Starting phenix.real_space_refine
on Fri May  9 19:46:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9byn_45039/05_2025/9byn_45039.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9byn_45039/05_2025/9byn_45039.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9byn_45039/05_2025/9byn_45039.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9byn_45039/05_2025/9byn_45039.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9byn_45039/05_2025/9byn_45039.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9byn_45039/05_2025/9byn_45039.cif"
  }
  resolution = 3.36
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    2300      2.51       5
     N     585      2.21       5
     O     665      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 3560
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 712
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.10, per 1000 atoms: 0.59
  Number of scatterers: 3560
  At special positions: 0
  Unit cell: (92.708, 70.004, 41.624, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     665      8.00
     N     585      7.00
     C    2300      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=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 428.9 milliseconds
  

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  860

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 39.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16
      removed outlier: 6.376A  pdb=" N   VAL A  14 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL C  14 " --> pdb=" O   LYS E  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21
      removed outlier: 6.454A  pdb=" N   ALA B  19 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ALA A  19 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 27
      removed outlier: 6.683A  pdb=" N   ALA B  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ALA A  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 30 through 32
      removed outlier: 6.526A  pdb=" N   HIS B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 62
      removed outlier: 6.571A  pdb=" N   THR B  60 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   THR A  60 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 68
      removed outlier: 7.064A  pdb=" N   ILE D  68 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ILE B  68 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   GLU A  66 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   GLU C  66 " --> pdb=" O   GLY E  67 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 73
      removed outlier: 6.556A  pdb=" N   GLU A  72 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLU C  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 78 through 80
      removed outlier: 8.027A  pdb=" N   TYR B  78 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   TYR A  78 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   LYS C  80 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LYS E  80 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 99
      removed outlier: 6.561A  pdb=" N   VAL B  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   THR D  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   PHE B  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ASN D  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   ALA B  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 103 through 108
      removed outlier: 6.827A  pdb=" N   ARG A 104 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   ILE C 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   THR A 106 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ARG C 104 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   ILE E 107 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   THR C 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.017A  pdb=" N   TYR A 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   TYR C 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 118 through 122
      removed outlier: 5.922A  pdb=" N   THR B 118 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   VAL D 121 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ALA B 120 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   THR A 118 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   VAL B 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ALA A 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)

    68 hydrogen bonds defined for protein.
    204 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: 0.91

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1110
        1.34 -     1.45: 516
        1.45 -     1.57: 1994
        1.57 -     1.69: 0
        1.69 -     1.80: 20
  Bond restraints: 3640
  Sorted by residual:
  bond pdb=" CG1 ILE E 107 "
       pdb=" CD1 ILE E 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.480  0.033 3.90e-02 6.57e+02 7.18e-01
  bond pdb=" CG1 ILE D 107 "
       pdb=" CD1 ILE D 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.90e-01
  bond pdb=" CG1 ILE C 107 "
       pdb=" CD1 ILE C 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.85e-01
  bond pdb=" CG1 ILE A 107 "
       pdb=" CD1 ILE A 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.78e-01
  bond pdb=" CG1 ILE B 107 "
       pdb=" CD1 ILE B 107 "
    ideal  model  delta    sigma   weight residual
    1.513  1.481  0.032 3.90e-02 6.57e+02 6.68e-01
  ... (remaining 3635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 4576
        1.06 -     2.12: 278
        2.12 -     3.18: 61
        3.18 -     4.24: 25
        4.24 -     5.30: 5
  Bond angle restraints: 4945
  Sorted by residual:
  angle pdb=" N   SER C  23 "
        pdb=" CA  SER C  23 "
        pdb=" C   SER C  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.11   -5.30 2.21e+00 2.05e-01 5.76e+00
  angle pdb=" N   SER A  23 "
        pdb=" CA  SER A  23 "
        pdb=" C   SER A  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.09   -5.28 2.21e+00 2.05e-01 5.71e+00
  angle pdb=" N   SER E  23 "
        pdb=" CA  SER E  23 "
        pdb=" C   SER E  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.08   -5.27 2.21e+00 2.05e-01 5.69e+00
  angle pdb=" N   SER B  23 "
        pdb=" CA  SER B  23 "
        pdb=" C   SER B  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.08   -5.27 2.21e+00 2.05e-01 5.69e+00
  angle pdb=" N   SER D  23 "
        pdb=" CA  SER D  23 "
        pdb=" C   SER D  23 "
      ideal   model   delta    sigma   weight residual
     109.81  115.08   -5.27 2.21e+00 2.05e-01 5.68e+00
  ... (remaining 4940 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.16: 1780
       10.16 -    20.32: 222
       20.32 -    30.48: 98
       30.48 -    40.64: 20
       40.64 -    50.80: 25
  Dihedral angle restraints: 2145
    sinusoidal: 815
      harmonic: 1330
  Sorted by residual:
  dihedral pdb=" CA  GLY D  67 "
           pdb=" C   GLY D  67 "
           pdb=" N   ILE D  68 "
           pdb=" CA  ILE D  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.03   15.97     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  GLY E  67 "
           pdb=" C   GLY E  67 "
           pdb=" N   ILE E  68 "
           pdb=" CA  ILE E  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.03   15.97     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  GLY A  67 "
           pdb=" C   GLY A  67 "
           pdb=" N   ILE A  68 "
           pdb=" CA  ILE A  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.03   15.97     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 2142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 242
       0.025 -    0.050: 168
       0.050 -    0.075: 66
       0.075 -    0.100: 50
       0.100 -    0.125: 54
  Chirality restraints: 580
  Sorted by residual:
  chirality pdb=" CA  SER E  85 "
            pdb=" N   SER E  85 "
            pdb=" C   SER E  85 "
            pdb=" CB  SER E  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.89e-01
  chirality pdb=" CA  SER A  85 "
            pdb=" N   SER A  85 "
            pdb=" C   SER A  85 "
            pdb=" CB  SER A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  SER D  85 "
            pdb=" N   SER D  85 "
            pdb=" C   SER D  85 "
            pdb=" CB  SER D  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 577 not shown)

  Planarity restraints: 610
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 100 "   -0.006 2.00e-02 2.50e+03   1.26e-02 1.58e+00
        pdb=" C   SER C 100 "    0.022 2.00e-02 2.50e+03
        pdb=" O   SER C 100 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY C 101 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 100 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" C   SER E 100 "    0.022 2.00e-02 2.50e+03
        pdb=" O   SER E 100 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY E 101 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 100 "   -0.006 2.00e-02 2.50e+03   1.24e-02 1.54e+00
        pdb=" C   SER D 100 "    0.021 2.00e-02 2.50e+03
        pdb=" O   SER D 100 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLY D 101 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 607 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 151
        2.72 -     3.27: 3132
        3.27 -     3.81: 5694
        3.81 -     4.36: 6366
        4.36 -     4.90: 11140
  Nonbonded interactions: 26483
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 112 "
            pdb=" O   SER B 112 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   SER A 112 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   SER D  85 "
            pdb=" OG  SER D  85 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O   SER A  85 "
            pdb=" OG  SER A  85 "
     model   vdw
     2.190 3.040
  ... (remaining 26478 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  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:             0.880
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.480
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
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      :  0.006   0.033   3640  Z= 0.248
  Angle     :  0.659   5.303   4945  Z= 0.357
  Chirality :  0.052   0.125    580
  Planarity :  0.005   0.027    610
  Dihedral  : 12.739  50.799   1285
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.58 %
    Favored  : 84.42 %
  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: -2.21 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP E  79 
 HIS   0.002   0.001   HIS E  90 
 PHE   0.014   0.003   PHE B  33 
 TYR   0.017   0.003   TYR D  78 
 ARG   0.003   0.001   ARG C 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25280 (   68)
  hydrogen bonds       : angle       8.32210 (  204)
  covalent geometry    : bond        0.00563 ( 3640)
  covalent geometry    : angle       0.65912 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.403 
Fit side-chains
REVERT: B   35 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7428 (mttt)
REVERT: D   35 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7473 (tttt)
REVERT: D   80 LYS cc_start: 0.8776 (tttt) cc_final: 0.8567 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2048
  time to fit residues: 12.3069
Evaluate side-chains
  49 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.117554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.088680 restraints weight = 3937.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.86
r_work: 0.3299 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.0991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3640  Z= 0.180
  Angle     :  0.607   5.562   4945  Z= 0.328
  Chirality :  0.049   0.171    580
  Planarity :  0.004   0.035    610
  Dihedral  :  5.386  16.198    490
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 11.95 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.29 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.002   0.001   HIS C  31 
 PHE   0.010   0.002   PHE D  33 
 TYR   0.021   0.002   TYR C  78 
 ARG   0.001   0.000   ARG A 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04816 (   68)
  hydrogen bonds       : angle       5.84629 (  204)
  covalent geometry    : bond        0.00423 ( 3640)
  covalent geometry    : angle       0.60738 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7518 (mtt-85)
REVERT: C  104 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7677 (mtt-85)
REVERT: D   35 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7542 (mttt)
REVERT: D   62 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7563 (tt0)
REVERT: D   80 LYS cc_start: 0.8441 (tttt) cc_final: 0.8232 (tttm)
REVERT: E   92 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7354 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 55
  average time/residue: 0.2259
  time to fit residues: 14.5883
Evaluate side-chains
  57 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.116201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.086677 restraints weight = 3878.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.86
r_work: 0.3251 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3640  Z= 0.223
  Angle     :  0.645   5.585   4945  Z= 0.349
  Chirality :  0.052   0.184    580
  Planarity :  0.004   0.036    610
  Dihedral  :  5.552  17.176    490
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.77 %
    Favored  : 83.38 %
  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: -2.37 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.003   0.001   HIS D  31 
 PHE   0.013   0.002   PHE E  95 
 TYR   0.024   0.003   TYR A  78 
 ARG   0.002   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04929 (   68)
  hydrogen bonds       : angle       5.57829 (  204)
  covalent geometry    : bond        0.00539 ( 3640)
  covalent geometry    : angle       0.64453 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7462 (tt0) cc_final: 0.6907 (tt0)
REVERT: A  104 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7433 (mtt-85)
REVERT: C  104 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7597 (mtt-85)
REVERT: D   35 LYS cc_start: 0.7751 (mtpt) cc_final: 0.7519 (mttt)
REVERT: D   80 LYS cc_start: 0.8402 (tttt) cc_final: 0.8172 (tttm)
REVERT: E   92 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7406 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 51
  average time/residue: 0.2370
  time to fit residues: 14.1527
Evaluate side-chains
  58 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
B  31 HIS
D  31 HIS
E  31 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.116132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.086515 restraints weight = 3974.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.89
r_work: 0.3250 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3640  Z= 0.204
  Angle     :  0.614   5.523   4945  Z= 0.332
  Chirality :  0.051   0.168    580
  Planarity :  0.003   0.030    610
  Dihedral  :  5.542  16.451    490
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.77 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  79 
 HIS   0.001   0.000   HIS A  31 
 PHE   0.012   0.002   PHE E  95 
 TYR   0.022   0.003   TYR C  78 
 ARG   0.002   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (   68)
  hydrogen bonds       : angle       5.27760 (  204)
  covalent geometry    : bond        0.00491 ( 3640)
  covalent geometry    : angle       0.61394 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7433 (tt0) cc_final: 0.6907 (tt0)
REVERT: A  104 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7486 (mtt-85)
REVERT: B   61 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7274 (mp0)
REVERT: C  104 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7793 (mtt-85)
REVERT: D   61 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7264 (pm20)
REVERT: D   80 LYS cc_start: 0.8394 (tttt) cc_final: 0.8153 (tttp)
REVERT: E   92 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7427 (tm-30)
REVERT: E  104 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7828 (mtt-85)
  outliers start: 10
  outliers final: 7
  residues processed: 52
  average time/residue: 0.2546
  time to fit residues: 15.3277
Evaluate side-chains
  59 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 10 optimal weight:    0.2980
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3916 r_free = 0.3916 target = 0.121097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.090853 restraints weight = 3869.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.89
r_work: 0.3329 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3640  Z= 0.131
  Angle     :  0.559   5.282   4945  Z= 0.301
  Chirality :  0.049   0.161    580
  Planarity :  0.003   0.033    610
  Dihedral  :  5.297  15.384    490
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.81 %
    Favored  : 83.12 %
  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: -2.39 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A  79 
 HIS   0.003   0.001   HIS A  31 
 PHE   0.008   0.001   PHE E  95 
 TYR   0.016   0.002   TYR C  78 
 ARG   0.001   0.000   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03199 (   68)
  hydrogen bonds       : angle       5.12393 (  204)
  covalent geometry    : bond        0.00315 ( 3640)
  covalent geometry    : angle       0.55854 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7464 (tt0) cc_final: 0.6956 (tt0)
REVERT: A  104 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7494 (mtt-85)
REVERT: C   30 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7242 (tpp)
REVERT: C  104 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7841 (mtt-85)
REVERT: D   35 LYS cc_start: 0.8068 (mttt) cc_final: 0.7847 (mmmt)
REVERT: D   80 LYS cc_start: 0.8409 (tttt) cc_final: 0.8185 (tttm)
REVERT: E   92 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7426 (tm-30)
REVERT: E  104 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7776 (mtt-85)
  outliers start: 8
  outliers final: 4
  residues processed: 53
  average time/residue: 0.2493
  time to fit residues: 15.3716
Evaluate side-chains
  56 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   61 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0770
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    2.8146

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.113586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.083943 restraints weight = 4022.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.90
r_work: 0.3238 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.046   3640  Z= 0.326
  Angle     :  0.698   5.844   4945  Z= 0.382
  Chirality :  0.054   0.181    580
  Planarity :  0.004   0.027    610
  Dihedral  :  5.777  17.863    490
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.55 %
    Favored  : 82.08 %
  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: -2.76 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.004   0.001   HIS B  31 
 PHE   0.018   0.003   PHE E  95 
 TYR   0.025   0.004   TYR C  78 
 ARG   0.003   0.000   ARG C  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05025 (   68)
  hydrogen bonds       : angle       5.27907 (  204)
  covalent geometry    : bond        0.00788 ( 3640)
  covalent geometry    : angle       0.69830 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7457 (tt0) cc_final: 0.6930 (tt0)
REVERT: A  104 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7647 (mtt-85)
REVERT: C  104 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7846 (mtt-85)
REVERT: D   35 LYS cc_start: 0.8144 (mttt) cc_final: 0.7849 (mmmt)
REVERT: D   80 LYS cc_start: 0.8450 (tttt) cc_final: 0.8224 (tttp)
REVERT: E   92 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7530 (tm-30)
REVERT: E  104 ARG cc_start: 0.8262 (mtt180) cc_final: 0.8000 (mtt-85)
  outliers start: 13
  outliers final: 10
  residues processed: 54
  average time/residue: 0.2651
  time to fit residues: 16.4722
Evaluate side-chains
  60 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   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 = 0.3904 r_free = 0.3904 target = 0.120246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.092518 restraints weight = 3897.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.67
r_work: 0.3340 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3640  Z= 0.113
  Angle     :  0.557   5.298   4945  Z= 0.299
  Chirality :  0.050   0.168    580
  Planarity :  0.003   0.027    610
  Dihedral  :  5.352  15.986    490
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.40 %
    Favored  : 81.04 %
  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: -2.49 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A  79 
 HIS   0.003   0.001   HIS A  31 
 PHE   0.007   0.001   PHE E  95 
 TYR   0.014   0.002   TYR C  78 
 ARG   0.002   0.000   ARG C 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02883 (   68)
  hydrogen bonds       : angle       5.03158 (  204)
  covalent geometry    : bond        0.00268 ( 3640)
  covalent geometry    : angle       0.55678 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7495 (tt0) cc_final: 0.7003 (tt0)
REVERT: A  104 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7633 (mtt-85)
REVERT: C   30 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7509 (tpp)
REVERT: C  104 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7740 (mtt90)
REVERT: D   35 LYS cc_start: 0.8177 (mttt) cc_final: 0.7903 (mmmt)
REVERT: D   80 LYS cc_start: 0.8527 (tttt) cc_final: 0.8301 (tttm)
REVERT: E   92 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7586 (tm-30)
REVERT: E  104 ARG cc_start: 0.8345 (mtt180) cc_final: 0.8043 (mtt-85)
  outliers start: 6
  outliers final: 4
  residues processed: 54
  average time/residue: 0.2561
  time to fit residues: 16.0539
Evaluate side-chains
  57 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   61 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0570
   chunk 31 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.9304

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.115174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.085859 restraints weight = 3920.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.84
r_work: 0.3271 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   3640  Z= 0.231
  Angle     :  0.622   5.644   4945  Z= 0.339
  Chirality :  0.052   0.171    580
  Planarity :  0.003   0.025    610
  Dihedral  :  5.552  17.224    490
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.14 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.003   0.001   HIS E  31 
 PHE   0.013   0.002   PHE E  95 
 TYR   0.020   0.003   TYR A  78 
 ARG   0.002   0.000   ARG C  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04194 (   68)
  hydrogen bonds       : angle       5.09857 (  204)
  covalent geometry    : bond        0.00558 ( 3640)
  covalent geometry    : angle       0.62231 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7411 (tt0) cc_final: 0.6900 (tt0)
REVERT: A  104 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7622 (mtt-85)
REVERT: C  104 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7572 (mtt90)
REVERT: D   35 LYS cc_start: 0.8046 (mttt) cc_final: 0.7753 (mmmt)
REVERT: D   80 LYS cc_start: 0.8454 (tttt) cc_final: 0.8237 (tttp)
REVERT: E   92 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7474 (tm-30)
REVERT: E  104 ARG cc_start: 0.8254 (mtt180) cc_final: 0.8012 (mtt-85)
  outliers start: 9
  outliers final: 8
  residues processed: 55
  average time/residue: 0.2615
  time to fit residues: 16.5946
Evaluate side-chains
  62 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3863 r_free = 0.3863 target = 0.116610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.087496 restraints weight = 3827.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.80
r_work: 0.3329 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3640  Z= 0.165
  Angle     :  0.583   5.479   4945  Z= 0.316
  Chirality :  0.050   0.168    580
  Planarity :  0.003   0.027    610
  Dihedral  :  5.452  16.548    490
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.40 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A  79 
 HIS   0.003   0.001   HIS A  31 
 PHE   0.010   0.002   PHE E  95 
 TYR   0.018   0.002   TYR C  78 
 ARG   0.001   0.000   ARG C  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (   68)
  hydrogen bonds       : angle       5.02499 (  204)
  covalent geometry    : bond        0.00401 ( 3640)
  covalent geometry    : angle       0.58290 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7442 (tt0) cc_final: 0.6923 (tt0)
REVERT: A  104 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7606 (mtt-85)
REVERT: C  104 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7661 (mtt90)
REVERT: D   35 LYS cc_start: 0.8060 (mttt) cc_final: 0.7804 (mmmt)
REVERT: D   80 LYS cc_start: 0.8495 (tttt) cc_final: 0.8275 (tttp)
REVERT: E   13 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6582 (tmm)
REVERT: E   92 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7483 (tm-30)
REVERT: E  104 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7971 (mtt-85)
  outliers start: 9
  outliers final: 7
  residues processed: 52
  average time/residue: 0.2601
  time to fit residues: 15.6329
Evaluate side-chains
  59 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.111412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.082559 restraints weight = 4024.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 2.86
r_work: 0.3264 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.052   3640  Z= 0.353
  Angle     :  0.709   5.992   4945  Z= 0.390
  Chirality :  0.055   0.175    580
  Planarity :  0.004   0.025    610
  Dihedral  :  5.907  18.471    490
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.88 %
    Favored  : 80.52 %
  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 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.004   0.001   HIS B  31 
 PHE   0.019   0.003   PHE D  95 
 TYR   0.025   0.004   TYR A  78 
 ARG   0.003   0.001   ARG C  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05186 (   68)
  hydrogen bonds       : angle       5.21808 (  204)
  covalent geometry    : bond        0.00850 ( 3640)
  covalent geometry    : angle       0.70898 ( 4945)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7537 (tt0) cc_final: 0.7011 (tt0)
REVERT: A  104 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7648 (mtt-85)
REVERT: C  104 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7923 (mtt-85)
REVERT: D   35 LYS cc_start: 0.8135 (mttt) cc_final: 0.7889 (mmmt)
REVERT: D   80 LYS cc_start: 0.8543 (tttt) cc_final: 0.8328 (tttp)
REVERT: E   92 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7571 (tm-30)
REVERT: E  104 ARG cc_start: 0.8375 (mtt180) cc_final: 0.8138 (mtt-85)
  outliers start: 10
  outliers final: 9
  residues processed: 55
  average time/residue: 0.2817
  time to fit residues: 17.7420
Evaluate side-chains
  62 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   61 GLU
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0370
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.7658

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.123788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.096642 restraints weight = 3936.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.68
r_work: 0.3337 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3640  Z= 0.119
  Angle     :  0.565   5.550   4945  Z= 0.304
  Chirality :  0.050   0.168    580
  Planarity :  0.003   0.027    610
  Dihedral  :  5.425  16.610    490
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.40 %
    Favored  : 80.52 %
  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: -2.63 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP C  79 
 HIS   0.003   0.000   HIS A  31 
 PHE   0.006   0.001   PHE E  95 
 TYR   0.016   0.002   TYR C  78 
 ARG   0.002   0.000   ARG C 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02938 (   68)
  hydrogen bonds       : angle       4.95995 (  204)
  covalent geometry    : bond        0.00290 ( 3640)
  covalent geometry    : angle       0.56498 ( 4945)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1988.65 seconds
wall clock time: 35 minutes 5.89 seconds (2105.89 seconds total)