Starting phenix.real_space_refine
on Wed Sep 17 03:23:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xwf_38734/09_2025/8xwf_38734.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xwf_38734/09_2025/8xwf_38734.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xwf_38734/09_2025/8xwf_38734.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xwf_38734/09_2025/8xwf_38734.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xwf_38734/09_2025/8xwf_38734.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xwf_38734/09_2025/8xwf_38734.map"
  }
  resolution = 3.65
  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=   1.000
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      21      5.16       5
     C    2024      2.51       5
     N     527      2.21       5
     O     518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3090
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 336
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "D"
      Number of atoms: 467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 467
          Classifications: {'peptide': 67}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 62}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "R"
      Number of atoms: 2287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2287
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 9, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 7, 'TYR:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 71
  Time building chain proxies: 1.13, per 1000 atoms: 0.37
  Number of scatterers: 3090
  At special positions: 0
  Unit cell: (68.475, 78.85, 94.4125, 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      21     16.00
     O     518      8.00
     N     527      7.00
     C    2024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS D   9 " - pdb=" SG  CYS D  35 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  11 " - pdb=" SG  CYS D  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  39 " - pdb=" SG  CYS R 286 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 119 " - pdb=" SG  CYS R 196 " distance=2.04

  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: 0.17
  Conformation dependent library (CDL) restraints added in 131.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  798

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 2 sheets defined
      65.8% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'E' and resid 19 through 21
      No H-bonds generated for 'chain 'E' and resid 19 through 21'
    Processing helix  chain 'E' and resid 56 through 69
      removed outlier: 3.915A  pdb=" N   GLN E  60 " --> pdb=" O   SER E  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 67
    Processing helix  chain 'R' and resid 44 through 76
      removed outlier: 4.005A  pdb=" N   LYS R  48 " --> pdb=" O   LEU R  44 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL R  52 " --> pdb=" O   LYS R  48 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ILE R  53 " --> pdb=" O   TYR R  49 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   SER R  76 " --> pdb=" O   VAL R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 111
      Proline residue:  R 102  - end of helix
    Processing helix  chain 'R' and resid 116 through 149
    Processing helix  chain 'R' and resid 154 through 160
      removed outlier: 3.735A  pdb=" N   GLN R 157 " --> pdb=" O   THR R 154 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   TYR R 160 " --> pdb=" O   GLN R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 177
    Processing helix  chain 'R' and resid 177 through 183
      removed outlier: 3.582A  pdb=" N   LEU R 181 " --> pdb=" O   ALA R 177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 203 through 212
    Processing helix  chain 'R' and resid 212 through 218
      removed outlier: 3.560A  pdb=" N   GLN R 216 " --> pdb=" O   ARG R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 220 through 240
      removed outlier: 3.789A  pdb=" N   LYS R 240 " --> pdb=" O   ARG R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 279
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 285 through 304
    Processing helix  chain 'R' and resid 304 through 315
      removed outlier: 4.389A  pdb=" N   CYS R 308 " --> pdb=" O   ILE R 304 " (cutoff:3.500A)
      Proline residue:  R 311  - end of helix
    Processing helix  chain 'R' and resid 318 through 329
      removed outlier: 3.596A  pdb=" N   ARG R 322 " --> pdb=" O   GLY R 318 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU R 329 " --> pdb=" O   LEU R 325 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 49 through 52
      removed outlier: 4.136A  pdb=" N   VAL E  40 " --> pdb=" O   LEU E  52 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   VAL D  40 " --> pdb=" O   LEU D  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187

    217 hydrogen bonds defined for protein.
    636 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: 0.46

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 964
        1.34 -     1.46: 600
        1.46 -     1.58: 1559
        1.58 -     1.70: 0
        1.70 -     1.83: 27
  Bond restraints: 3150
  Sorted by residual:
  bond pdb=" N   GLY E  17 "
       pdb=" CA  GLY E  17 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.37e+00
  bond pdb=" N   LYS D  65 "
       pdb=" CA  LYS D  65 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.30e-02 5.92e+03 4.66e+00
  bond pdb=" C   PRO E  33 "
       pdb=" O   PRO E  33 "
    ideal  model  delta    sigma   weight residual
    1.237  1.213  0.025 1.26e-02 6.30e+03 3.81e+00
  bond pdb=" CA  LYS D  65 "
       pdb=" C   LYS D  65 "
    ideal  model  delta    sigma   weight residual
    1.523  1.498  0.025 1.37e-02 5.33e+03 3.27e+00
  bond pdb=" CA  ILE R  46 "
       pdb=" CB  ILE R  46 "
    ideal  model  delta    sigma   weight residual
    1.540  1.522  0.018 1.17e-02 7.31e+03 2.35e+00
  ... (remaining 3145 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 4234
        1.69 -     3.38: 53
        3.38 -     5.07: 22
        5.07 -     6.76: 0
        6.76 -     8.45: 1
  Bond angle restraints: 4310
  Sorted by residual:
  angle pdb=" N   LYS D  65 "
        pdb=" CA  LYS D  65 "
        pdb=" C   LYS D  65 "
      ideal   model   delta    sigma   weight residual
     112.23  103.78    8.45 1.26e+00 6.30e-01 4.50e+01
  angle pdb=" O   GLY E  32 "
        pdb=" C   GLY E  32 "
        pdb=" N   PRO E  33 "
      ideal   model   delta    sigma   weight residual
     121.77  118.46    3.31 1.00e+00 1.00e+00 1.09e+01
  angle pdb=" O   ILE D  66 "
        pdb=" C   ILE D  66 "
        pdb=" N   LEU D  67 "
      ideal   model   delta    sigma   weight residual
     121.91  125.08   -3.17 9.80e-01 1.04e+00 1.05e+01
  angle pdb=" N   ILE D  66 "
        pdb=" CA  ILE D  66 "
        pdb=" C   ILE D  66 "
      ideal   model   delta    sigma   weight residual
     110.42  107.33    3.09 9.60e-01 1.09e+00 1.04e+01
  angle pdb=" N   ILE R 317 "
        pdb=" CA  ILE R 317 "
        pdb=" C   ILE R 317 "
      ideal   model   delta    sigma   weight residual
     112.98  109.08    3.90 1.25e+00 6.40e-01 9.72e+00
  ... (remaining 4305 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 1712
       16.96 -    33.91: 143
       33.91 -    50.86: 20
       50.86 -    67.82: 5
       67.82 -    84.77: 3
  Dihedral angle restraints: 1883
    sinusoidal: 660
      harmonic: 1223
  Sorted by residual:
  dihedral pdb=" CB  CYS R  39 "
           pdb=" SG  CYS R  39 "
           pdb=" SG  CYS R 286 "
           pdb=" CB  CYS R 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.53   30.47     1      1.00e+01 1.00e-02 1.33e+01
  dihedral pdb=" C   LYS D  65 "
           pdb=" N   LYS D  65 "
           pdb=" CA  LYS D  65 "
           pdb=" CB  LYS D  65 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.37   -8.23     0      2.50e+00 1.60e-01 1.08e+01
  dihedral pdb=" CG  ARG R 322 "
           pdb=" CD  ARG R 322 "
           pdb=" NE  ARG R 322 "
           pdb=" CZ  ARG R 322 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.99  -43.99     2      1.50e+01 4.44e-03 1.03e+01
  ... (remaining 1880 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 493
       0.063 -    0.126: 57
       0.126 -    0.188: 1
       0.188 -    0.251: 0
       0.251 -    0.314: 2
  Chirality restraints: 553
  Sorted by residual:
  chirality pdb=" CA  ILE D  66 "
            pdb=" N   ILE D  66 "
            pdb=" C   ILE D  66 "
            pdb=" CB  ILE D  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.75   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" CA  LYS D  65 "
            pdb=" N   LYS D  65 "
            pdb=" C   LYS D  65 "
            pdb=" CB  LYS D  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CA  GLU D  64 "
            pdb=" N   GLU D  64 "
            pdb=" C   GLU D  64 "
            pdb=" CB  GLU D  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.37e-01
  ... (remaining 550 not shown)

  Planarity restraints: 527
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 310 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.89e+00
        pdb=" N   PRO R 311 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO R 311 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO R 311 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  30 "    0.016 5.00e-02 4.00e+02   2.44e-02 9.51e-01
        pdb=" N   PRO D  31 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO D  31 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO D  31 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 214 "    0.015 5.00e-02 4.00e+02   2.28e-02 8.35e-01
        pdb=" N   PRO R 215 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO R 215 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 215 "    0.013 5.00e-02 4.00e+02
  ... (remaining 524 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1047
        2.85 -     3.36: 3159
        3.36 -     3.88: 4845
        3.88 -     4.39: 5082
        4.39 -     4.90: 9214
  Nonbonded interactions: 23347
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D  10 "
            pdb=" ND2 ASN R 191 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O   GLY R 201 "
            pdb=" OG1 THR R 204 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" NH2 ARG D   8 "
            pdb=" OD1 ASP R 293 "
     model   vdw
     2.379 3.120
  nonbonded pdb=" O   SER D   2 "
            pdb=" OG  SER R 193 "
     model   vdw
     2.434 3.040
  nonbonded pdb=" NE2 HIS D  34 "
            pdb=" OG  SER R 189 "
     model   vdw
     2.442 3.120
  ... (remaining 23342 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  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:             0.020
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.970
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
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      :  0.004   0.040   3154  Z= 0.196
  Angle     :  0.584   8.448   4318  Z= 0.364
  Chirality :  0.043   0.314    553
  Planarity :  0.004   0.034    527
  Dihedral  : 13.120  84.772   1073
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.95 (0.43), residues: 412
  helix:  2.68 (0.33), residues: 258
  sheet:  1.33 (0.69), residues: 49
  loop :  0.45 (0.63), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 185 
 TYR   0.006   0.001   TYR R 160 
 PHE   0.009   0.001   PHE R 220 
 TRP   0.005   0.001   TRP R 104 
 HIS   0.003   0.001   HIS R 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3150)
  covalent geometry    : angle       0.58035 ( 4310)
  SS BOND              : bond        0.00325 (    4)
  SS BOND              : angle       1.66181 (    8)
  hydrogen bonds       : bond        0.09586 (  217)
  hydrogen bonds       : angle       4.91654 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  187 VAL cc_start: 0.9330 (t) cc_final: 0.9090 (m)
REVERT: R  243 MET cc_start: 0.7788 (mtm) cc_final: 0.7332 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0509
  time to fit residues: 6.7284
Evaluate side-chains
  69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D  16 GLN
R  66 ASN
R  89 ASN
R 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.118696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.090991 restraints weight = 6358.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.093433 restraints weight = 3339.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.094856 restraints weight = 2219.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.095938 restraints weight = 1756.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.096429 restraints weight = 1511.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3154  Z= 0.136
  Angle     :  0.566   6.926   4318  Z= 0.287
  Chirality :  0.041   0.158    553
  Planarity :  0.004   0.032    527
  Dihedral  :  3.751  16.604    441
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 13.79 %
    Favored  : 82.45 %
  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 aren not related in a simple way.
  whole:  3.19 (0.43), residues: 412
  helix:  2.88 (0.33), residues: 261
  sheet:  1.18 (0.73), residues: 47
  loop :  0.59 (0.64), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  29 
 TYR   0.009   0.001   TYR R 188 
 PHE   0.006   0.001   PHE R 183 
 TRP   0.007   0.001   TRP R 112 
 HIS   0.003   0.001   HIS E  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3150)
  covalent geometry    : angle       0.55989 ( 4310)
  SS BOND              : bond        0.00560 (    4)
  SS BOND              : angle       1.95845 (    8)
  hydrogen bonds       : bond        0.04643 (  217)
  hydrogen bonds       : angle       4.09877 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   22 ASN cc_start: 0.8972 (m-40) cc_final: 0.8666 (t0)
REVERT: D   44 LEU cc_start: 0.8870 (mt) cc_final: 0.8426 (tp)
REVERT: D   52 LEU cc_start: 0.9077 (mt) cc_final: 0.8823 (mt)
REVERT: R  240 LYS cc_start: 0.8501 (mtpp) cc_final: 0.8149 (mtmm)
REVERT: R  262 LEU cc_start: 0.8329 (tp) cc_final: 0.8102 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0564
  time to fit residues: 5.2797
Evaluate side-chains
  68 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   51 CYS
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  227 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
E  19 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.116515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.088161 restraints weight = 6407.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.090576 restraints weight = 3330.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.092009 restraints weight = 2207.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.093018 restraints weight = 1744.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.093522 restraints weight = 1510.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
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      :  0.004   0.045   3154  Z= 0.162
  Angle     :  0.590   7.435   4318  Z= 0.297
  Chirality :  0.040   0.147    553
  Planarity :  0.005   0.062    527
  Dihedral  :  3.784  19.439    441
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 17.24 %
    Favored  : 78.06 %
  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 aren not related in a simple way.
  whole:  2.95 (0.42), residues: 412
  helix:  2.72 (0.32), residues: 260
  sheet:  1.01 (0.72), residues: 50
  loop :  0.46 (0.64), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG D  29 
 TYR   0.009   0.001   TYR R  86 
 PHE   0.008   0.001   PHE R 117 
 TRP   0.008   0.001   TRP R 112 
 HIS   0.007   0.001   HIS D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3150)
  covalent geometry    : angle       0.58636 ( 4310)
  SS BOND              : bond        0.00351 (    4)
  SS BOND              : angle       1.62238 (    8)
  hydrogen bonds       : bond        0.04724 (  217)
  hydrogen bonds       : angle       4.08787 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: R   94 ASP cc_start: 0.8822 (m-30) cc_final: 0.8530 (t0)
REVERT: R  240 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8345 (mtmm)
  outliers start: 15
  outliers final: 12
  residues processed: 73
  average time/residue: 0.0530
  time to fit residues: 4.8479
Evaluate side-chains
  71 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   19 HIS
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue  132 SER
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  227 MET
Chi-restraints excluded: chain R residue  237 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** D  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 ASN
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 306 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.115270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.087249 restraints weight = 6428.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.089674 restraints weight = 3368.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.091095 restraints weight = 2232.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.092177 restraints weight = 1759.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.092668 restraints weight = 1511.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3154  Z= 0.197
  Angle     :  0.614   7.661   4318  Z= 0.308
  Chirality :  0.041   0.154    553
  Planarity :  0.005   0.070    527
  Dihedral  :  3.774  16.964    441
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 16.93 %
    Favored  : 77.43 %
  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 aren not related in a simple way.
  whole:  2.74 (0.41), residues: 412
  helix:  2.65 (0.32), residues: 260
  sheet:  0.85 (0.75), residues: 48
  loop :  0.14 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  29 
 TYR   0.009   0.001   TYR R  55 
 PHE   0.009   0.001   PHE R 117 
 TRP   0.006   0.001   TRP R 112 
 HIS   0.010   0.002   HIS E  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 3150)
  covalent geometry    : angle       0.61041 ( 4310)
  SS BOND              : bond        0.00222 (    4)
  SS BOND              : angle       1.57512 (    8)
  hydrogen bonds       : bond        0.04934 (  217)
  hydrogen bonds       : angle       4.18015 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: D    6 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8243 (mt-10)
REVERT: D   24 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7575 (tm-30)
REVERT: R  199 ASP cc_start: 0.8610 (t0) cc_final: 0.8301 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 68
  average time/residue: 0.0535
  time to fit residues: 4.6437
Evaluate side-chains
  70 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   51 CYS
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  227 MET
Chi-restraints excluded: chain R residue  237 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** D  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.114630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.086582 restraints weight = 6448.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.088792 restraints weight = 3481.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.090383 restraints weight = 2381.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.091081 restraints weight = 1867.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.091704 restraints weight = 1660.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3154  Z= 0.205
  Angle     :  0.616   7.394   4318  Z= 0.312
  Chirality :  0.041   0.156    553
  Planarity :  0.004   0.068    527
  Dihedral  :  3.770  17.021    441
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 19.44 %
    Favored  : 74.61 %
  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 aren not related in a simple way.
  whole:  2.54 (0.41), residues: 412
  helix:  2.52 (0.31), residues: 260
  sheet:  0.84 (0.83), residues: 43
  loop : -0.00 (0.54), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  29 
 TYR   0.009   0.001   TYR R  55 
 PHE   0.009   0.001   PHE R 117 
 TRP   0.005   0.001   TRP R 112 
 HIS   0.008   0.002   HIS D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 3150)
  covalent geometry    : angle       0.61272 ( 4310)
  SS BOND              : bond        0.00291 (    4)
  SS BOND              : angle       1.49300 (    8)
  hydrogen bonds       : bond        0.05098 (  217)
  hydrogen bonds       : angle       4.25560 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: D    6 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8253 (mt-10)
REVERT: D   24 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7595 (tm-30)
REVERT: D   44 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8356 (tp)
  outliers start: 19
  outliers final: 17
  residues processed: 70
  average time/residue: 0.0528
  time to fit residues: 4.6828
Evaluate side-chains
  77 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   51 CYS
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue    9 CYS
Chi-restraints excluded: chain D residue   44 LEU
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  132 SER
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  227 MET
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  279 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 8 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.124211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.098530 restraints weight = 6390.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.100687 restraints weight = 3274.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.102249 restraints weight = 2225.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.102984 restraints weight = 1765.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.102990 restraints weight = 1570.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3154  Z= 0.123
  Angle     :  0.550   7.459   4318  Z= 0.281
  Chirality :  0.039   0.158    553
  Planarity :  0.003   0.038    527
  Dihedral  :  3.583  17.065    441
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.51 %
    Favored  : 73.98 %
  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 aren not related in a simple way.
  whole:  2.59 (0.41), residues: 412
  helix:  2.62 (0.32), residues: 255
  sheet:  0.55 (0.84), residues: 45
  loop :  0.10 (0.52), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  29 
 TYR   0.007   0.001   TYR R  55 
 PHE   0.005   0.001   PHE R 130 
 TRP   0.008   0.001   TRP R 112 
 HIS   0.006   0.001   HIS D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3150)
  covalent geometry    : angle       0.54845 ( 4310)
  SS BOND              : bond        0.00211 (    4)
  SS BOND              : angle       1.13660 (    8)
  hydrogen bonds       : bond        0.04346 (  217)
  hydrogen bonds       : angle       3.98462 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   24 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7661 (tm-30)
REVERT: D   44 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8295 (tp)
REVERT: R   94 ASP cc_start: 0.8637 (m-30) cc_final: 0.8422 (t0)
REVERT: R  199 ASP cc_start: 0.8481 (t0) cc_final: 0.7897 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0562
  time to fit residues: 4.9572
Evaluate side-chains
  70 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   44 LEU
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain R residue   61 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.117807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.089983 restraints weight = 6431.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.092421 restraints weight = 3400.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.093856 restraints weight = 2268.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.094819 restraints weight = 1798.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.095382 restraints weight = 1568.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3154  Z= 0.127
  Angle     :  0.556   6.996   4318  Z= 0.285
  Chirality :  0.039   0.173    553
  Planarity :  0.003   0.021    527
  Dihedral  :  3.541  16.284    441
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 25.08 %
    Favored  : 73.04 %
  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 aren not related in a simple way.
  whole:  2.63 (0.41), residues: 412
  helix:  2.62 (0.32), residues: 255
  sheet:  0.65 (0.86), residues: 45
  loop :  0.15 (0.54), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 185 
 TYR   0.008   0.001   TYR R  86 
 PHE   0.005   0.001   PHE R 130 
 TRP   0.007   0.001   TRP R 112 
 HIS   0.007   0.001   HIS D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3150)
  covalent geometry    : angle       0.55457 ( 4310)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       1.17180 (    8)
  hydrogen bonds       : bond        0.04227 (  217)
  hydrogen bonds       : angle       3.98065 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: D    6 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8162 (mt-10)
REVERT: D   24 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7682 (tm-30)
REVERT: R   94 ASP cc_start: 0.8805 (m-30) cc_final: 0.8500 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 68
  average time/residue: 0.0430
  time to fit residues: 3.9562
Evaluate side-chains
  68 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue  279 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** D  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.117132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.092385 restraints weight = 6557.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.092289 restraints weight = 3511.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.093244 restraints weight = 2883.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.093449 restraints weight = 2173.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.094380 restraints weight = 2067.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3154  Z= 0.135
  Angle     :  0.613  13.244   4318  Z= 0.300
  Chirality :  0.040   0.162    553
  Planarity :  0.003   0.039    527
  Dihedral  :  3.517  16.239    441
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.88 %
    Favored  : 73.98 %
  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 aren not related in a simple way.
  whole:  2.63 (0.41), residues: 412
  helix:  2.57 (0.32), residues: 260
  sheet:  0.83 (0.86), residues: 43
  loop :  0.10 (0.55), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  29 
 TYR   0.007   0.001   TYR R  86 
 PHE   0.006   0.001   PHE R 117 
 TRP   0.007   0.001   TRP R 112 
 HIS   0.004   0.001   HIS R 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3150)
  covalent geometry    : angle       0.61082 ( 4310)
  SS BOND              : bond        0.00193 (    4)
  SS BOND              : angle       1.22212 (    8)
  hydrogen bonds       : bond        0.04345 (  217)
  hydrogen bonds       : angle       3.94661 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: D    6 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8125 (mt-10)
REVERT: D   24 GLN cc_start: 0.8493 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: R   94 ASP cc_start: 0.8819 (m-30) cc_final: 0.8516 (t0)
REVERT: R  274 ASP cc_start: 0.8893 (t0) cc_final: 0.8685 (t0)
  outliers start: 10
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0454
  time to fit residues: 3.9069
Evaluate side-chains
  69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  279 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 4 optimal weight:    0.2980
   chunk 28 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    0.1980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.118422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.090345 restraints weight = 6516.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.092839 restraints weight = 3444.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094246 restraints weight = 2295.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.095307 restraints weight = 1823.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.095531 restraints weight = 1576.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3154  Z= 0.115
  Angle     :  0.602  11.943   4318  Z= 0.292
  Chirality :  0.039   0.160    553
  Planarity :  0.003   0.032    527
  Dihedral  :  3.457  16.545    441
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.51 %
    Favored  : 73.98 %
  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 aren not related in a simple way.
  whole:  2.58 (0.41), residues: 412
  helix:  2.66 (0.32), residues: 255
  sheet:  0.42 (0.87), residues: 45
  loop :  0.04 (0.52), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  29 
 TYR   0.007   0.001   TYR R  86 
 PHE   0.004   0.001   PHE R 130 
 TRP   0.008   0.001   TRP R 112 
 HIS   0.003   0.000   HIS R 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3150)
  covalent geometry    : angle       0.60013 ( 4310)
  SS BOND              : bond        0.00180 (    4)
  SS BOND              : angle       1.16210 (    8)
  hydrogen bonds       : bond        0.04010 (  217)
  hydrogen bonds       : angle       3.81744 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: D    6 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8114 (mt-10)
REVERT: D   24 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: R   94 ASP cc_start: 0.8815 (m-30) cc_final: 0.8498 (t0)
REVERT: R  274 ASP cc_start: 0.8870 (t0) cc_final: 0.8655 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 68
  average time/residue: 0.0522
  time to fit residues: 4.4830
Evaluate side-chains
  69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue  141 SER
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  279 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** D  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  13 GLN
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.114139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.086291 restraints weight = 6437.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.088680 restraints weight = 3382.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.090218 restraints weight = 2254.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.090767 restraints weight = 1767.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.091374 restraints weight = 1584.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3154  Z= 0.220
  Angle     :  0.690  11.999   4318  Z= 0.343
  Chirality :  0.043   0.168    553
  Planarity :  0.004   0.025    527
  Dihedral  :  3.685  16.132    441
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.45 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.41), residues: 412
  helix:  2.40 (0.32), residues: 260
  sheet:  0.77 (0.86), residues: 45
  loop : -0.10 (0.56), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  29 
 TYR   0.010   0.002   TYR R 145 
 PHE   0.011   0.001   PHE R 117 
 TRP   0.007   0.002   TRP R 112 
 HIS   0.006   0.001   HIS D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 3150)
  covalent geometry    : angle       0.68742 ( 4310)
  SS BOND              : bond        0.00341 (    4)
  SS BOND              : angle       1.51176 (    8)
  hydrogen bonds       : bond        0.05091 (  217)
  hydrogen bonds       : angle       4.20277 (  636)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: D   24 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7672 (tm-30)
REVERT: R   94 ASP cc_start: 0.8895 (m-30) cc_final: 0.8537 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0452
  time to fit residues: 3.8434
Evaluate side-chains
  66 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   62 ILE
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  279 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0060
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 0 optimal weight:    0.8980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** D  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.117525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.089890 restraints weight = 6454.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.092468 restraints weight = 3281.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094152 restraints weight = 2144.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.095100 restraints weight = 1649.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.095387 restraints weight = 1420.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3154  Z= 0.124
  Angle     :  0.621  11.755   4318  Z= 0.310
  Chirality :  0.040   0.161    553
  Planarity :  0.003   0.020    527
  Dihedral  :  3.561  17.634    441
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 26.02 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.41), residues: 412
  helix:  2.57 (0.32), residues: 255
  sheet:  0.47 (0.85), residues: 47
  loop : -0.01 (0.54), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  29 
 TYR   0.006   0.001   TYR R  86 
 PHE   0.006   0.001   PHE R 233 
 TRP   0.008   0.001   TRP R 112 
 HIS   0.004   0.001   HIS D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3150)
  covalent geometry    : angle       0.61937 ( 4310)
  SS BOND              : bond        0.00165 (    4)
  SS BOND              : angle       1.16190 (    8)
  hydrogen bonds       : bond        0.04298 (  217)
  hydrogen bonds       : angle       3.98462 (  636)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 697.91 seconds
wall clock time: 12 minutes 39.80 seconds (759.80 seconds total)