Starting phenix.real_space_refine
on Wed Jun  3 12:26:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/21tw_67994/06_2026/21tw_67994.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/21tw_67994/06_2026/21tw_67994.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/21tw_67994/06_2026/21tw_67994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/21tw_67994/06_2026/21tw_67994.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/21tw_67994/06_2026/21tw_67994.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/21tw_67994/06_2026/21tw_67994.cif"
  }
  resolution = 2.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      14      5.16       5
     C    3183      2.51       5
     N     861      2.21       5
     O     921      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4979
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1732
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 10, 'TRANS': 213}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1092
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 8, 'TRANS': 130}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1075
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 8, 'TRANS': 128}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1080
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 8, 'TRANS': 129}
          Chain breaks: 1
  Time building chain proxies: 1.64, per 1000 atoms: 0.33
  Number of scatterers: 4979
  At special positions: 0
  Unit cell: (65.404, 82.74, 95.348, 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      14     16.00
     O     921      8.00
     N     861      7.00
     C    3183      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 270 " - pdb=" SG  CYS A 344 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  69 " - pdb=" SG  CYS B 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  69 " - pdb=" SG  CYS C 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  69 " - pdb=" SG  CYS D 101 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 197.7 milliseconds
  

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 13 sheets defined
      3.9% alpha, 42.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 87 through 91
    Processing helix  chain 'A' and resid 276 through 280
    Processing helix  chain 'A' and resid 335 through 339
    Processing helix  chain 'B' and resid 138 through 142
    Processing helix  chain 'C' and resid 138 through 142
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.626A  pdb=" N   LEU A  18 " --> pdb=" O   MET A  83 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59
      removed outlier: 6.570A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   GLU A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   MET A  34 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL A  93 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73
    Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 254
    Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 307
      removed outlier: 6.306A  pdb=" N   TRP A 284 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   GLU A 298 " --> pdb=" O   MET A 282 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   MET A 282 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL A 285 " --> pdb=" O   TYR A 343 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 29
      removed outlier: 3.859A  pdb=" N   LEU B  55 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 38
      removed outlier: 3.592A  pdb=" N   VAL B  13 " --> pdb=" O   ALA B  38 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LEU B  55 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 44
      removed outlier: 5.809A  pdb=" N   ARG B  82 " --> pdb=" O   ASN B  92 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   ASN B  92 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AB1, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 44
      removed outlier: 6.118A  pdb=" N   ARG C  82 " --> pdb=" O   ASN C  92 " (cutoff:3.500A)
      removed outlier: 5.771A  pdb=" N   ASN C  92 " --> pdb=" O   ARG C  82 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 36 through 38
      removed outlier: 3.717A  pdb=" N   VAL D  13 " --> pdb=" O   ALA D  38 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY D  54 " --> pdb=" O   LEU D 126 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY D  66 " --> pdb=" O   TRP D 114 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 43
      removed outlier: 4.162A  pdb=" N   GLU D  42 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG D 131 " --> pdb=" O   ILE D  83 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ARG D  82 " --> pdb=" O   ASN D  92 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   ASN D  92 " --> pdb=" O   ARG D  82 " (cutoff:3.500A)

    205 hydrogen bonds defined for protein.
    489 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: 0.84

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1622
        1.34 -     1.46: 988
        1.46 -     1.58: 2463
        1.58 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 5091
  Sorted by residual:
  bond pdb=" N   SER A  99 "
       pdb=" CA  SER A  99 "
    ideal  model  delta    sigma   weight residual
    1.453  1.484 -0.031 8.30e-03 1.45e+04 1.35e+01
  bond pdb=" CA  SER A  99 "
       pdb=" CB  SER A  99 "
    ideal  model  delta    sigma   weight residual
    1.536  1.499  0.037 1.23e-02 6.61e+03 9.29e+00
  bond pdb=" N   VAL B  74 "
       pdb=" CA  VAL B  74 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.19e-02 7.06e+03 8.85e+00
  bond pdb=" N   TYR B  87 "
       pdb=" CA  TYR B  87 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.18e-02 7.18e+03 8.76e+00
  bond pdb=" N   LYS A 307 "
       pdb=" CA  LYS A 307 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.17e-02 7.31e+03 8.39e+00
  ... (remaining 5086 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 6297
        1.37 -     2.74: 464
        2.74 -     4.12: 135
        4.12 -     5.49: 20
        5.49 -     6.86: 3
  Bond angle restraints: 6919
  Sorted by residual:
  angle pdb=" C   TYR A 343 "
        pdb=" CA  TYR A 343 "
        pdb=" CB  TYR A 343 "
      ideal   model   delta    sigma   weight residual
     111.51  104.65    6.86 1.66e+00 3.63e-01 1.71e+01
  angle pdb=" CA  LEU C  48 "
        pdb=" C   LEU C  48 "
        pdb=" O   LEU C  48 "
      ideal   model   delta    sigma   weight residual
     121.55  117.37    4.18 1.06e+00 8.90e-01 1.55e+01
  angle pdb=" N   VAL A 296 "
        pdb=" CA  VAL A 296 "
        pdb=" C   VAL A 296 "
      ideal   model   delta    sigma   weight residual
     113.53  109.74    3.79 9.80e-01 1.04e+00 1.49e+01
  angle pdb=" C   ASP C 130 "
        pdb=" CA  ASP C 130 "
        pdb=" CB  ASP C 130 "
      ideal   model   delta    sigma   weight residual
     110.67  116.19   -5.52 1.52e+00 4.33e-01 1.32e+01
  angle pdb=" N   GLY A  26 "
        pdb=" CA  GLY A  26 "
        pdb=" C   GLY A  26 "
      ideal   model   delta    sigma   weight residual
     115.30  110.52    4.78 1.39e+00 5.18e-01 1.18e+01
  ... (remaining 6914 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 2578
       15.99 -    31.97: 295
       31.97 -    47.96: 102
       47.96 -    63.95: 41
       63.95 -    79.93: 10
  Dihedral angle restraints: 3026
    sinusoidal: 1199
      harmonic: 1827
  Sorted by residual:
  dihedral pdb=" CA  TYR A 280 "
           pdb=" C   TYR A 280 "
           pdb=" N   TRP A 281 "
           pdb=" CA  TRP A 281 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.22   19.78     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CB  CYS A 270 "
           pdb=" SG  CYS A 270 "
           pdb=" SG  CYS A 344 "
           pdb=" CB  CYS A 344 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -56.00  -30.00     1      1.00e+01 1.00e-02 1.29e+01
  dihedral pdb=" CB  CYS C  69 "
           pdb=" SG  CYS C  69 "
           pdb=" SG  CYS C 101 "
           pdb=" CB  CYS C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -58.45  -27.55     1      1.00e+01 1.00e-02 1.09e+01
  ... (remaining 3023 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 536
       0.051 -    0.101: 158
       0.101 -    0.152: 62
       0.152 -    0.203: 9
       0.203 -    0.253: 2
  Chirality restraints: 767
  Sorted by residual:
  chirality pdb=" CA  ILE C  80 "
            pdb=" N   ILE C  80 "
            pdb=" C   ILE C  80 "
            pdb=" CB  ILE C  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  ILE B  83 "
            pdb=" N   ILE B  83 "
            pdb=" C   ILE B  83 "
            pdb=" CB  ILE B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  LEU D  94 "
            pdb=" N   LEU D  94 "
            pdb=" C   LEU D  94 "
            pdb=" CB  LEU D  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 764 not shown)

  Planarity restraints: 892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  72 "    0.248 9.50e-02 1.11e+02   1.11e-01 7.73e+00
        pdb=" NE  ARG A  72 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  72 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  72 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  72 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  82 "    0.222 9.50e-02 1.11e+02   9.94e-02 6.07e+00
        pdb=" NE  ARG C  82 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  82 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  82 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  82 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C 125 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.24e+00
        pdb=" C   GLN C 125 "    0.040 2.00e-02 2.50e+03
        pdb=" O   GLN C 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU C 126 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 889 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 228
        2.70 -     3.25: 4959
        3.25 -     3.80: 8910
        3.80 -     4.35: 12182
        4.35 -     4.90: 19467
  Nonbonded interactions: 45746
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 332 "
            pdb=" N   SER A 333 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" O   PHE A 277 "
            pdb=" NH2 ARG A 320 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" NZ  LYS D  98 "
            pdb=" O   PRO D 117 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" N   GLN A 107 "
            pdb=" OE1 GLN A 107 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" CD1 TRP B  28 "
            pdb=" OD1 ASN B  46 "
     model   vdw
     2.288 3.260
  ... (remaining 45741 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 11 through 101 or resid 112 through 156))
  selection = (chain 'C' and resid 11 through 156)
  selection = (chain 'D' and (resid 11 through 101 or resid 112 through 156))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.970
  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:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     7.500
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   5096  Z= 0.399
  Angle     :  0.856   6.859   6929  Z= 0.541
  Chirality :  0.057   0.253    767
  Planarity :  0.007   0.111    892
  Dihedral  : 17.451  79.935   1847
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 19.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 29.29 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.34), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.98 (0.29), residues: 283
  loop : -0.23 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  72 
 TYR   0.016   0.002   TYR A 343 
 PHE   0.012   0.002   PHE B 144 
 TRP   0.014   0.002   TRP A 284 
 HIS   0.003   0.001   HIS C  78 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00599 /  0.40 ( 5091)
  covalent geometry    : angle       0.85580 /  0.54 ( 6919)
  SS BOND              : bond        0.00245 /  0.13 (    5)
  SS BOND              : angle       0.82991 /  0.42 (   10)
  hydrogen bonds       : bond        0.25278 / 17.45 (  192)
  hydrogen bonds       : angle      11.84268 /  8.18 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A  280 TYR cc_start: 0.7879 (m-80) cc_final: 0.7029 (m-80)
REVERT: B   27 GLN cc_start: 0.7211 (tt0) cc_final: 0.6733 (tm-30)
REVERT: B   42 GLU cc_start: 0.6483 (mt-10) cc_final: 0.5982 (mm-30)
REVERT: B  112 LYS cc_start: 0.7183 (ttmt) cc_final: 0.6708 (ttpt)
REVERT: B  131 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7295 (mmm-85)
  outliers start: 5
  outliers final: 2
  residues processed: 81
  average time/residue: 0.6681
  time to fit residues: 56.0437
Evaluate side-chains
  69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 PHE
Chi-restraints excluded: chain C residue   48 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0670
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.196477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.159622 restraints weight = 4779.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 2.42
r_work: 0.3995 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3848 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5096  Z= 0.191
  Angle     :  0.638   8.046   6929  Z= 0.335
  Chirality :  0.047   0.180    767
  Planarity :  0.004   0.028    892
  Dihedral  :  5.485  39.898    699
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 26.49 %
    Favored  : 67.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.33), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.70 (0.29), residues: 284
  loop : -0.04 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  72 
 TYR   0.018   0.002   TYR A  95 
 PHE   0.014   0.002   PHE B 124 
 TRP   0.021   0.002   TRP A 284 
 HIS   0.005   0.001   HIS B  73 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.19 ( 5091)
  covalent geometry    : angle       0.63870 /  0.34 ( 6919)
  SS BOND              : bond        0.00209 /  0.10 (    5)
  SS BOND              : angle       0.39272 /  0.20 (   10)
  hydrogen bonds       : bond        0.04148 /  2.93 (  192)
  hydrogen bonds       : angle       8.40667 /  5.58 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 69
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.5586 (mtm) cc_final: 0.3403 (mpt)
REVERT: A   87 ARG cc_start: 0.7621 (mtt90) cc_final: 0.6992 (mtt90)
REVERT: A  280 TYR cc_start: 0.7733 (m-80) cc_final: 0.6978 (m-80)
REVERT: A  307 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6630 (mtpp)
REVERT: B   27 GLN cc_start: 0.7325 (tt0) cc_final: 0.6703 (tm-30)
REVERT: B   42 GLU cc_start: 0.6436 (mt-10) cc_final: 0.5743 (mm-30)
REVERT: B  112 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6428 (ttpt)
REVERT: B  131 ARG cc_start: 0.7490 (mmt90) cc_final: 0.6939 (mmm-85)
REVERT: C   98 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7086 (tttt)
REVERT: D   44 ARG cc_start: 0.7690 (ptt-90) cc_final: 0.7455 (ptt-90)
  outliers start: 32
  outliers final: 10
  residues processed: 93
  average time/residue: 0.6014
  time to fit residues: 58.0822
Evaluate side-chains
  70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  112 LYS
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   98 LYS
Chi-restraints excluded: chain D residue   41 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0570
   chunk 51 optimal weight:    0.0370
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0670
   chunk 1 optimal weight:    0.1980
   overall best weight:    0.1914

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
B  15 HIS
B  46 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.202187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.166443 restraints weight = 4722.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.4191 rms_B_bonded: 2.46
r_work: 0.4075 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3931 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5096  Z= 0.129
  Angle     :  0.562   6.329   6929  Z= 0.293
  Chirality :  0.046   0.185    767
  Planarity :  0.004   0.032    892
  Dihedral  :  4.969  39.572    697
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 15.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 26.12 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.33), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.52 (0.29), residues: 288
  loop :  0.14 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 131 
 TYR   0.018   0.002   TYR A  95 
 PHE   0.008   0.001   PHE B 124 
 TRP   0.016   0.002   TRP A 284 
 HIS   0.003   0.001   HIS B  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 ( 5091)
  covalent geometry    : angle       0.56206 /  0.29 ( 6919)
  SS BOND              : bond        0.00092 /  0.05 (    5)
  SS BOND              : angle       0.51737 /  0.26 (   10)
  hydrogen bonds       : bond        0.03382 /  2.35 (  192)
  hydrogen bonds       : angle       7.72485 /  5.09 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 64
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7442 (tpp80)
REVERT: A   87 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7070 (mpt-90)
REVERT: A  280 TYR cc_start: 0.7533 (m-80) cc_final: 0.6759 (m-80)
REVERT: B   27 GLN cc_start: 0.7469 (tt0) cc_final: 0.6848 (tm-30)
REVERT: B   42 GLU cc_start: 0.6440 (mt-10) cc_final: 0.5674 (mm-30)
REVERT: B   47 GLN cc_start: 0.6571 (mt0) cc_final: 0.6181 (mp10)
REVERT: B   76 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7480 (mt)
REVERT: B  112 LYS cc_start: 0.6940 (ttmt) cc_final: 0.6248 (ttpt)
REVERT: B  131 ARG cc_start: 0.7466 (mmt90) cc_final: 0.6996 (mmm-85)
REVERT: C   42 GLU cc_start: 0.7920 (mp0) cc_final: 0.7470 (mp0)
REVERT: C   45 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6890 (m-30)
REVERT: C   98 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7023 (tttt)
REVERT: C  138 ARG cc_start: 0.5324 (mmm160) cc_final: 0.4739 (mmm160)
REVERT: C  143 ASP cc_start: 0.6706 (t70) cc_final: 0.6150 (t70)
REVERT: D   44 ARG cc_start: 0.7779 (ptt-90) cc_final: 0.7431 (ptt-90)
REVERT: D  131 ARG cc_start: 0.7380 (ptp90) cc_final: 0.7180 (ptp90)
REVERT: D  135 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6098 (tp30)
  outliers start: 32
  outliers final: 8
  residues processed: 91
  average time/residue: 0.6406
  time to fit residues: 60.4790
Evaluate side-chains
  69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain A residue  357 THR
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue   98 LYS
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   93 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0770
   chunk 34 optimal weight:    0.8980
   chunk 17 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    9.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
B 149 GLN
C  61 GLN
C  67 GLN
C  73 HIS
D  61 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.195201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.158181 restraints weight = 4708.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 2.42
r_work: 0.3973 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3828 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5096  Z= 0.195
  Angle     :  0.602   6.032   6929  Z= 0.315
  Chirality :  0.047   0.204    767
  Planarity :  0.004   0.031    892
  Dihedral  :  4.885  19.306    695
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 24.44 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.33), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.39 (0.29), residues: 294
  loop :  0.26 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 131 
 TYR   0.017   0.002   TYR A  95 
 PHE   0.011   0.002   PHE B 124 
 TRP   0.019   0.002   TRP A 284 
 HIS   0.003   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.19 ( 5091)
  covalent geometry    : angle       0.60224 /  0.31 ( 6919)
  SS BOND              : bond        0.00128 /  0.06 (    5)
  SS BOND              : angle       0.64743 /  0.32 (   10)
  hydrogen bonds       : bond        0.03524 /  2.46 (  192)
  hydrogen bonds       : angle       7.68916 /  5.10 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 63
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   19 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7404 (tpp80)
REVERT: A  103 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5704 (t80)
REVERT: A  104 ASN cc_start: 0.5933 (m-40) cc_final: 0.5685 (m-40)
REVERT: A  280 TYR cc_start: 0.7701 (m-80) cc_final: 0.6920 (m-80)
REVERT: B   42 GLU cc_start: 0.6504 (mt-10) cc_final: 0.5775 (mm-30)
REVERT: B   76 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7466 (mt)
REVERT: B  112 LYS cc_start: 0.7022 (ttmt) cc_final: 0.6434 (ttpt)
REVERT: B  131 ARG cc_start: 0.7525 (mmt90) cc_final: 0.6969 (mmm-85)
REVERT: C   45 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6852 (m-30)
REVERT: C   48 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7391 (tp)
REVERT: C   57 LEU cc_start: 0.7751 (tp) cc_final: 0.7493 (tm)
REVERT: C   98 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7175 (tttt)
REVERT: C  131 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6491 (mmt90)
REVERT: C  138 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.4809 (mmm160)
REVERT: D   44 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7361 (ptt-90)
REVERT: D   74 VAL cc_start: 0.5965 (OUTLIER) cc_final: 0.5700 (t)
REVERT: D  135 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6220 (tp30)
  outliers start: 41
  outliers final: 13
  residues processed: 98
  average time/residue: 0.6266
  time to fit residues: 63.6903
Evaluate side-chains
  78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   98 LYS
Chi-restraints excluded: chain C residue  131 ARG
Chi-restraints excluded: chain C residue  138 ARG
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   93 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0980
   chunk 27 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
B  61 GLN
C  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.193177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.156262 restraints weight = 4800.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 2.44
r_work: 0.3952 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3806 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5096  Z= 0.206
  Angle     :  0.617   6.629   6929  Z= 0.323
  Chirality :  0.047   0.247    767
  Planarity :  0.004   0.031    892
  Dihedral  :  4.982  20.061    695
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 25.19 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.34), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.33 (0.29), residues: 294
  loop :  0.25 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 131 
 TYR   0.013   0.002   TYR A  95 
 PHE   0.011   0.002   PHE B 124 
 TRP   0.021   0.002   TRP A 284 
 HIS   0.004   0.001   HIS B  73 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.21 ( 5091)
  covalent geometry    : angle       0.61745 /  0.32 ( 6919)
  SS BOND              : bond        0.00123 /  0.06 (    5)
  SS BOND              : angle       0.65112 /  0.33 (   10)
  hydrogen bonds       : bond        0.03454 /  2.42 (  192)
  hydrogen bonds       : angle       7.74943 /  5.14 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 62
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   19 ARG cc_start: 0.7775 (tpp80) cc_final: 0.7327 (tpp80)
REVERT: A   67 ARG cc_start: 0.6875 (ttp-110) cc_final: 0.6655 (ttp-110)
REVERT: A  104 ASN cc_start: 0.5958 (m-40) cc_final: 0.5749 (m-40)
REVERT: A  280 TYR cc_start: 0.7756 (m-80) cc_final: 0.6930 (m-80)
REVERT: A  294 GLU cc_start: 0.7285 (pt0) cc_final: 0.6996 (pp20)
REVERT: A  321 ASP cc_start: 0.6960 (t0) cc_final: 0.6293 (m-30)
REVERT: B   27 GLN cc_start: 0.7376 (tt0) cc_final: 0.6779 (tm-30)
REVERT: B   42 GLU cc_start: 0.6554 (mt-10) cc_final: 0.5807 (mm-30)
REVERT: B   76 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7551 (mt)
REVERT: B  131 ARG cc_start: 0.7456 (mmt90) cc_final: 0.7046 (mmm-85)
REVERT: C   45 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6846 (m-30)
REVERT: C   48 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7395 (tp)
REVERT: C   98 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7180 (tttt)
REVERT: C  131 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6403 (mmt90)
REVERT: C  143 ASP cc_start: 0.6745 (t70) cc_final: 0.6262 (t70)
REVERT: D   44 ARG cc_start: 0.7678 (ptt-90) cc_final: 0.7281 (ptt-90)
REVERT: D  135 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6242 (tp30)
  outliers start: 38
  outliers final: 17
  residues processed: 97
  average time/residue: 0.6029
  time to fit residues: 60.5419
Evaluate side-chains
  80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   98 LYS
Chi-restraints excluded: chain C residue  131 ARG
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   93 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 38 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
B  61 GLN
C  27 GLN
C  61 GLN
D  61 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.188280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.150921 restraints weight = 4895.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 2.43
r_work: 0.3892 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3745 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   5096  Z= 0.288
  Angle     :  0.692   7.047   6929  Z= 0.364
  Chirality :  0.050   0.340    767
  Planarity :  0.004   0.033    892
  Dihedral  :  5.325  20.945    695
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 20.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  7.28 %
    Allowed  : 25.19 %
    Favored  : 67.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.34), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.44 (0.30), residues: 291
  loop :  0.08 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 131 
 TYR   0.018   0.002   TYR A  95 
 PHE   0.014   0.002   PHE C 124 
 TRP   0.026   0.003   TRP A 284 
 HIS   0.005   0.002   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00609 /  0.29 ( 5091)
  covalent geometry    : angle       0.69148 /  0.36 ( 6919)
  SS BOND              : bond        0.00185 /  0.09 (    5)
  SS BOND              : angle       0.88947 /  0.46 (   10)
  hydrogen bonds       : bond        0.03834 /  2.69 (  192)
  hydrogen bonds       : angle       8.05458 /  5.36 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 60
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A   19 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7345 (tpp80)
REVERT: A  280 TYR cc_start: 0.7863 (m-80) cc_final: 0.6957 (m-80)
REVERT: A  294 GLU cc_start: 0.7309 (pt0) cc_final: 0.6925 (pp20)
REVERT: A  321 ASP cc_start: 0.7143 (t0) cc_final: 0.6460 (m-30)
REVERT: B   42 GLU cc_start: 0.6570 (mt-10) cc_final: 0.5867 (mm-30)
REVERT: B   45 ASP cc_start: 0.7487 (m-30) cc_final: 0.7175 (m-30)
REVERT: B   61 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7906 (tm130)
REVERT: B   76 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7482 (mt)
REVERT: B  131 ARG cc_start: 0.7429 (mmt90) cc_final: 0.7023 (mmm-85)
REVERT: C   45 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.6862 (m-30)
REVERT: C   48 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7430 (tp)
REVERT: C   98 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7261 (tttt)
REVERT: C  131 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6441 (mmt90)
REVERT: D   44 ARG cc_start: 0.7730 (ptt-90) cc_final: 0.7296 (ptt-90)
REVERT: D  135 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6326 (tp30)
  outliers start: 39
  outliers final: 16
  residues processed: 96
  average time/residue: 0.6330
  time to fit residues: 63.0610
Evaluate side-chains
  81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   98 LYS
Chi-restraints excluded: chain C residue  131 ARG
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   93 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
B  61 GLN
C  27 GLN
D  61 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.189601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.152349 restraints weight = 4774.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 2.43
r_work: 0.3909 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3761 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5096  Z= 0.248
  Angle     :  0.670   7.620   6929  Z= 0.351
  Chirality :  0.050   0.381    767
  Planarity :  0.004   0.032    892
  Dihedral  :  5.307  21.095    695
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 20.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 25.56 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.33), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.50 (0.30), residues: 290
  loop :  0.09 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 131 
 TYR   0.013   0.002   TYR A  95 
 PHE   0.012   0.002   PHE C 124 
 TRP   0.027   0.002   TRP A 284 
 HIS   0.004   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00525 /  0.25 ( 5091)
  covalent geometry    : angle       0.66982 /  0.35 ( 6919)
  SS BOND              : bond        0.00160 /  0.08 (    5)
  SS BOND              : angle       0.73824 /  0.39 (   10)
  hydrogen bonds       : bond        0.03599 /  2.53 (  192)
  hydrogen bonds       : angle       8.06695 /  5.39 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 65
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   19 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7356 (tpp80)
REVERT: A  103 PHE cc_start: 0.6082 (OUTLIER) cc_final: 0.5851 (t80)
REVERT: A  280 TYR cc_start: 0.7807 (m-80) cc_final: 0.6912 (m-80)
REVERT: A  294 GLU cc_start: 0.7323 (pt0) cc_final: 0.6933 (pp20)
REVERT: A  321 ASP cc_start: 0.7127 (t0) cc_final: 0.6441 (m-30)
REVERT: B   27 GLN cc_start: 0.7330 (tt0) cc_final: 0.6757 (tm-30)
REVERT: B   42 GLU cc_start: 0.6542 (mt-10) cc_final: 0.5852 (mm-30)
REVERT: B   45 ASP cc_start: 0.7471 (m-30) cc_final: 0.7150 (m-30)
REVERT: B   76 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7502 (mt)
REVERT: B  131 ARG cc_start: 0.7408 (mmt90) cc_final: 0.6983 (mmm-85)
REVERT: C   45 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6846 (m-30)
REVERT: C   48 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7430 (tp)
REVERT: C   98 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7219 (tttt)
REVERT: C  131 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6335 (mmt90)
REVERT: C  143 ASP cc_start: 0.7000 (t70) cc_final: 0.6302 (t70)
REVERT: D   44 ARG cc_start: 0.7656 (ptt-90) cc_final: 0.7306 (ptt-90)
REVERT: D  135 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6216 (tp30)
  outliers start: 35
  outliers final: 16
  residues processed: 96
  average time/residue: 0.5691
  time to fit residues: 56.7296
Evaluate side-chains
  81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue   98 LYS
Chi-restraints excluded: chain C residue  131 ARG
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   93 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 56 optimal weight:    0.3980
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0570
   chunk 43 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
A 332 ASN
** B  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  46 ASN
B  61 GLN
C  27 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.192351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.155791 restraints weight = 4830.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 2.42
r_work: 0.3946 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3799 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5096  Z= 0.203
  Angle     :  0.638   7.489   6929  Z= 0.334
  Chirality :  0.048   0.298    767
  Planarity :  0.004   0.033    892
  Dihedral  :  5.179  20.763    695
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 19.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 26.49 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.34), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.45 (0.29), residues: 293
  loop :  0.18 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 131 
 TYR   0.019   0.002   TYR A  95 
 PHE   0.014   0.002   PHE A 103 
 TRP   0.026   0.002   TRP A 284 
 HIS   0.004   0.001   HIS B  73 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.20 ( 5091)
  covalent geometry    : angle       0.63790 /  0.33 ( 6919)
  SS BOND              : bond        0.00120 /  0.06 (    5)
  SS BOND              : angle       0.69285 /  0.36 (   10)
  hydrogen bonds       : bond        0.03315 /  2.30 (  192)
  hydrogen bonds       : angle       7.88253 /  5.26 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 65
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7400 (tpp80)
REVERT: A  280 TYR cc_start: 0.7768 (m-80) cc_final: 0.6894 (m-80)
REVERT: A  321 ASP cc_start: 0.7095 (t0) cc_final: 0.6413 (m-30)
REVERT: B   42 GLU cc_start: 0.6503 (mt-10) cc_final: 0.5824 (mm-30)
REVERT: B   76 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7537 (mt)
REVERT: B  131 ARG cc_start: 0.7416 (mmt90) cc_final: 0.7022 (mmm-85)
REVERT: C   48 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7429 (tp)
REVERT: C  143 ASP cc_start: 0.7092 (t70) cc_final: 0.6490 (t70)
REVERT: D   44 ARG cc_start: 0.7639 (ptt-90) cc_final: 0.7328 (ptt-90)
REVERT: D  135 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6213 (tp30)
  outliers start: 31
  outliers final: 16
  residues processed: 91
  average time/residue: 0.6304
  time to fit residues: 59.7189
Evaluate side-chains
  79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   93 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0980
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 332 ASN
** B  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  61 GLN
C  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.190884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.154154 restraints weight = 4797.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 2.41
r_work: 0.3936 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3790 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.106   5096  Z= 0.227
  Angle     :  0.673   8.993   6929  Z= 0.351
  Chirality :  0.051   0.435    767
  Planarity :  0.004   0.033    892
  Dihedral  :  5.304  20.692    695
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 19.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 27.61 %
    Favored  : 66.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.34), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.43 (0.30), residues: 293
  loop :  0.19 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 131 
 TYR   0.013   0.002   TYR A  95 
 PHE   0.026   0.002   PHE A 103 
 TRP   0.031   0.002   TRP A 284 
 HIS   0.004   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00504 /  0.23 ( 5091)
  covalent geometry    : angle       0.67306 /  0.35 ( 6919)
  SS BOND              : bond        0.00142 /  0.07 (    5)
  SS BOND              : angle       0.78940 /  0.41 (   10)
  hydrogen bonds       : bond        0.03434 /  2.40 (  192)
  hydrogen bonds       : angle       7.99647 /  5.40 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 59
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   19 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7395 (tpp80)
REVERT: A  103 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5410 (t80)
REVERT: A  280 TYR cc_start: 0.7750 (m-80) cc_final: 0.6849 (m-80)
REVERT: A  294 GLU cc_start: 0.7287 (pt0) cc_final: 0.6953 (pp20)
REVERT: A  321 ASP cc_start: 0.7085 (t0) cc_final: 0.6401 (m-30)
REVERT: B   42 GLU cc_start: 0.6510 (mt-10) cc_final: 0.5831 (mm-30)
REVERT: B   76 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7526 (mt)
REVERT: B  131 ARG cc_start: 0.7417 (mmt90) cc_final: 0.7027 (mmm-85)
REVERT: C   45 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6962 (m-30)
REVERT: C   48 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7430 (tp)
REVERT: C  143 ASP cc_start: 0.7143 (t70) cc_final: 0.6542 (t70)
REVERT: D   44 ARG cc_start: 0.7650 (ptt-90) cc_final: 0.7330 (ptt-90)
REVERT: D  135 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6211 (tp30)
  outliers start: 29
  outliers final: 19
  residues processed: 84
  average time/residue: 0.5979
  time to fit residues: 52.1465
Evaluate side-chains
  79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 55
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  103 PHE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  144 PHE
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   93 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 43 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  61 GLN
C  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.190897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.154316 restraints weight = 4795.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.4060 rms_B_bonded: 2.43
r_work: 0.3939 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3794 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.101   5096  Z= 0.236
  Angle     :  0.689   8.338   6929  Z= 0.359
  Chirality :  0.051   0.400    767
  Planarity :  0.004   0.032    892
  Dihedral  :  5.382  20.952    695
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 20.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 27.61 %
    Favored  : 67.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.34), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.43 (0.30), residues: 291
  loop :  0.18 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  32 
 TYR   0.018   0.002   TYR A  95 
 PHE   0.018   0.002   PHE A 103 
 TRP   0.036   0.003   TRP A 284 
 HIS   0.004   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00523 /  0.24 ( 5091)
  covalent geometry    : angle       0.68909 /  0.36 ( 6919)
  SS BOND              : bond        0.00158 /  0.08 (    5)
  SS BOND              : angle       0.81322 /  0.42 (   10)
  hydrogen bonds       : bond        0.03485 /  2.43 (  192)
  hydrogen bonds       : angle       8.02621 /  5.41 (  489)

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

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

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1244 Ramachandran restraints generated.
    622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 55
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  280 TYR cc_start: 0.7760 (m-80) cc_final: 0.6818 (m-80)
REVERT: A  294 GLU cc_start: 0.7287 (pt0) cc_final: 0.6942 (pp20)
REVERT: A  321 ASP cc_start: 0.7100 (t0) cc_final: 0.6397 (m-30)
REVERT: B   11 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5495 (ptmt)
REVERT: B   42 GLU cc_start: 0.6473 (mt-10) cc_final: 0.5809 (mm-30)
REVERT: B   76 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7499 (mt)
REVERT: B  131 ARG cc_start: 0.7465 (mmt90) cc_final: 0.7073 (mmm-85)
REVERT: C   45 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6950 (m-30)
REVERT: C   48 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7435 (tp)
REVERT: C  143 ASP cc_start: 0.7128 (t70) cc_final: 0.6471 (t70)
REVERT: D  135 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6223 (tp30)
  outliers start: 28
  outliers final: 19
  residues processed: 79
  average time/residue: 0.5461
  time to fit residues: 44.9413
Evaluate side-chains
  78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 54
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  347 SER
Chi-restraints excluded: chain B residue   11 LYS
Chi-restraints excluded: chain B residue   61 GLN
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  144 PHE
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   57 LEU
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   43 LEU
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   81 SER
Chi-restraints excluded: chain D residue   93 LEU
Chi-restraints excluded: chain D residue  135 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0670
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** B  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  61 GLN
C  27 GLN
** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.192834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.156275 restraints weight = 4833.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 2.45
r_work: 0.3961 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3816 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100   5096  Z= 0.207
  Angle     :  0.675   8.164   6929  Z= 0.349
  Chirality :  0.051   0.535    767
  Planarity :  0.004   0.033    892
  Dihedral  :  5.260  20.799    695
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 27.99 %
    Favored  : 67.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.34), residues: 622
  helix:  None (None), residues: 0
  sheet: -1.41 (0.30), residues: 293
  loop :  0.22 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  32 
 TYR   0.020   0.002   TYR A 308 
 PHE   0.012   0.002   PHE C 152 
 TRP   0.038   0.002   TRP A 284 
 HIS   0.003   0.001   HIS B  73 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.21 ( 5091)
  covalent geometry    : angle       0.67469 /  0.35 ( 6919)
  SS BOND              : bond        0.00132 /  0.06 (    5)
  SS BOND              : angle       0.69732 /  0.36 (   10)
  hydrogen bonds       : bond        0.03312 /  2.31 (  192)
  hydrogen bonds       : angle       7.94932 /  5.35 (  489)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2936.84 seconds
wall clock time: 50 minutes 52.91 seconds (3052.91 seconds total)