Starting phenix.real_space_refine
on Sun Apr 27 00:04:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hn1_34906/04_2025/8hn1_34906.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hn1_34906/04_2025/8hn1_34906.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hn1_34906/04_2025/8hn1_34906.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hn1_34906/04_2025/8hn1_34906.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hn1_34906/04_2025/8hn1_34906.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hn1_34906/04_2025/8hn1_34906.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.111
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 505 atoms to isotropic.
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      27      5.16       5
     C    2314      2.51       5
     N     593      2.21       5
     O     626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3560
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 510
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 65, 505
          Classifications: {'peptide': 65}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
      Conformer: "B"
        Number of residues, atoms: 65, 505
          Classifications: {'peptide': 65}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
          bond proxies already assigned to first conformer: 509
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2217
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 14, 'TRANS': 265}
    Chain: "D"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 833
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 3.00, per 1000 atoms: 0.84
  Number of scatterers: 3560
  At special positions: 0
  Unit cell: (88.765, 84.435, 102.837, 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      27     16.00
     O     626      8.00
     N     593      7.00
     C    2314      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C   3 " - pdb=" SG  CYS C  24 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  17 " - pdb=" SG  CYS C  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  46 " - pdb=" SG  CYS C  57 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  58 " - pdb=" SG  CYS C  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  24 " - pdb=" SG  CYS D  97 " 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: 0.86
  Conformation dependent library (CDL) restraints added in 510.9 milliseconds
  

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  842

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 5 sheets defined
      54.4% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 53
    Processing helix  chain 'A' and resid 59 through 79
      removed outlier: 3.551A  pdb=" N   TYR A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
    Processing helix  chain 'A' and resid 94 through 130
      removed outlier: 4.123A  pdb=" N   PHE A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE A 101 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
    Processing helix  chain 'A' and resid 139 through 160
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 181 through 193
    Processing helix  chain 'A' and resid 193 through 214
      removed outlier: 3.611A  pdb=" N   ALA A 198 " --> pdb=" O   TYR A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 298
      removed outlier: 3.686A  pdb=" N   ALA A 270 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
      Proline residue:  A 293  - end of helix
    Processing helix  chain 'A' and resid 304 through 317
      removed outlier: 3.590A  pdb=" N   PHE A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 330
      Proline residue:  A 323  - end of helix
      Proline residue:  A 327  - end of helix
    Processing helix  chain 'A' and resid 331 through 343
      removed outlier: 3.870A  pdb=" N   ILE A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 3
      removed outlier: 3.612A  pdb=" N   GLU C  15 " --> pdb=" O   CYS C   3 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 8
    Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 32
      removed outlier: 3.768A  pdb=" N   GLY C  41 " --> pdb=" O   PHE C  25 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ILE C  35 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 6
      removed outlier: 3.759A  pdb=" N   THR D  79 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 61
      removed outlier: 3.591A  pdb=" N   ALA D  51 " --> pdb=" O   TRP D  38 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   LEU D  33 " --> pdb=" O   ARG D 102 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ARG D 102 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASP D  35 " --> pdb=" O   GLU D 100 " (cutoff:3.500A)

    212 hydrogen bonds defined for protein.
    618 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: 0.88

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1111
        1.34 -     1.46: 897
        1.46 -     1.58: 1606
        1.58 -     1.70: 0
        1.70 -     1.81: 32
  Bond restraints: 3646
  Sorted by residual:
  bond pdb=" CE2 PHE A  86 "
       pdb=" CZ  PHE A  86 "
    ideal  model  delta    sigma   weight residual
    1.382  1.353  0.029 3.00e-02 1.11e+03 9.13e-01
  bond pdb=" CE1 PHE A  86 "
       pdb=" CZ  PHE A  86 "
    ideal  model  delta    sigma   weight residual
    1.382  1.355  0.027 3.00e-02 1.11e+03 8.33e-01
  bond pdb=" CA  ILE C  48 "
       pdb=" CB  ILE C  48 "
    ideal  model  delta    sigma   weight residual
    1.526  1.539 -0.013 1.55e-02 4.16e+03 7.22e-01
  bond pdb=" C   GLN A 167 "
       pdb=" N   PRO A 168 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.020 2.34e-02 1.83e+03 7.00e-01
  bond pdb=" CG  PRO A 196 "
       pdb=" CD  PRO A 196 "
    ideal  model  delta    sigma   weight residual
    1.503  1.477  0.026 3.40e-02 8.65e+02 5.92e-01
  ... (remaining 3641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 4686
        1.06 -     2.12: 216
        2.12 -     3.18: 36
        3.18 -     4.24: 15
        4.24 -     5.30: 7
  Bond angle restraints: 4960
  Sorted by residual:
  angle pdb=" N   GLY D  37 "
        pdb=" CA  GLY D  37 "
        pdb=" C   GLY D  37 "
      ideal   model   delta    sigma   weight residual
     110.18  114.00   -3.82 1.56e+00 4.11e-01 6.00e+00
  angle pdb=" N   ALA A 169 "
        pdb=" CA  ALA A 169 "
        pdb=" C   ALA A 169 "
      ideal   model   delta    sigma   weight residual
     109.81  115.11   -5.30 2.21e+00 2.05e-01 5.74e+00
  angle pdb=" N   PRO C  33 "
        pdb=" CA  PRO C  33 "
        pdb=" C   PRO C  33 "
      ideal   model   delta    sigma   weight residual
     112.47  117.22   -4.75 2.06e+00 2.36e-01 5.32e+00
  angle pdb=" CA  ALA A 169 "
        pdb=" C   ALA A 169 "
        pdb=" N   PRO A 170 "
      ideal   model   delta    sigma   weight residual
     118.44  121.83   -3.39 1.59e+00 3.96e-01 4.54e+00
  angle pdb=" N   VAL A 207 "
        pdb=" CA  VAL A 207 "
        pdb=" C   VAL A 207 "
      ideal   model   delta    sigma   weight residual
     110.62  108.52    2.10 1.02e+00 9.61e-01 4.22e+00
  ... (remaining 4955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 1984
       17.41 -    34.82: 147
       34.82 -    52.23: 13
       52.23 -    69.64: 4
       69.64 -    87.05: 3
  Dihedral angle restraints: 2151
    sinusoidal: 833
      harmonic: 1318
  Sorted by residual:
  dihedral pdb=" CA  GLN A 167 "
           pdb=" C   GLN A 167 "
           pdb=" N   PRO A 168 "
           pdb=" CA  PRO A 168 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.46  -23.54     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ALA A 169 "
           pdb=" C   ALA A 169 "
           pdb=" N   PRO A 170 "
           pdb=" CA  PRO A 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.31  -17.69     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ASP A 172 "
           pdb=" CB  ASP A 172 "
           pdb=" CG  ASP A 172 "
           pdb=" OD1 ASP A 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.98   59.98     1      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 2148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 418
       0.042 -    0.083: 118
       0.083 -    0.125: 32
       0.125 -    0.166: 1
       0.166 -    0.208: 1
  Chirality restraints: 570
  Sorted by residual:
  chirality pdb=" CA  PRO C  33 "
            pdb=" N   PRO C  33 "
            pdb=" C   PRO C  33 "
            pdb=" CB  PRO C  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  PRO A 168 "
            pdb=" N   PRO A 168 "
            pdb=" C   PRO A 168 "
            pdb=" CB  PRO A 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  VAL C  32 "
            pdb=" N   VAL C  32 "
            pdb=" C   VAL C  32 "
            pdb=" CB  VAL C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 567 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  32 "   -0.029 5.00e-02 4.00e+02   4.35e-02 3.03e+00
        pdb=" N   PRO C  33 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO C  33 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  33 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 298 "   -0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO A 299 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 299 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 299 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  86 "    0.014 2.00e-02 2.50e+03   1.20e-02 2.51e+00
        pdb=" CG  PHE A  86 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  86 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  86 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  86 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  86 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  86 "    0.003 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 23
        2.57 -     3.15: 2954
        3.15 -     3.74: 5332
        3.74 -     4.32: 7471
        4.32 -     4.90: 12587
  Nonbonded interactions: 28367
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 103 "
            pdb=" OE1 GLU D 107 "
     model   vdw
     1.991 3.040
  nonbonded pdb=" O   ARG D  68 "
            pdb=" OG  SER D  85 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" NH2 ARG D  68 "
            pdb=" O   SER D  86 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OD2 ASP D  74 "
            pdb=" NZ  LYS D  77 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   THR C   5 "
            pdb=" OG  SER C   6 "
     model   vdw
     2.299 3.040
  ... (remaining 28362 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=0.42 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:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.190
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3652  Z= 0.146
  Angle     :  0.578   5.296   4972  Z= 0.325
  Chirality :  0.040   0.208    570
  Planarity :  0.004   0.044    616
  Dihedral  : 12.060  87.052   1291
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.40), residues: 449
  helix:  1.35 (0.35), residues: 217
  sheet: -2.36 (0.60), residues: 72
  loop : -2.02 (0.46), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 165 
 HIS   0.002   0.000   HIS C  29 
 PHE   0.027   0.001   PHE A  86 
 TYR   0.006   0.001   TYR A 204 
 ARG   0.003   0.000   ARG A  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20403 (  212)
  hydrogen bonds       : angle       7.64056 (  618)
  SS BOND              : bond        0.00147 (    6)
  SS BOND              : angle       0.67889 (   12)
  covalent geometry    : bond        0.00320 ( 3646)
  covalent geometry    : angle       0.57756 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: D  108 GLU cc_start: 0.8247 (pt0) cc_final: 0.7832 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.6627
  time to fit residues: 47.4813
Evaluate side-chains
  55 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 34 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.189764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.110546 restraints weight = 9027.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 3.38
r_work: 0.3008 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3652  Z= 0.174
  Angle     :  0.648   7.047   4972  Z= 0.337
  Chirality :  0.045   0.200    570
  Planarity :  0.005   0.040    616
  Dihedral  :  4.415  23.313    502
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  :  9.07 %
    Favored  : 88.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.40), residues: 449
  helix:  1.52 (0.34), residues: 229
  sheet: -1.96 (0.57), residues: 82
  loop : -2.33 (0.45), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 
 PHE   0.010   0.002   PHE A 308 
 TYR   0.012   0.001   TYR A 316 
 ARG   0.004   0.000   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05283 (  212)
  hydrogen bonds       : angle       5.20630 (  618)
  SS BOND              : bond        0.00302 (    6)
  SS BOND              : angle       1.23800 (   12)
  covalent geometry    : bond        0.00416 ( 3646)
  covalent geometry    : angle       0.64624 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  107 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6936 (tp30)
REVERT: D  108 GLU cc_start: 0.8167 (pt0) cc_final: 0.7802 (pt0)
  outliers start: 10
  outliers final: 5
  residues processed: 58
  average time/residue: 0.7442
  time to fit residues: 45.3422
Evaluate side-chains
  56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain D residue  107 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 38 optimal weight:    9.9990
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.190365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.115978 restraints weight = 3882.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.46
r_work: 0.3116 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3652  Z= 0.142
  Angle     :  0.592   7.282   4972  Z= 0.304
  Chirality :  0.044   0.196    570
  Planarity :  0.004   0.036    616
  Dihedral  :  4.177  21.517    502
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 10.62 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.41), residues: 449
  helix:  1.82 (0.35), residues: 230
  sheet: -1.67 (0.58), residues: 82
  loop : -2.21 (0.47), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 165 
 HIS   0.001   0.000   HIS A  54 
 PHE   0.007   0.001   PHE D  69 
 TYR   0.010   0.001   TYR A 316 
 ARG   0.004   0.000   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04644 (  212)
  hydrogen bonds       : angle       4.81660 (  618)
  SS BOND              : bond        0.00205 (    6)
  SS BOND              : angle       0.82605 (   12)
  covalent geometry    : bond        0.00332 ( 3646)
  covalent geometry    : angle       0.59083 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5986 (tpm170)
REVERT: A  179 ASN cc_start: 0.7913 (m-40) cc_final: 0.7602 (t0)
REVERT: A  307 VAL cc_start: 0.7925 (p) cc_final: 0.7690 (m)
REVERT: D  108 GLU cc_start: 0.8225 (pt0) cc_final: 0.7776 (pt0)
  outliers start: 9
  outliers final: 6
  residues processed: 56
  average time/residue: 0.8103
  time to fit residues: 47.4492
Evaluate side-chains
  57 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   55 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0470
   chunk 36 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6478

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.191278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.113708 restraints weight = 6720.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.03
r_work: 0.3093 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3652  Z= 0.130
  Angle     :  0.568   7.270   4972  Z= 0.292
  Chirality :  0.043   0.191    570
  Planarity :  0.004   0.035    616
  Dihedral  :  4.018  21.505    502
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 10.88 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.41), residues: 449
  helix:  2.07 (0.35), residues: 231
  sheet: -1.51 (0.58), residues: 82
  loop : -2.16 (0.48), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 
 PHE   0.008   0.001   PHE A 312 
 TYR   0.011   0.001   TYR A 316 
 ARG   0.002   0.000   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  212)
  hydrogen bonds       : angle       4.57800 (  618)
  SS BOND              : bond        0.00202 (    6)
  SS BOND              : angle       0.72924 (   12)
  covalent geometry    : bond        0.00300 ( 3646)
  covalent geometry    : angle       0.56740 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 ASN cc_start: 0.7814 (m-40) cc_final: 0.7313 (t0)
REVERT: A  213 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7365 (ttp-170)
REVERT: A  339 ASN cc_start: 0.7604 (t0) cc_final: 0.7393 (t0)
REVERT: D  107 GLU cc_start: 0.7356 (tt0) cc_final: 0.7103 (tp30)
REVERT: D  108 GLU cc_start: 0.8271 (pt0) cc_final: 0.7838 (pt0)
  outliers start: 10
  outliers final: 7
  residues processed: 58
  average time/residue: 0.8034
  time to fit residues: 48.9097
Evaluate side-chains
  58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0070
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 40 optimal weight:    9.9990
   overall best weight:    0.5600

-------------------------------------------------------------------------------
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 = 0.4120 r_free = 0.4120 target = 0.191540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.115240 restraints weight = 6931.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 3.01
r_work: 0.3094 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3652  Z= 0.122
  Angle     :  0.563   7.257   4972  Z= 0.286
  Chirality :  0.042   0.190    570
  Planarity :  0.004   0.034    616
  Dihedral  :  3.900  21.437    502
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 12.18 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.42), residues: 449
  helix:  2.19 (0.35), residues: 233
  sheet: -1.32 (0.59), residues: 83
  loop : -2.01 (0.50), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 165 
 HIS   0.001   0.000   HIS A  54 
 PHE   0.008   0.001   PHE A 312 
 TYR   0.010   0.001   TYR A 316 
 ARG   0.002   0.000   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04111 (  212)
  hydrogen bonds       : angle       4.43031 (  618)
  SS BOND              : bond        0.00199 (    6)
  SS BOND              : angle       0.67941 (   12)
  covalent geometry    : bond        0.00279 ( 3646)
  covalent geometry    : angle       0.56241 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7118 (tt)
REVERT: A  179 ASN cc_start: 0.7786 (m-40) cc_final: 0.7299 (t0)
REVERT: A  213 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7358 (ttp-170)
REVERT: D  107 GLU cc_start: 0.7419 (tt0) cc_final: 0.7183 (tp30)
REVERT: D  108 GLU cc_start: 0.8244 (pt0) cc_final: 0.7940 (pt0)
  outliers start: 12
  outliers final: 5
  residues processed: 59
  average time/residue: 0.7809
  time to fit residues: 48.4303
Evaluate side-chains
  58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 3 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.187532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.109050 restraints weight = 7215.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 3.13
r_work: 0.3014 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3652  Z= 0.186
  Angle     :  0.622   7.486   4972  Z= 0.319
  Chirality :  0.045   0.227    570
  Planarity :  0.004   0.038    616
  Dihedral  :  4.085  21.024    502
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 12.69 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.40), residues: 449
  helix:  1.85 (0.34), residues: 231
  sheet: -1.36 (0.59), residues: 83
  loop : -2.16 (0.47), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 165 
 HIS   0.002   0.001   HIS C  29 
 PHE   0.009   0.002   PHE A 289 
 TYR   0.012   0.001   TYR A 326 
 ARG   0.002   0.000   ARG D 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05134 (  212)
  hydrogen bonds       : angle       4.67702 (  618)
  SS BOND              : bond        0.00201 (    6)
  SS BOND              : angle       0.78410 (   12)
  covalent geometry    : bond        0.00456 ( 3646)
  covalent geometry    : angle       0.62107 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7037 (tt)
REVERT: A  179 ASN cc_start: 0.7800 (m-40) cc_final: 0.7227 (t0)
REVERT: A  213 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7368 (ttp-170)
REVERT: D   36 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7317 (mtm)
REVERT: D  107 GLU cc_start: 0.7433 (tt0) cc_final: 0.7166 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 62
  average time/residue: 1.0321
  time to fit residues: 67.7492
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain D residue   36 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:   20.0000
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 35 optimal weight:   30.0000
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.189362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.114425 restraints weight = 3881.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.46
r_work: 0.2977 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3652  Z= 0.147
  Angle     :  0.584   7.210   4972  Z= 0.300
  Chirality :  0.044   0.206    570
  Planarity :  0.004   0.038    616
  Dihedral  :  3.995  21.253    502
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 13.99 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.41), residues: 449
  helix:  2.03 (0.34), residues: 231
  sheet: -1.31 (0.59), residues: 83
  loop : -2.10 (0.48), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 
 PHE   0.008   0.001   PHE A 289 
 TYR   0.010   0.001   TYR A 316 
 ARG   0.002   0.000   ARG D 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04588 (  212)
  hydrogen bonds       : angle       4.54161 (  618)
  SS BOND              : bond        0.00194 (    6)
  SS BOND              : angle       0.75909 (   12)
  covalent geometry    : bond        0.00352 ( 3646)
  covalent geometry    : angle       0.58302 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7051 (tt)
REVERT: A  179 ASN cc_start: 0.7805 (m-40) cc_final: 0.7274 (t0)
REVERT: A  213 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7406 (ttp-170)
REVERT: D  107 GLU cc_start: 0.7461 (tt0) cc_final: 0.7229 (tp30)
  outliers start: 13
  outliers final: 10
  residues processed: 58
  average time/residue: 1.1646
  time to fit residues: 73.0525
Evaluate side-chains
  60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  321 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0010
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.6186

-------------------------------------------------------------------------------
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 = 0.4116 r_free = 0.4116 target = 0.191000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.113386 restraints weight = 8951.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 3.28
r_work: 0.3002 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3652  Z= 0.125
  Angle     :  0.563   7.134   4972  Z= 0.288
  Chirality :  0.043   0.193    570
  Planarity :  0.004   0.035    616
  Dihedral  :  3.866  21.064    502
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.03 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.41), residues: 449
  helix:  2.23 (0.34), residues: 232
  sheet: -1.14 (0.59), residues: 82
  loop : -1.95 (0.49), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 
 PHE   0.008   0.001   PHE A 312 
 TYR   0.010   0.001   TYR A 316 
 ARG   0.001   0.000   ARG C  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  212)
  hydrogen bonds       : angle       4.41764 (  618)
  SS BOND              : bond        0.00182 (    6)
  SS BOND              : angle       0.73468 (   12)
  covalent geometry    : bond        0.00290 ( 3646)
  covalent geometry    : angle       0.56256 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7005 (tt)
REVERT: A  179 ASN cc_start: 0.7746 (m-40) cc_final: 0.7233 (t0)
REVERT: A  213 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7329 (ttp-170)
REVERT: D   36 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.6968 (ptp)
REVERT: D  107 GLU cc_start: 0.7467 (tt0) cc_final: 0.7243 (tp30)
  outliers start: 8
  outliers final: 6
  residues processed: 57
  average time/residue: 0.7047
  time to fit residues: 42.4547
Evaluate side-chains
  58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain D residue   36 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.188720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.111689 restraints weight = 5778.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.84
r_work: 0.2997 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3652  Z= 0.163
  Angle     :  0.597   7.157   4972  Z= 0.306
  Chirality :  0.044   0.217    570
  Planarity :  0.004   0.037    616
  Dihedral  :  3.977  20.842    502
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 14.51 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.41), residues: 449
  helix:  2.05 (0.34), residues: 231
  sheet: -1.10 (0.63), residues: 76
  loop : -1.93 (0.48), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 
 PHE   0.008   0.001   PHE A 289 
 TYR   0.009   0.001   TYR A 316 
 ARG   0.002   0.000   ARG D 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04787 (  212)
  hydrogen bonds       : angle       4.54431 (  618)
  SS BOND              : bond        0.00189 (    6)
  SS BOND              : angle       0.82741 (   12)
  covalent geometry    : bond        0.00394 ( 3646)
  covalent geometry    : angle       0.59634 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   50 GLU cc_start: 0.7310 (tt0) cc_final: 0.6867 (pt0)
REVERT: A   28 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7010 (tt)
REVERT: A  179 ASN cc_start: 0.7776 (m-40) cc_final: 0.7252 (t0)
REVERT: A  213 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7543 (ttp-170)
REVERT: D   36 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7068 (ptp)
REVERT: D  107 GLU cc_start: 0.7543 (tt0) cc_final: 0.7307 (tp30)
  outliers start: 14
  outliers final: 10
  residues processed: 59
  average time/residue: 1.2342
  time to fit residues: 77.2951
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   54 SER
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain D residue   36 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   chunk 32 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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 = 0.4115 r_free = 0.4115 target = 0.190850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.113218 restraints weight = 8955.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 3.25
r_work: 0.3054 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3652  Z= 0.127
  Angle     :  0.565   6.997   4972  Z= 0.290
  Chirality :  0.043   0.195    570
  Planarity :  0.004   0.035    616
  Dihedral  :  3.857  20.795    502
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.28 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.41), residues: 449
  helix:  2.27 (0.34), residues: 232
  sheet: -1.01 (0.63), residues: 75
  loop : -1.83 (0.49), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 
 PHE   0.008   0.001   PHE A 312 
 TYR   0.009   0.001   TYR A 316 
 ARG   0.002   0.000   ARG D  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  212)
  hydrogen bonds       : angle       4.40924 (  618)
  SS BOND              : bond        0.00180 (    6)
  SS BOND              : angle       0.77584 (   12)
  covalent geometry    : bond        0.00293 ( 3646)
  covalent geometry    : angle       0.56460 ( 4960)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   50 GLU cc_start: 0.7336 (tt0) cc_final: 0.6955 (pt0)
REVERT: A   28 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6956 (tt)
REVERT: A  179 ASN cc_start: 0.7729 (m-40) cc_final: 0.7165 (t0)
REVERT: A  213 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7439 (ttp-170)
REVERT: D   36 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7055 (ptp)
REVERT: D  107 GLU cc_start: 0.7481 (tt0) cc_final: 0.7255 (tp30)
  outliers start: 11
  outliers final: 9
  residues processed: 59
  average time/residue: 0.7035
  time to fit residues: 43.8369
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  165 TRP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain D residue   36 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 44 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 37 optimal weight:    9.9990
   chunk 5 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4124 r_free = 0.4124 target = 0.191809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.118936 restraints weight = 12182.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 4.01
r_work: 0.3004 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3652  Z= 0.125
  Angle     :  0.563   7.076   4972  Z= 0.288
  Chirality :  0.042   0.195    570
  Planarity :  0.004   0.035    616
  Dihedral  :  3.817  20.922    502
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.03 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.41), residues: 449
  helix:  2.36 (0.34), residues: 232
  sheet: -0.88 (0.64), residues: 75
  loop : -1.79 (0.49), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 165 
 HIS   0.002   0.000   HIS A  54 
 PHE   0.008   0.001   PHE A 312 
 TYR   0.010   0.001   TYR A 316 
 ARG   0.002   0.000   ARG D  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04153 (  212)
  hydrogen bonds       : angle       4.36599 (  618)
  SS BOND              : bond        0.00173 (    6)
  SS BOND              : angle       0.74903 (   12)
  covalent geometry    : bond        0.00290 ( 3646)
  covalent geometry    : angle       0.56246 ( 4960)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4052.00 seconds
wall clock time: 71 minutes 48.11 seconds (4308.11 seconds total)