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8670 (m-40) cc_final: 0.8263 (t0)
REVERT: A  168 ARG cc_start: 0.7634 (mtt180) cc_final: 0.7050 (ttp-110)
REVERT: A  180 ASN cc_start: 0.7949 (m-40) cc_final: 0.7623 (p0)
REVERT: A  195 GLU cc_start: 0.8231 (mp0) cc_final: 0.7844 (mp0)
REVERT: A  224 ARG cc_start: 0.8491 (mtt90) cc_final: 0.7689 (mtp-110)
REVERT: B  154 THR cc_start: 0.6955 (p) cc_final: 0.6747 (t)
REVERT: B  168 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7140 (ttp-110)
REVERT: B  180 ASN cc_start: 0.7938 (m-40) cc_final: 0.7406 (p0)
REVERT: B  195 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8144 (mm-30)
REVERT: B  224 ARG cc_start: 0.8565 (mtt90) cc_final: 0.7753 (mtp-110)
REVERT: B  228 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8600 (pt0)
REVERT: C  131 ASN cc_start: 0.8036 (m-40) cc_final: 0.7569 (m-40)
REVERT: C  154 THR cc_start: 0.6404 (p) cc_final: 0.6176 (t)
REVERT: C  168 ARG cc_start: 0.7747 (mtt180) cc_final: 0.6823 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7783 (m-40) cc_final: 0.7397 (p0)
REVERT: C  195 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8165 (mm-30)
REVERT: C  224 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7908 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8641 (m-40) cc_final: 0.8307 (t0)
REVERT: D  168 ARG cc_start: 0.7652 (mtt180) cc_final: 0.6953 (ttp-110)
REVERT: D  180 ASN cc_start: 0.7921 (m-40) cc_final: 0.7476 (p0)
REVERT: D  195 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8217 (mm-30)
REVERT: D  224 ARG cc_start: 0.8541 (mtt90) cc_final: 0.7889 (mtp-110)
  outliers start: 30
  outliers final: 22
  residues processed: 155
  average time/residue: 0.2347
  time to fit residues: 47.7367
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  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue   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  228 GLU
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 D residue   74 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  192 LEU
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:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 80 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    2.3990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.105019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.073008 restraints weight = 27497.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.075042 restraints weight = 16270.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.076296 restraints weight = 11923.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.4477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8096  Z= 0.265
  Angle     :  0.728  13.532  10932  Z= 0.346
  Chirality :  0.037   0.199   1300
  Planarity :  0.005   0.042   1468
  Dihedral  :  3.454  12.630   1148
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.12 %
    Favored  : 75.36 %
  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:  2.46 (0.24), residues: 1032
  helix:  1.93 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.37 (0.67), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A   4 
 TYR   0.018   0.003   TYR C  24 
 ARG   0.005   0.000   ARG D 179 

*********************** 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
  167 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8742 (m-40) cc_final: 0.8249 (t0)
REVERT: A  168 ARG cc_start: 0.7634 (mtt180) cc_final: 0.7079 (ttp-110)
REVERT: A  180 ASN cc_start: 0.8028 (m-40) cc_final: 0.7688 (p0)
REVERT: A  224 ARG cc_start: 0.8521 (mtt90) cc_final: 0.7720 (mtp-110)
REVERT: B  154 THR cc_start: 0.6942 (p) cc_final: 0.6723 (t)
REVERT: B  168 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7157 (ttp-110)
REVERT: B  180 ASN cc_start: 0.8045 (m-40) cc_final: 0.7466 (p0)
REVERT: B  195 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8203 (mm-30)
REVERT: B  224 ARG cc_start: 0.8571 (mtt90) cc_final: 0.7878 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8055 (m-40) cc_final: 0.7541 (m-40)
REVERT: C  154 THR cc_start: 0.6466 (p) cc_final: 0.6254 (t)
REVERT: C  168 ARG cc_start: 0.7776 (mtt180) cc_final: 0.6920 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7787 (m-40) cc_final: 0.7218 (p0)
REVERT: C  195 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8209 (mm-30)
REVERT: C  224 ARG cc_start: 0.8382 (mtt90) cc_final: 0.7910 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8670 (m-40) cc_final: 0.8262 (t0)
REVERT: D  168 ARG cc_start: 0.7623 (mtt180) cc_final: 0.6958 (ttp-110)
REVERT: D  180 ASN cc_start: 0.8049 (m-40) cc_final: 0.7526 (p0)
REVERT: D  195 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8245 (mm-30)
REVERT: D  224 ARG cc_start: 0.8535 (mtt90) cc_final: 0.7862 (mtp-110)
  outliers start: 29
  outliers final: 24
  residues processed: 148
  average time/residue: 0.2350
  time to fit residues: 45.4761
Evaluate side-chains
  152 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
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  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  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 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   80 LEU
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  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:    0.3980
   chunk 15 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 84 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.6788

-------------------------------------------------------------------------------
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 = 0.3932 r_free = 0.3932 target = 0.105845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074223 restraints weight = 26915.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.076278 restraints weight = 15899.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.077565 restraints weight = 11674.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.4552

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= 0.237
  Angle     :  0.738  14.140  10932  Z= 0.345
  Chirality :  0.037   0.173   1300
  Planarity :  0.004   0.042   1468
  Dihedral  :  3.480  14.629   1148
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.97 %
    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:  2.51 (0.24), residues: 1032
  helix:  1.96 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.31 (0.71), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A   4 
 TYR   0.016   0.003   TYR C  24 
 ARG   0.005   0.000   ARG B 102 

********************** 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
  159 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASN cc_start: 0.8703 (m-40) cc_final: 0.8204 (t0)
REVERT: A  168 ARG cc_start: 0.7620 (mtt180) cc_final: 0.6980 (ttp-110)
REVERT: A  180 ASN cc_start: 0.8036 (m-40) cc_final: 0.7687 (p0)
REVERT: A  195 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7900 (mp0)
REVERT: A  224 ARG cc_start: 0.8490 (mtt90) cc_final: 0.7693 (mtp-110)
REVERT: B  154 THR cc_start: 0.6933 (p) cc_final: 0.6709 (t)
REVERT: B  168 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7105 (ttp-110)
REVERT: B  180 ASN cc_start: 0.8027 (m-40) cc_final: 0.7427 (p0)
REVERT: B  195 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8182 (mm-30)
REVERT: B  224 ARG cc_start: 0.8656 (mtt90) cc_final: 0.8017 (mtp-110)
REVERT: C  131 ASN cc_start: 0.8070 (m-40) cc_final: 0.7606 (m-40)
REVERT: C  154 THR cc_start: 0.6442 (p) cc_final: 0.6232 (t)
REVERT: C  168 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6856 (ttp-110)
REVERT: C  180 ASN cc_start: 0.7850 (m-40) cc_final: 0.7366 (p0)
REVERT: C  195 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8208 (mm-30)
REVERT: C  224 ARG cc_start: 0.8373 (mtt90) cc_final: 0.7912 (tmt-80)
REVERT: D   15 ASN cc_start: 0.8677 (m-40) cc_final: 0.8303 (t0)
REVERT: D  168 ARG cc_start: 0.7593 (mtt180) cc_final: 0.6928 (ttp-110)
REVERT: D  180 ASN cc_start: 0.8075 (m-40) cc_final: 0.7512 (p0)
REVERT: D  195 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8225 (mm-30)
REVERT: D  224 ARG cc_start: 0.8523 (mtt90) cc_final: 0.7848 (mtp-110)
  outliers start: 25
  outliers final: 21
  residues processed: 143
  average time/residue: 0.2377
  time to fit residues: 44.4870
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  : 0.864 
-------------------------------------------------------------------------------
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  110 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  195 GLU
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  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  228 GLU
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  238 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 15 optimal weight:   20.0000
   chunk 76 optimal weight:    5.9990
   chunk 102 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 6 optimal weight:    6.9990
   overall best weight:    4.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.103172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.070929 restraints weight = 27244.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.072967 restraints weight = 16048.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.074205 restraints weight = 11751.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   8096  Z= 0.391
  Angle     :  0.822  13.199  10932  Z= 0.400
  Chirality :  0.041   0.191   1300
  Planarity :  0.005   0.044   1468
  Dihedral  :  3.567  13.145   1148
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 20.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.72 %
    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:  2.00 (0.24), residues: 1032
  helix:  1.65 (0.15), residues: 988
  sheet:  None (None), residues: 0
  loop : -5.90 (0.60), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C   4 
 TYR   0.018   0.004   TYR C  24 
 ARG   0.012   0.001   ARG D 202 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2624.43 seconds
wall clock time: 47 minutes 32.92 seconds (2852.92 seconds total)