Starting phenix.real_space_refine
on Wed Sep 17 04:46:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqq_45819/09_2025/9cqq_45819.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqq_45819/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqq_45819/09_2025/9cqq_45819.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqq_45819/09_2025/9cqq_45819.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqq_45819/09_2025/9cqq_45819.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqq_45819/09_2025/9cqq_45819.map"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.019
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.42, per 1000 atoms: 0.32
  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: 0.48
  Conformation dependent library (CDL) restraints added in 176.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.15
  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: 0.72

  Time building geometry restraints manager: 0.59 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: 0.00
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:             4.210
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.850
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.100
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.28 (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
 ARG   0.002   0.000   ARG D  40 
 TYR   0.007   0.001   TYR B  35 
 PHE   0.007   0.001   PHE A  43 
 TRP   0.011   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 4610)
  covalent geometry    : angle       0.68592 ( 6330)
  hydrogen bonds       : bond        0.11681 (  343)
  hydrogen bonds       : angle       4.62247 (  981)
  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  : 0.167 
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: 0.7635
  time to fit residues: 43.2435
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  : 0.161 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.156027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.130257 restraints weight = 4320.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.31
r_work: 0.3191 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.0847

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= 0.152
  Angle     :  0.577   5.600   6330  Z= 0.272
  Chirality :  0.040   0.130    692
  Planarity :  0.006   0.046    790
  Dihedral  :  9.933  86.055    619
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 11.67 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.99 (0.36), residues: 558
  helix:  2.40 (0.25), residues: 436
  sheet:  None (None), residues: 0
  loop :  0.50 (0.59), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.009   0.001   PHE C 128 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.005   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 4610)
  covalent geometry    : angle       0.57699 ( 6330)
  hydrogen bonds       : bond        0.04019 (  343)
  hydrogen bonds       : angle       4.09187 (  981)
  Misc. bond           : bond        0.06321 (    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
  67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.8056 (tptp) cc_final: 0.7758 (tptp)
REVERT: C  116 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7394 (mp0)
REVERT: D  104 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7976 (ptm-80)
REVERT: D  121 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7186 (mt-10)
  outliers start: 16
  outliers final: 9
  residues processed: 63
  average time/residue: 0.7075
  time to fit residues: 46.0282
Evaluate side-chains
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
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 43 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 46 optimal weight:    0.1980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.150282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.126748 restraints weight = 4362.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.16
r_work: 0.3158 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0921

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= 0.130
  Angle     :  0.552   5.572   6330  Z= 0.257
  Chirality :  0.039   0.117    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.654  84.598    617
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.78 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.01 (0.36), residues: 558
  helix:  2.41 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.51 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  92 
 TYR   0.006   0.001   TYR D  35 
 PHE   0.008   0.001   PHE C 128 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 4610)
  covalent geometry    : angle       0.55164 ( 6330)
  hydrogen bonds       : bond        0.03576 (  343)
  hydrogen bonds       : angle       3.92750 (  981)
  Misc. bond           : bond        0.05558 (    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
  60 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.8100 (tptp) cc_final: 0.7822 (tptp)
REVERT: A   92 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8154 (mtm180)
REVERT: C  116 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7382 (mp0)
REVERT: D  121 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7117 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 56
  average time/residue: 0.7636
  time to fit residues: 44.1002
Evaluate side-chains
  54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
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  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 53 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0770
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.3574 r_free = 0.3574 target = 0.150229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.126920 restraints weight = 4349.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.17
r_work: 0.3133 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   4614  Z= 0.126
  Angle     :  0.546   5.532   6330  Z= 0.254
  Chirality :  0.038   0.117    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.640  84.102    616
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 13.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.01 (0.36), residues: 558
  helix:  2.42 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.44 (0.58), residues: 120

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4610)
  covalent geometry    : angle       0.54589 ( 6330)
  hydrogen bonds       : bond        0.03507 (  343)
  hydrogen bonds       : angle       3.86453 (  981)
  Misc. bond           : bond        0.05518 (    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
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.8094 (tptp) cc_final: 0.7868 (tptp)
REVERT: A   92 ARG cc_start: 0.8727 (mtm110) cc_final: 0.8191 (mtm180)
REVERT: C  116 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7376 (mp0)
REVERT: D  121 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7211 (mt-10)
  outliers start: 14
  outliers final: 6
  residues processed: 61
  average time/residue: 0.7265
  time to fit residues: 45.6954
Evaluate side-chains
  54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.1980
   chunk 21 optimal weight:    0.7980
   chunk 52 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.151092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.128438 restraints weight = 4341.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.12
r_work: 0.3148 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   4614  Z= 0.124
  Angle     :  0.542   5.515   6330  Z= 0.252
  Chirality :  0.038   0.117    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.631  83.631    616
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.54 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.36), residues: 558
  helix:  2.44 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.45 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 104 
 TYR   0.008   0.001   TYR C 140 
 PHE   0.008   0.001   PHE C 128 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4610)
  covalent geometry    : angle       0.54236 ( 6330)
  hydrogen bonds       : bond        0.03449 (  343)
  hydrogen bonds       : angle       3.83622 (  981)
  Misc. bond           : bond        0.05529 (    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
  61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8729 (mtm110) cc_final: 0.8170 (mtm180)
REVERT: C  116 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7400 (mp0)
REVERT: D  121 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7230 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 58
  average time/residue: 0.7513
  time to fit residues: 44.9212
Evaluate side-chains
  53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.149952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.125667 restraints weight = 4411.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.23
r_work: 0.3122 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   4614  Z= 0.132
  Angle     :  0.550   5.505   6330  Z= 0.256
  Chirality :  0.039   0.118    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.703  84.293    616
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.20 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.98 (0.36), residues: 558
  helix:  2.39 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.48 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.009   0.001   TYR C 140 
 PHE   0.009   0.001   PHE C 128 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4610)
  covalent geometry    : angle       0.55046 ( 6330)
  hydrogen bonds       : bond        0.03586 (  343)
  hydrogen bonds       : angle       3.86528 (  981)
  Misc. bond           : bond        0.06084 (    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: 12
    poor density    : 49
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8745 (mtm110) cc_final: 0.8338 (mtm180)
REVERT: C  116 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7442 (mp0)
REVERT: D  121 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7272 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 59
  average time/residue: 0.7353
  time to fit residues: 44.7343
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0770
   chunk 31 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.150428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.126460 restraints weight = 4404.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.22
r_work: 0.3139 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4614  Z= 0.125
  Angle     :  0.546   5.497   6330  Z= 0.253
  Chirality :  0.038   0.117    692
  Planarity :  0.005   0.046    790
  Dihedral  :  9.676  83.576    616
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.98 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.06 (0.36), residues: 558
  helix:  2.45 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.49 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 104 
 TYR   0.010   0.001   TYR C 140 
 PHE   0.009   0.001   PHE C 128 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4610)
  covalent geometry    : angle       0.54590 ( 6330)
  hydrogen bonds       : bond        0.03434 (  343)
  hydrogen bonds       : angle       3.81367 (  981)
  Misc. bond           : bond        0.05466 (    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
  63 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8748 (mtm110) cc_final: 0.8331 (mtm180)
REVERT: C  116 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7441 (mp0)
REVERT: D  121 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7234 (mt-10)
  outliers start: 15
  outliers final: 10
  residues processed: 60
  average time/residue: 0.7181
  time to fit residues: 44.4928
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  : 0.174 
-------------------------------------------------------------------------------
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   68 LEU
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  121 GLU
Chi-restraints excluded: chain D residue  141 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0770
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.151789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.128580 restraints weight = 4355.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.16
r_work: 0.3159 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
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   0.088   4614  Z= 0.118
  Angle     :  0.535   5.524   6330  Z= 0.247
  Chirality :  0.038   0.117    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.629  82.605    616
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.74 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.14 (0.36), residues: 558
  helix:  2.50 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.54 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 104 
 TYR   0.010   0.001   TYR C 140 
 PHE   0.008   0.001   PHE C 128 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.003   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4610)
  covalent geometry    : angle       0.53456 ( 6330)
  hydrogen bonds       : bond        0.03279 (  343)
  hydrogen bonds       : angle       3.77238 (  981)
  Misc. bond           : bond        0.05077 (    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: 9
    poor density    : 49
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8750 (mtm110) cc_final: 0.8338 (mtm180)
REVERT: C  116 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7537 (mp0)
REVERT: D  121 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7307 (mt-10)
  outliers start: 9
  outliers final: 7
  residues processed: 56
  average time/residue: 0.7481
  time to fit residues: 43.2416
Evaluate side-chains
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 50 optimal weight:    0.1980
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.154158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.128636 restraints weight = 4309.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.28
r_work: 0.3172 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.129   4614  Z= 0.174
  Angle     :  0.591   5.526   6330  Z= 0.277
  Chirality :  0.041   0.124    692
  Planarity :  0.006   0.045    790
  Dihedral  :  9.967  87.432    616
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.30 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.35), residues: 558
  helix:  2.20 (0.24), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.32 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 104 
 TYR   0.013   0.002   TYR C 140 
 PHE   0.012   0.001   PHE C 128 
 TRP   0.012   0.002   TRP C  14 
 HIS   0.006   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 4610)
  covalent geometry    : angle       0.59060 ( 6330)
  hydrogen bonds       : bond        0.04195 (  343)
  hydrogen bonds       : angle       4.01127 (  981)
  Misc. bond           : bond        0.07926 (    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
  57 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8745 (mtm110) cc_final: 0.8314 (mtm180)
REVERT: C  116 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7494 (mp0)
REVERT: D  121 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7202 (mt-10)
  outliers start: 10
  outliers final: 8
  residues processed: 55
  average time/residue: 0.7739
  time to fit residues: 43.8350
Evaluate side-chains
  56 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
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   78 LEU
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0980
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 1 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    0.1980
   chunk 44 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.3580

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.153201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.130084 restraints weight = 4300.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.15
r_work: 0.3173 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   4614  Z= 0.107
  Angle     :  0.526   5.506   6330  Z= 0.242
  Chirality :  0.037   0.113    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.677  83.325    616
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.64 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.17 (0.36), residues: 558
  helix:  2.54 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.45 (0.60), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 104 
 TYR   0.012   0.001   TYR C 140 
 PHE   0.007   0.001   PHE B 118 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4610)
  covalent geometry    : angle       0.52595 ( 6330)
  hydrogen bonds       : bond        0.03025 (  343)
  hydrogen bonds       : angle       3.75726 (  981)
  Misc. bond           : bond        0.03866 (    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
  59 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   52 SER cc_start: 0.8240 (t) cc_final: 0.7926 (m)
REVERT: A   92 ARG cc_start: 0.8741 (mtm110) cc_final: 0.8329 (mtm180)
REVERT: B   66 LYS cc_start: 0.8031 (mttp) cc_final: 0.7317 (mtpt)
REVERT: C   40 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7780 (mtpt)
REVERT: C  116 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7456 (mp0)
REVERT: D  121 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7144 (mt-10)
  outliers start: 11
  outliers final: 4
  residues processed: 55
  average time/residue: 0.7664
  time to fit residues: 43.3399
Evaluate side-chains
  51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   78 LEU
Chi-restraints excluded: chain D residue  121 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 55 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.150778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.126872 restraints weight = 4296.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.21
r_work: 0.3124 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1288

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= 0.127
  Angle     :  0.543   5.518   6330  Z= 0.252
  Chirality :  0.038   0.118    692
  Planarity :  0.005   0.045    790
  Dihedral  :  9.761  84.817    616
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.52 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.06 (0.36), residues: 558
  helix:  2.47 (0.25), residues: 438
  sheet:  None (None), residues: 0
  loop :  0.38 (0.59), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 104 
 TYR   0.013   0.001   TYR C 140 
 PHE   0.009   0.001   PHE C 128 
 TRP   0.012   0.001   TRP C  14 
 HIS   0.004   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4610)
  covalent geometry    : angle       0.54255 ( 6330)
  hydrogen bonds       : bond        0.03482 (  343)
  hydrogen bonds       : angle       3.81793 (  981)
  Misc. bond           : bond        0.06026 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1749.17 seconds
wall clock time: 30 minutes 39.88 seconds (1839.88 seconds total)