Starting phenix.real_space_refine
on Thu Jul 24 03:01:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xlt_33286/07_2025/7xlt_33286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xlt_33286/07_2025/7xlt_33286.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2025/7xlt_33286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2025/7xlt_33286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2025/7xlt_33286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xlt_33286/07_2025/7xlt_33286.cif"
  }
  resolution = 4.4
  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=   0.046
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: 5
    Type Number    sf(0)   Gaussians
     P      78      5.49       5
     S      14      5.16       5
     C    2869      2.51       5
     N     845      2.21       5
     O    1179      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4985
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1635
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 11, 'TRANS': 203}
    Chain: "L"
      Number of atoms: 1676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1676
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 11, 'TRANS': 204}
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 801
          Classifications: {'DNA': 40}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 39}
    Chain: "B"
      Number of atoms: 873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 873
          Classifications: {'RNA': 40}
          Modifications used: {'5*END': 1, 'rna3p_pur': 32, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 39}
  Time building chain proxies: 6.86, per 1000 atoms: 1.38
  Number of scatterers: 4985
  At special positions: 0
  Unit cell: (125.465, 106.918, 93.826, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P      78     15.00
     O    1179      8.00
     N     845      7.00
     C    2869      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 201 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 139 " - pdb=" SG  CYS L 199 " 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: 2.57
  Conformation dependent library (CDL) restraints added in 647.9 milliseconds
  

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  796

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 9 sheets defined
      5.6% alpha, 36.0% beta
      41 base pairs and 55 stacking pairs defined.
    Time for finding SS restraints: 3.58
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.606A  pdb=" N   ASP H  90 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'H' and resid 176 through 180
    Processing helix  chain 'H' and resid 192 through 194
      No H-bonds generated for 'chain 'H' and resid 192 through 194'
    Processing helix  chain 'L' and resid 126 through 131
    Processing helix  chain 'L' and resid 188 through 192
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.340A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   VAL H  33 " --> pdb=" O   ASP H  99 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   MET H  34 " --> pdb=" O   PHE H  50 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   PHE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.340A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TYR H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 129
      removed outlier: 3.988A  pdb=" N   SER H 186 " --> pdb=" O   HIS H 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 50 through 53
      removed outlier: 5.817A  pdb=" N   LEU L  51 " --> pdb=" O   LEU L  42 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   LEU L  42 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR L 107 " --> pdb=" O   TYR L  91 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   CYS L  93 " --> pdb=" O   GLY L 105 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   GLY L 105 " --> pdb=" O   CYS L  93 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 119 through 123
    Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 155

    108 hydrogen bonds defined for protein.
    264 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      102 hydrogen bonds
      200 hydrogen bond angles
      0 basepair planarities
      41 basepair parallelities
      55 stacking parallelities
  Total time for adding SS restraints: 5.69

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1253
        1.34 -     1.46: 1731
        1.46 -     1.58: 2107
        1.58 -     1.70: 156
        1.70 -     1.82: 19
  Bond restraints: 5266
  Sorted by residual:
  bond pdb=" CA  VAL L  99 "
       pdb=" CB  VAL L  99 "
    ideal  model  delta    sigma   weight residual
    1.534  1.551 -0.017 6.80e-03 2.16e+04 6.17e+00
  bond pdb=" C   GLU H 154 "
       pdb=" N   PRO H 155 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 5.02e+00
  bond pdb=" C   VAL L  99 "
       pdb=" N   PRO L 100 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 5.00e+00
  bond pdb=" CA  VAL L  99 "
       pdb=" C   VAL L  99 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 8.80e-03 1.29e+04 4.68e+00
  bond pdb=" O5'   C B  10 "
       pdb=" C5'   C B  10 "
    ideal  model  delta    sigma   weight residual
    1.420  1.452 -0.032 1.50e-02 4.44e+03 4.65e+00
  ... (remaining 5261 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 7219
        2.07 -     4.14: 247
        4.14 -     6.21: 41
        6.21 -     8.29: 10
        8.29 -    10.36: 3
  Bond angle restraints: 7520
  Sorted by residual:
  angle pdb=" C   HIS L  98 "
        pdb=" N   VAL L  99 "
        pdb=" CA  VAL L  99 "
      ideal   model   delta    sigma   weight residual
     120.24  123.82   -3.58 6.30e-01 2.52e+00 3.22e+01
  angle pdb=" C   PRO H 153 "
        pdb=" N   GLU H 154 "
        pdb=" CA  GLU H 154 "
      ideal   model   delta    sigma   weight residual
     120.09  125.72   -5.63 1.25e+00 6.40e-01 2.03e+01
  angle pdb=" CA  VAL L  99 "
        pdb=" C   VAL L  99 "
        pdb=" N   PRO L 100 "
      ideal   model   delta    sigma   weight residual
     121.00  123.99   -2.99 8.30e-01 1.45e+00 1.30e+01
  angle pdb=" CA  GLU H  82 "
        pdb=" CB  GLU H  82 "
        pdb=" CG  GLU H  82 "
      ideal   model   delta    sigma   weight residual
     114.10  121.30   -7.20 2.00e+00 2.50e-01 1.30e+01
  angle pdb=" CB  MET L 180 "
        pdb=" CG  MET L 180 "
        pdb=" SD  MET L 180 "
      ideal   model   delta    sigma   weight residual
     112.70  123.06  -10.36 3.00e+00 1.11e-01 1.19e+01
  ... (remaining 7515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.74: 2374
       15.74 -    31.49: 398
       31.49 -    47.23: 133
       47.23 -    62.97: 53
       62.97 -    78.72: 33
  Dihedral angle restraints: 2991
    sinusoidal: 1743
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CA  ASN L  58 "
           pdb=" C   ASN L  58 "
           pdb=" N   ARG L  59 "
           pdb=" CA  ARG L  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.04  -24.96     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  VAL H 156 "
           pdb=" C   VAL H 156 "
           pdb=" N   THR H 157 "
           pdb=" CA  THR H 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.62  -24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  TYR H  80 "
           pdb=" C   TYR H  80 "
           pdb=" N   MET H  81 "
           pdb=" CA  MET H  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.33   22.67     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 2988 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 807
       0.086 -    0.172: 59
       0.172 -    0.258: 4
       0.258 -    0.344: 3
       0.344 -    0.430: 1
  Chirality restraints: 874
  Sorted by residual:
  chirality pdb=" P     C B  37 "
            pdb=" OP1   C B  37 "
            pdb=" OP2   C B  37 "
            pdb=" O5'   C B  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.84   -0.43 2.00e-01 2.50e+01 4.62e+00
  chirality pdb=" CB  ILE L 155 "
            pdb=" CA  ILE L 155 "
            pdb=" CG1 ILE L 155 "
            pdb=" CG2 ILE L 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" P     C B  10 "
            pdb=" OP1   C B  10 "
            pdb=" OP2   C B  10 "
            pdb=" O5'   C B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.71   -0.30 2.00e-01 2.50e+01 2.30e+00
  ... (remaining 871 not shown)

  Planarity restraints: 662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR L   7 "   -0.036 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO L   8 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 108 "    0.016 2.00e-02 2.50e+03   1.50e-02 4.50e+00
        pdb=" CG  TYR H 108 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 108 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 108 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 108 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 108 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H 108 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP H 107 "   -0.009 2.00e-02 2.50e+03   1.92e-02 3.70e+00
        pdb=" CG  ASP H 107 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASP H 107 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP H 107 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 659 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1322
        2.81 -     3.33: 3795
        3.33 -     3.86: 9088
        3.86 -     4.38: 9680
        4.38 -     4.90: 15108
  Nonbonded interactions: 38993
  Sorted by model distance:
  nonbonded pdb=" O   GLY H   8 "
            pdb=" OG1 THR H 113 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OG  SER H 141 "
            pdb=" O   VAL H 189 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OG  SER L  57 "
            pdb=" O   GLY L  69 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG  SER L  25 "
            pdb=" O   GLN L  27 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" NH1 ARG L  66 "
            pdb=" OE2 GLU L  84 "
     model   vdw
     2.369 3.120
  ... (remaining 38988 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:             30.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     29.040
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:8.790
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   68.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5953
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   0.052   5270  Z= 0.214
  Angle     :  0.888  10.357   7528  Z= 0.482
  Chirality :  0.050   0.430    874
  Planarity :  0.006   0.055    662
  Dihedral  : 18.802  78.716   2183
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 34.30 %
    Favored  : 64.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.39), residues: 427
  helix: -3.85 (0.81), residues: 12
  sheet:  0.01 (0.39), residues: 188
  loop : -2.75 (0.37), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP L 168 
 HIS   0.012   0.002   HIS H  35 
 PHE   0.024   0.002   PHE L  94 
 TYR   0.037   0.002   TYR H 108 
 ARG   0.009   0.001   ARG L  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10362 (  206)
  hydrogen bonds       : angle       7.41819 (  464)
  SS BOND              : bond        0.00513 (    4)
  SS BOND              : angle       1.39737 (    8)
  covalent geometry    : bond        0.00431 ( 5266)
  covalent geometry    : angle       0.88698 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  107 THR cc_start: 0.6878 (m) cc_final: 0.6517 (m)
REVERT: L  144 PHE cc_start: 0.6641 (m-10) cc_final: 0.6319 (m-10)
REVERT: L  171 GLN cc_start: 0.6884 (tp40) cc_final: 0.6116 (tp-100)
  outliers start: 3
  outliers final: 1
  residues processed: 71
  average time/residue: 0.3478
  time to fit residues: 31.2118
Evaluate side-chains
  62 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 202 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.138315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.111446 restraints weight = 32775.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.111104 restraints weight = 22835.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.111274 restraints weight = 18702.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069   5270  Z= 0.304
  Angle     :  0.821   9.076   7528  Z= 0.438
  Chirality :  0.042   0.179    874
  Planarity :  0.006   0.064    662
  Dihedral  : 16.760  74.066   1436
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 24.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.38), residues: 427
  helix: -3.79 (0.68), residues: 19
  sheet: -0.50 (0.38), residues: 177
  loop : -2.68 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.004   TRP H 105 
 HIS   0.006   0.002   HIS H  35 
 PHE   0.030   0.003   PHE L  76 
 TYR   0.019   0.003   TYR L  91 
 ARG   0.007   0.001   ARG L  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07925 (  206)
  hydrogen bonds       : angle       7.22409 (  464)
  SS BOND              : bond        0.03395 (    4)
  SS BOND              : angle       1.11575 (    8)
  covalent geometry    : bond        0.00654 ( 5266)
  covalent geometry    : angle       0.82076 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
REVERT: L   61 SER cc_start: 0.8674 (m) cc_final: 0.8188 (p)
REVERT: L   78 LEU cc_start: 0.8916 (tt) cc_final: 0.8662 (tt)
REVERT: L   92 TYR cc_start: 0.8091 (m-10) cc_final: 0.7705 (m-10)
REVERT: L  129 GLN cc_start: 0.6573 (pt0) cc_final: 0.6087 (pm20)
REVERT: L  144 PHE cc_start: 0.7653 (m-10) cc_final: 0.7421 (m-10)
REVERT: L  149 ILE cc_start: 0.6896 (mm) cc_final: 0.6656 (mm)
REVERT: L  180 MET cc_start: 0.7606 (mmm) cc_final: 0.7120 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.3550
  time to fit residues: 27.8449
Evaluate side-chains
  47 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 49 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 46 optimal weight:   20.0000
   chunk 35 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 129 GLN
** L 166 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 = 0.4476 r_free = 0.4476 target = 0.137052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.111880 restraints weight = 33977.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.110565 restraints weight = 26618.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.110899 restraints weight = 21128.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5270  Z= 0.210
  Angle     :  0.715   6.556   7528  Z= 0.384
  Chirality :  0.039   0.168    874
  Planarity :  0.006   0.050    662
  Dihedral  : 16.905  74.057   1436
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 24.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.01 %
    Favored  : 94.72 %
  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: -2.58 (0.38), residues: 427
  helix: -3.51 (0.76), residues: 19
  sheet: -0.28 (0.40), residues: 169
  loop : -2.78 (0.36), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  47 
 HIS   0.009   0.002   HIS H  35 
 PHE   0.018   0.002   PHE L  76 
 TYR   0.014   0.002   TYR H  54 
 ARG   0.006   0.001   ARG L  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06281 (  206)
  hydrogen bonds       : angle       7.01229 (  464)
  SS BOND              : bond        0.00481 (    4)
  SS BOND              : angle       1.46955 (    8)
  covalent geometry    : bond        0.00456 ( 5266)
  covalent geometry    : angle       0.71385 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: H   45 LEU cc_start: 0.8555 (mm) cc_final: 0.8216 (mt)
REVERT: L   42 LEU cc_start: 0.8516 (tp) cc_final: 0.8250 (tp)
REVERT: L   50 LYS cc_start: 0.7550 (mmpt) cc_final: 0.7028 (mmmt)
REVERT: L   61 SER cc_start: 0.8775 (m) cc_final: 0.8316 (p)
REVERT: L   78 LEU cc_start: 0.9104 (tt) cc_final: 0.8896 (tt)
REVERT: L   92 TYR cc_start: 0.8193 (m-10) cc_final: 0.7755 (m-10)
REVERT: L  129 GLN cc_start: 0.6711 (pt0) cc_final: 0.6094 (pm20)
REVERT: L  149 ILE cc_start: 0.6512 (mm) cc_final: 0.6257 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 54
  average time/residue: 0.1640
  time to fit residues: 11.6493
Evaluate side-chains
  48 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** 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 = 0.4488 r_free = 0.4488 target = 0.138508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.107501 restraints weight = 32699.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.109556 restraints weight = 20388.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.110600 restraints weight = 14846.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5270  Z= 0.175
  Angle     :  0.665   6.564   7528  Z= 0.360
  Chirality :  0.038   0.164    874
  Planarity :  0.005   0.045    662
  Dihedral  : 16.824  73.902   1436
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 22.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.39), residues: 427
  helix: -3.64 (0.73), residues: 19
  sheet: -0.18 (0.40), residues: 169
  loop : -2.68 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 109 
 HIS   0.002   0.001   HIS H 170 
 PHE   0.020   0.002   PHE L  76 
 TYR   0.019   0.002   TYR L 191 
 ARG   0.007   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05529 (  206)
  hydrogen bonds       : angle       6.68817 (  464)
  SS BOND              : bond        0.00421 (    4)
  SS BOND              : angle       1.61700 (    8)
  covalent geometry    : bond        0.00387 ( 5266)
  covalent geometry    : angle       0.66327 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.526 
Fit side-chains
REVERT: H   45 LEU cc_start: 0.8524 (mm) cc_final: 0.8241 (mt)
REVERT: H  107 ASP cc_start: 0.6712 (p0) cc_final: 0.6480 (p0)
REVERT: L   24 ARG cc_start: 0.7549 (tmt170) cc_final: 0.7314 (tmt170)
REVERT: L   50 LYS cc_start: 0.7231 (mmpt) cc_final: 0.6703 (mmmt)
REVERT: L   92 TYR cc_start: 0.8132 (m-80) cc_final: 0.7507 (m-10)
REVERT: L  149 ILE cc_start: 0.6229 (mm) cc_final: 0.5998 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2220
  time to fit residues: 15.6926
Evaluate side-chains
  46 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:   10.9990
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** 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 = 0.4453 r_free = 0.4453 target = 0.134696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.104301 restraints weight = 33072.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.106182 restraints weight = 21173.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.107111 restraints weight = 15595.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5270  Z= 0.210
  Angle     :  0.712   6.592   7528  Z= 0.381
  Chirality :  0.039   0.164    874
  Planarity :  0.005   0.048    662
  Dihedral  : 16.923  74.029   1436
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 25.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.39), residues: 427
  helix: -3.83 (0.70), residues: 19
  sheet: -0.30 (0.40), residues: 173
  loop : -2.67 (0.38), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP H 109 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.018   0.002   PHE L  76 
 TYR   0.028   0.002   TYR H  27 
 ARG   0.003   0.001   ARG H 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06480 (  206)
  hydrogen bonds       : angle       6.96049 (  464)
  SS BOND              : bond        0.00521 (    4)
  SS BOND              : angle       1.63896 (    8)
  covalent geometry    : bond        0.00456 ( 5266)
  covalent geometry    : angle       0.71000 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 1.139 
Fit side-chains
REVERT: H   20 MET cc_start: 0.8140 (tpp) cc_final: 0.7770 (tpt)
REVERT: H  107 ASP cc_start: 0.6948 (p0) cc_final: 0.6336 (p0)
REVERT: L   42 LEU cc_start: 0.8562 (tp) cc_final: 0.8353 (tp)
REVERT: L  149 ILE cc_start: 0.6449 (mm) cc_final: 0.6144 (mm)
REVERT: L  180 MET cc_start: 0.7575 (mmm) cc_final: 0.6888 (tpp)
REVERT: L  192 GLU cc_start: 0.7961 (mp0) cc_final: 0.7394 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1985
  time to fit residues: 14.5912
Evaluate side-chains
  44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 48 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 3 optimal weight:    0.3980
   chunk 41 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** 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 = 0.4482 r_free = 0.4482 target = 0.137574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.111523 restraints weight = 33670.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.111245 restraints weight = 22669.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.111392 restraints weight = 18064.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5270  Z= 0.157
  Angle     :  0.658   6.365   7528  Z= 0.354
  Chirality :  0.039   0.250    874
  Planarity :  0.005   0.045    662
  Dihedral  : 16.804  73.845   1436
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 20.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.40), residues: 427
  helix: -3.57 (0.79), residues: 19
  sheet: -0.15 (0.40), residues: 169
  loop : -2.58 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP H  36 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.017   0.002   PHE L  76 
 TYR   0.024   0.002   TYR L 191 
 ARG   0.005   0.001   ARG H  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05254 (  206)
  hydrogen bonds       : angle       6.46256 (  464)
  SS BOND              : bond        0.00541 (    4)
  SS BOND              : angle       1.32728 (    8)
  covalent geometry    : bond        0.00341 ( 5266)
  covalent geometry    : angle       0.65713 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 1.048 
Fit side-chains
REVERT: H  107 ASP cc_start: 0.6811 (p0) cc_final: 0.6230 (p0)
REVERT: L   42 LEU cc_start: 0.8613 (tp) cc_final: 0.8388 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.3113
  time to fit residues: 21.8473
Evaluate side-chains
  46 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 46 optimal weight:   30.0000
   chunk 23 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    4.3386

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 166 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.132974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.102802 restraints weight = 32141.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.103140 restraints weight = 20699.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.104316 restraints weight = 15626.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.4785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5270  Z= 0.239
  Angle     :  0.745   8.811   7528  Z= 0.401
  Chirality :  0.041   0.231    874
  Planarity :  0.005   0.051    662
  Dihedral  : 16.968  74.124   1436
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 27.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.40), residues: 427
  helix: -3.29 (0.91), residues: 19
  sheet: -0.51 (0.39), residues: 173
  loop : -2.72 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP H  36 
 HIS   0.008   0.002   HIS H  35 
 PHE   0.019   0.003   PHE L  76 
 TYR   0.017   0.002   TYR H  95 
 ARG   0.004   0.001   ARG L  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07050 (  206)
  hydrogen bonds       : angle       7.09895 (  464)
  SS BOND              : bond        0.00531 (    4)
  SS BOND              : angle       1.51803 (    8)
  covalent geometry    : bond        0.00525 ( 5266)
  covalent geometry    : angle       0.74347 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: H  107 ASP cc_start: 0.6791 (p0) cc_final: 0.6482 (p0)
REVERT: L    4 MET cc_start: 0.8517 (tmm) cc_final: 0.8288 (tmm)
REVERT: L   94 PHE cc_start: 0.7335 (t80) cc_final: 0.7029 (t80)
REVERT: L  180 MET cc_start: 0.7971 (tpp) cc_final: 0.7599 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1492
  time to fit residues: 10.4403
Evaluate side-chains
  43 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:   30.0000
   chunk 16 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   chunk 41 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:   30.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  61 ASN
** H 205 HIS ** 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 = 0.4443 r_free = 0.4443 target = 0.134087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.107763 restraints weight = 33833.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.106596 restraints weight = 24090.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.106932 restraints weight = 20412.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.4999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5270  Z= 0.210
  Angle     :  0.714   6.629   7528  Z= 0.384
  Chirality :  0.041   0.224    874
  Planarity :  0.006   0.062    662
  Dihedral  : 17.037  74.040   1436
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 26.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.39), residues: 427
  helix: -3.20 (0.95), residues: 19
  sheet: -0.46 (0.39), residues: 169
  loop : -2.79 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP H  36 
 HIS   0.011   0.002   HIS H  35 
 PHE   0.026   0.003   PHE L  76 
 TYR   0.016   0.002   TYR H 100 
 ARG   0.008   0.001   ARG L  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06360 (  206)
  hydrogen bonds       : angle       6.87783 (  464)
  SS BOND              : bond        0.00577 (    4)
  SS BOND              : angle       1.52885 (    8)
  covalent geometry    : bond        0.00463 ( 5266)
  covalent geometry    : angle       0.71267 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.458 
Fit side-chains
REVERT: L    4 MET cc_start: 0.8505 (tmm) cc_final: 0.8229 (tmm)
REVERT: L   42 LEU cc_start: 0.8743 (tp) cc_final: 0.8424 (tp)
REVERT: L  180 MET cc_start: 0.7896 (tpp) cc_final: 0.7218 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1838
  time to fit residues: 13.0035
Evaluate side-chains
  43 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 42 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** 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 = 0.4459 r_free = 0.4459 target = 0.135467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.108846 restraints weight = 32580.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.108466 restraints weight = 26707.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.108413 restraints weight = 19502.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5270  Z= 0.172
  Angle     :  0.687   6.669   7528  Z= 0.370
  Chirality :  0.040   0.237    874
  Planarity :  0.005   0.051    662
  Dihedral  : 16.930  73.874   1436
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 22.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.39), residues: 427
  helix: -3.60 (0.80), residues: 18
  sheet: -0.41 (0.39), residues: 169
  loop : -2.70 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP H 105 
 HIS   0.008   0.002   HIS H  35 
 PHE   0.018   0.002   PHE L  76 
 TYR   0.029   0.002   TYR L 191 
 ARG   0.009   0.001   ARG L  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05499 (  206)
  hydrogen bonds       : angle       6.73720 (  464)
  SS BOND              : bond        0.00497 (    4)
  SS BOND              : angle       1.44783 (    8)
  covalent geometry    : bond        0.00385 ( 5266)
  covalent geometry    : angle       0.68570 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.454 
Fit side-chains
REVERT: H  107 ASP cc_start: 0.6433 (p0) cc_final: 0.6140 (p0)
REVERT: L    4 MET cc_start: 0.8515 (tmm) cc_final: 0.8187 (tmm)
REVERT: L   42 LEU cc_start: 0.8665 (tp) cc_final: 0.8421 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1670
  time to fit residues: 12.1745
Evaluate side-chains
  44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 19 optimal weight:   20.0000
   chunk 16 optimal weight:   20.0000
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** 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 = 0.4470 r_free = 0.4470 target = 0.135159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.110001 restraints weight = 33896.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.109203 restraints weight = 27998.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.109705 restraints weight = 19977.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.5119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5270  Z= 0.167
  Angle     :  0.697  10.857   7528  Z= 0.370
  Chirality :  0.039   0.220    874
  Planarity :  0.005   0.048    662
  Dihedral  : 16.867  73.838   1436
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 22.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  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: -2.55 (0.40), residues: 427
  helix: -3.59 (0.78), residues: 18
  sheet: -0.46 (0.40), residues: 174
  loop : -2.62 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP H 105 
 HIS   0.008   0.001   HIS H  35 
 PHE   0.020   0.002   PHE L  76 
 TYR   0.040   0.003   TYR H  27 
 ARG   0.008   0.001   ARG L  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05389 (  206)
  hydrogen bonds       : angle       6.69475 (  464)
  SS BOND              : bond        0.00483 (    4)
  SS BOND              : angle       1.30270 (    8)
  covalent geometry    : bond        0.00371 ( 5266)
  covalent geometry    : angle       0.69642 ( 7520)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.473 
Fit side-chains
REVERT: H  107 ASP cc_start: 0.6624 (p0) cc_final: 0.6381 (p0)
REVERT: L    4 MET cc_start: 0.8479 (tmm) cc_final: 0.8106 (tmm)
REVERT: L   42 LEU cc_start: 0.8709 (tp) cc_final: 0.8363 (tp)
REVERT: L  180 MET cc_start: 0.7229 (mmm) cc_final: 0.6142 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1688
  time to fit residues: 11.6988
Evaluate side-chains
  44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 13 optimal weight:   50.0000
   chunk 38 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0370
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 1 optimal weight:   20.0000
   chunk 49 optimal weight:   30.0000
   chunk 16 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    2.3062

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** 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 = 0.4479 r_free = 0.4479 target = 0.136064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.111237 restraints weight = 33827.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.110376 restraints weight = 27539.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.110725 restraints weight = 19856.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.5191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5270  Z= 0.162
  Angle     :  0.682   8.005   7528  Z= 0.366
  Chirality :  0.039   0.206    874
  Planarity :  0.005   0.050    662
  Dihedral  : 16.784  73.813   1436
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 22.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  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: -2.51 (0.40), residues: 427
  helix: -3.72 (0.72), residues: 18
  sheet: -0.27 (0.41), residues: 169
  loop : -2.68 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP H 105 
 HIS   0.007   0.001   HIS H  35 
 PHE   0.018   0.002   PHE L  76 
 TYR   0.031   0.002   TYR H  27 
 ARG   0.008   0.001   ARG L  59 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05271 (  206)
  hydrogen bonds       : angle       6.48021 (  464)
  SS BOND              : bond        0.00509 (    4)
  SS BOND              : angle       1.43504 (    8)
  covalent geometry    : bond        0.00361 ( 5266)
  covalent geometry    : angle       0.68098 ( 7520)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3261.26 seconds
wall clock time: 62 minutes 39.51 seconds (3759.51 seconds total)