Starting phenix.real_space_refine
on Sat May 10 01:01:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqq_45819/05_2025/9cqq_45819.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqq_45819/05_2025/9cqq_45819.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqq_45819/05_2025/9cqq_45819.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqq_45819/05_2025/9cqq_45819.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqq_45819/05_2025/9cqq_45819.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqq_45819/05_2025/9cqq_45819.cif"
  }
  resolution = 2.91
  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=  -0.000 sd=   0.019
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
     Fe      4      7.16       5
     S      12      5.16       5
     C    2900      2.51       5
     N     760      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4470
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "C"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1058
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "D"
      Number of atoms: 1091
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1091
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 7, 'TRANS': 135}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.52, per 1000 atoms: 0.56
  Number of scatterers: 4470
  At special positions: 0
  Unit cell: (77.91, 72.03, 66.15, 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)
     Fe      4     26.01
     S      12     16.00
     O     794      8.00
     N     760      7.00
     C    2900      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.28
  Conformation dependent library (CDL) restraints added in 556.5 milliseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      88.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 89
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.676A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 17
      removed outlier: 3.769A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 3.527A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
      removed outlier: 3.532A  pdb=" N   ARG B  40 " --> pdb=" O   TRP B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 76
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 3.983A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 143
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 89
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.646A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 138
    Processing helix  chain 'D' and resid 4 through 17
    Processing helix  chain 'D' and resid 19 through 35
      removed outlier: 3.821A  pdb=" N   GLY D  25 " --> pdb=" O   ASP D  21 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 41
    Processing helix  chain 'D' and resid 42 through 46
      removed outlier: 3.808A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 4.108A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 143

    343 hydrogen bonds defined for protein.
    981 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: 1.20

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 1889
        1.39 -     1.56: 2687
        1.56 -     1.72: 0
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4610
  Sorted by residual:
  bond pdb=" N   VAL B  23 "
       pdb=" CA  VAL B  23 "
    ideal  model  delta    sigma   weight residual
    1.460  1.504 -0.044 1.21e-02 6.83e+03 1.34e+01
  bond pdb=" N   VAL A 132 "
       pdb=" CA  VAL A 132 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.39e+00
  bond pdb=" N   VAL B  18 "
       pdb=" CA  VAL B  18 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.034 1.20e-02 6.94e+03 8.21e+00
  bond pdb=" N   VAL D  11 "
       pdb=" CA  VAL D  11 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.84e+00
  bond pdb=" N   THR C 137 "
       pdb=" CA  THR C 137 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.21e-02 6.83e+03 7.60e+00
  ... (remaining 4605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 6015
        1.32 -     2.64: 204
        2.64 -     3.96: 81
        3.96 -     5.28: 24
        5.28 -     6.59: 6
  Bond angle restraints: 6330
  Sorted by residual:
  angle pdb=" N   GLU B  22 "
        pdb=" CA  GLU B  22 "
        pdb=" C   GLU B  22 "
      ideal   model   delta    sigma   weight residual
     111.14  115.31   -4.17 1.08e+00 8.57e-01 1.49e+01
  angle pdb=" CA  ALA D 142 "
        pdb=" C   ALA D 142 "
        pdb=" O   ALA D 142 "
      ideal   model   delta    sigma   weight residual
     120.55  116.49    4.06 1.06e+00 8.90e-01 1.47e+01
  angle pdb=" CA  VAL C 135 "
        pdb=" C   VAL C 135 "
        pdb=" O   VAL C 135 "
      ideal   model   delta    sigma   weight residual
     120.95  117.15    3.80 1.04e+00 9.25e-01 1.33e+01
  angle pdb=" CA  ALA B 142 "
        pdb=" C   ALA B 142 "
        pdb=" O   ALA B 142 "
      ideal   model   delta    sigma   weight residual
     120.55  116.71    3.84 1.06e+00 8.90e-01 1.32e+01
  angle pdb=" CA  SER A 133 "
        pdb=" C   SER A 133 "
        pdb=" O   SER A 133 "
      ideal   model   delta    sigma   weight residual
     120.55  116.80    3.75 1.06e+00 8.90e-01 1.25e+01
  ... (remaining 6325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 2314
       17.40 -    34.81: 217
       34.81 -    52.21: 58
       52.21 -    69.61: 19
       69.61 -    87.02: 6
  Dihedral angle restraints: 2614
    sinusoidal: 990
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" C   VAL B  23 "
           pdb=" N   VAL B  23 "
           pdb=" CA  VAL B  23 "
           pdb=" CB  VAL B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.00   12.00     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" N   VAL B  23 "
           pdb=" C   VAL B  23 "
           pdb=" CA  VAL B  23 "
           pdb=" CB  VAL B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  133.78  -10.38     0      2.50e+00 1.60e-01 1.72e+01
  dihedral pdb=" CA  ASP A 126 "
           pdb=" CB  ASP A 126 "
           pdb=" CG  ASP A 126 "
           pdb=" OD1 ASP A 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.99   59.99     1      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 2611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 675
       0.111 -    0.221: 14
       0.221 -    0.332: 2
       0.332 -    0.442: 0
       0.442 -    0.553: 1
  Chirality restraints: 692
  Sorted by residual:
  chirality pdb=" CB  VAL B  23 "
            pdb=" CA  VAL B  23 "
            pdb=" CG1 VAL B  23 "
            pdb=" CG2 VAL B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.08   -0.55 2.00e-01 2.50e+01 7.64e+00
  chirality pdb=" CA  VAL B  23 "
            pdb=" N   VAL B  23 "
            pdb=" C   VAL B  23 "
            pdb=" CB  VAL B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.17    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CB  VAL B  18 "
            pdb=" CA  VAL B  18 "
            pdb=" CG1 VAL B  18 "
            pdb=" CG2 VAL B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 689 not shown)

  Planarity restraints: 790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 123 "    0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO B 124 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 135 "   -0.009 2.00e-02 2.50e+03   1.79e-02 3.20e+00
        pdb=" C   VAL A 135 "    0.031 2.00e-02 2.50e+03
        pdb=" O   VAL A 135 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 136 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  94 "    0.029 5.00e-02 4.00e+02   4.36e-02 3.05e+00
        pdb=" N   PRO C  95 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.024 5.00e-02 4.00e+02
  ... (remaining 787 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 138
        2.72 -     3.26: 4418
        3.26 -     3.81: 7752
        3.81 -     4.35: 9454
        4.35 -     4.90: 15948
  Nonbonded interactions: 37710
  Sorted by model distance:
  nonbonded pdb=" O   PRO A  77 "
            pdb=" OH  TYR A 140 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OE1 GLU C  27 "
            pdb=" NE2 HIS C 112 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OE1 GLU A  27 "
            pdb=" NE2 HIS A 112 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   PRO C 114 "
            pdb=" NE2 HIS D 116 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" NZ  LYS B  17 "
            pdb=" OE1 GLU B 121 "
     model   vdw
     2.335 3.120
  ... (remaining 37705 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             9.340
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     12.340
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
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      :  0.005   0.089   4614  Z= 0.275
  Angle     :  0.686   6.595   6330  Z= 0.423
  Chirality :  0.050   0.553    692
  Planarity :  0.005   0.045    790
  Dihedral  : 15.962  87.016   1562
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.10 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.19 %
  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:  3.28 (0.36), residues: 558
  helix:  2.66 (0.25), residues: 434
  sheet:  None (None), residues: 0
  loop :  0.40 (0.59), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.007   0.001   PHE A  43 
 TYR   0.007   0.001   TYR B  35 
 ARG   0.002   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11681 (  343)
  hydrogen bonds       : angle       4.62247 (  981)
  covalent geometry    : bond        0.00441 ( 4610)
  covalent geometry    : angle       0.68592 ( 6330)
  Misc. bond           : bond        0.05809 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.425 
Fit side-chains
REVERT: C   40 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7854 (mtpt)
REVERT: D  104 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7056 (mmt-90)
  outliers start: 8
  outliers final: 2
  residues processed: 55
  average time/residue: 1.5331
  time to fit residues: 87.0049
Evaluate side-chains
  51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   23 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.2980
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0970
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN
D 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.152051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.128434 restraints weight = 4309.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.17
r_work: 0.3192 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.0741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   4614  Z= 0.124
  Angle     :  0.548   5.590   6330  Z= 0.256
  Chirality :  0.039   0.122    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.816  86.541    619
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 11.45 %
    Favored  : 85.24 %
  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:  3.21 (0.36), residues: 558
  helix:  2.56 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.54 (0.59), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.007   0.001   PHE C 128 
 TYR   0.006   0.001   TYR C  42 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03546 (  343)
  hydrogen bonds       : angle       3.96495 (  981)
  covalent geometry    : bond        0.00331 ( 4610)
  covalent geometry    : angle       0.54780 ( 6330)
  Misc. bond           : bond        0.04442 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.8016 (tptp) cc_final: 0.7735 (tptp)
REVERT: C  116 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7286 (mp0)
REVERT: D  121 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7059 (mt-10)
  outliers start: 15
  outliers final: 9
  residues processed: 60
  average time/residue: 1.5033
  time to fit residues: 93.2607
Evaluate side-chains
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   44 SER
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
D 143 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.149530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.125719 restraints weight = 4339.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.20
r_work: 0.3114 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   4614  Z= 0.143
  Angle     :  0.566   5.543   6330  Z= 0.264
  Chirality :  0.040   0.118    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.696  84.959    617
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 12.78 %
    Favored  : 84.14 %
  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:  2.94 (0.36), residues: 558
  helix:  2.36 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.44 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  14 
 HIS   0.005   0.001   HIS A  58 
 PHE   0.009   0.001   PHE C 128 
 TYR   0.007   0.001   TYR D  35 
 ARG   0.002   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03843 (  343)
  hydrogen bonds       : angle       3.97303 (  981)
  covalent geometry    : bond        0.00385 ( 4610)
  covalent geometry    : angle       0.56649 ( 6330)
  Misc. bond           : bond        0.06598 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.8151 (tptp) cc_final: 0.7892 (tptp)
REVERT: C  116 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7406 (mp0)
REVERT: D  121 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7210 (mt-10)
  outliers start: 14
  outliers final: 7
  residues processed: 59
  average time/residue: 1.5146
  time to fit residues: 92.4056
Evaluate side-chains
  54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0970
   chunk 31 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
B 127 GLN
D 143 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.150681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.126896 restraints weight = 4342.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.19
r_work: 0.3129 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089   4614  Z= 0.126
  Angle     :  0.546   5.531   6330  Z= 0.254
  Chirality :  0.038   0.117    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.623  84.012    616
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.54 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.01 (0.36), residues: 558
  helix:  2.42 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.42 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.008   0.001   PHE C 128 
 TYR   0.007   0.001   TYR C 140 
 ARG   0.002   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  343)
  hydrogen bonds       : angle       3.86800 (  981)
  covalent geometry    : bond        0.00340 ( 4610)
  covalent geometry    : angle       0.54604 ( 6330)
  Misc. bond           : bond        0.05443 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.8069 (tptp) cc_final: 0.7866 (tptp)
REVERT: A   92 ARG cc_start: 0.8737 (mtm110) cc_final: 0.8200 (mtm180)
REVERT: C  116 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7360 (mp0)
REVERT: D  121 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7205 (mt-10)
  outliers start: 11
  outliers final: 5
  residues processed: 55
  average time/residue: 1.4946
  time to fit residues: 84.8604
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.147785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.123782 restraints weight = 4423.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.22
r_work: 0.3089 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.121   4614  Z= 0.155
  Angle     :  0.577   5.501   6330  Z= 0.270
  Chirality :  0.040   0.121    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.840  86.420    616
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.66 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.83 (0.35), residues: 558
  helix:  2.28 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.42 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  14 
 HIS   0.005   0.001   HIS A  89 
 PHE   0.011   0.001   PHE C 128 
 TYR   0.009   0.001   TYR C 140 
 ARG   0.004   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  343)
  hydrogen bonds       : angle       3.99253 (  981)
  covalent geometry    : bond        0.00417 ( 4610)
  covalent geometry    : angle       0.57652 ( 6330)
  Misc. bond           : bond        0.07442 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8761 (mtm110) cc_final: 0.8357 (mtm180)
REVERT: C  116 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7371 (mp0)
REVERT: D  121 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7161 (mt-10)
  outliers start: 15
  outliers final: 6
  residues processed: 60
  average time/residue: 1.4160
  time to fit residues: 87.7902
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.0270
   chunk 7 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.149676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.125772 restraints weight = 4326.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.21
r_work: 0.3124 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.099   4614  Z= 0.131
  Angle     :  0.549   5.524   6330  Z= 0.256
  Chirality :  0.039   0.118    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.763  85.531    616
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.20 %
    Favored  : 82.38 %
  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:  2.96 (0.36), residues: 558
  helix:  2.37 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.45 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  89 
 PHE   0.009   0.001   PHE C 128 
 TYR   0.009   0.001   TYR C 140 
 ARG   0.004   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03539 (  343)
  hydrogen bonds       : angle       3.89042 (  981)
  covalent geometry    : bond        0.00352 ( 4610)
  covalent geometry    : angle       0.54937 ( 6330)
  Misc. bond           : bond        0.05917 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8758 (mtm110) cc_final: 0.8356 (mtm180)
REVERT: C  116 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7453 (mp0)
REVERT: D  121 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7256 (mt-10)
  outliers start: 11
  outliers final: 6
  residues processed: 59
  average time/residue: 1.5509
  time to fit residues: 94.5391
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.149439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.125628 restraints weight = 4361.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.21
r_work: 0.3131 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103   4614  Z= 0.135
  Angle     :  0.550   5.506   6330  Z= 0.256
  Chirality :  0.039   0.119    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.826  86.098    616
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.76 %
    Favored  : 82.60 %
  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:  2.93 (0.36), residues: 558
  helix:  2.36 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.41 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.009   0.001   PHE C 128 
 TYR   0.010   0.001   TYR C 140 
 ARG   0.003   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  343)
  hydrogen bonds       : angle       3.88344 (  981)
  covalent geometry    : bond        0.00365 ( 4610)
  covalent geometry    : angle       0.54988 ( 6330)
  Misc. bond           : bond        0.06221 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8343 (mtm180)
REVERT: C  116 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7444 (mp0)
REVERT: D  121 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7221 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 59
  average time/residue: 1.4404
  time to fit residues: 87.8150
Evaluate side-chains
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.148275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.124295 restraints weight = 4321.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.22
r_work: 0.3106 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   4614  Z= 0.147
  Angle     :  0.570   5.936   6330  Z= 0.267
  Chirality :  0.040   0.121    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.931  87.094    616
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.98 %
    Favored  : 82.60 %
  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:  2.86 (0.36), residues: 558
  helix:  2.31 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.41 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  89 
 PHE   0.011   0.001   PHE C 128 
 TYR   0.011   0.001   TYR C 140 
 ARG   0.005   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03828 (  343)
  hydrogen bonds       : angle       3.93387 (  981)
  covalent geometry    : bond        0.00396 ( 4610)
  covalent geometry    : angle       0.57049 ( 6330)
  Misc. bond           : bond        0.07005 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8369 (mtm180)
REVERT: C  116 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7481 (mp0)
REVERT: D  121 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7208 (mt-10)
  outliers start: 11
  outliers final: 8
  residues processed: 56
  average time/residue: 1.5034
  time to fit residues: 87.0220
Evaluate side-chains
  55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    0.2980
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3568 r_free = 0.3568 target = 0.149140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.125196 restraints weight = 4348.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.23
r_work: 0.3115 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   4614  Z= 0.140
  Angle     :  0.560   5.508   6330  Z= 0.261
  Chirality :  0.039   0.119    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.957  87.263    616
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.98 %
    Favored  : 82.60 %
  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:  2.88 (0.36), residues: 558
  helix:  2.33 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.40 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  14 
 HIS   0.004   0.001   HIS A  89 
 PHE   0.010   0.001   PHE C 128 
 TYR   0.012   0.001   TYR C 140 
 ARG   0.005   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03682 (  343)
  hydrogen bonds       : angle       3.91223 (  981)
  covalent geometry    : bond        0.00378 ( 4610)
  covalent geometry    : angle       0.55950 ( 6330)
  Misc. bond           : bond        0.06580 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8755 (mtm110) cc_final: 0.8349 (mtm180)
REVERT: C  116 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7447 (mp0)
REVERT: D  121 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7236 (mt-10)
  outliers start: 11
  outliers final: 9
  residues processed: 57
  average time/residue: 1.4413
  time to fit residues: 84.9426
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 38 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.159139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.134385 restraints weight = 4236.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.24
r_work: 0.3190 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   4614  Z= 0.143
  Angle     :  0.564   5.493   6330  Z= 0.264
  Chirality :  0.039   0.120    692
  Planarity :  0.005   0.046    790
  Dihedral  : 10.053  89.170    616
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.20 %
    Favored  : 82.60 %
  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:  2.86 (0.35), residues: 558
  helix:  2.34 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.30 (0.59), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  14 
 HIS   0.005   0.001   HIS A  89 
 PHE   0.010   0.001   PHE C 128 
 TYR   0.013   0.001   TYR C 140 
 ARG   0.004   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  343)
  hydrogen bonds       : angle       3.93304 (  981)
  covalent geometry    : bond        0.00387 ( 4610)
  covalent geometry    : angle       0.56422 ( 6330)
  Misc. bond           : bond        0.06926 (    4)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8738 (mtm110) cc_final: 0.8328 (mtm180)
REVERT: C  116 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7503 (mp0)
REVERT: D  121 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7152 (mt-10)
  outliers start: 10
  outliers final: 9
  residues processed: 55
  average time/residue: 1.4832
  time to fit residues: 84.3174
Evaluate side-chains
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Chi-restraints excluded: chain A residue   23 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain C residue    3 SER
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.149128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.124962 restraints weight = 4347.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.24
r_work: 0.3109 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109   4614  Z= 0.136
  Angle     :  0.556   5.500   6330  Z= 0.259
  Chirality :  0.039   0.119    692
  Planarity :  0.005   0.046    790
  Dihedral  : 10.046  89.790    616
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.20 %
    Favored  : 82.60 %
  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:  2.92 (0.36), residues: 558
  helix:  2.39 (0.24), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.28 (0.59), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  89 
 PHE   0.010   0.001   PHE C 128 
 TYR   0.012   0.001   TYR C 140 
 ARG   0.004   0.001   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03619 (  343)
  hydrogen bonds       : angle       3.90681 (  981)
  covalent geometry    : bond        0.00367 ( 4610)
  covalent geometry    : angle       0.55585 ( 6330)
  Misc. bond           : bond        0.06508 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3276.80 seconds
wall clock time: 57 minutes 33.52 seconds (3453.52 seconds total)