Starting phenix.real_space_refine
on Wed Sep 17 03:58:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9byn_45039/09_2025/9byn_45039.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9byn_45039/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9byn_45039/09_2025/9byn_45039.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9byn_45039/09_2025/9byn_45039.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9byn_45039/09_2025/9byn_45039.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9byn_45039/09_2025/9byn_45039.map"
  }
  resolution = 3.36
  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=   0.005
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): 0.00s

  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: 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:
    B, C, D, E
  Time building chain proxies: 0.78, per 1000 atoms: 0.22
  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: 0.26
  Conformation dependent library (CDL) restraints added in 170.5 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.19
  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: 0.52

  Time building geometry restraints manager: 0.38 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.160
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.310
  Find NCS groups from input model:        0.030
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.900
-------------------------------------------------------------------------------
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 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: -2.21 (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
 ARG   0.003   0.001   ARG C 103 
 TYR   0.017   0.003   TYR D  78 
 PHE   0.014   0.003   PHE B  33 
 TRP   0.010   0.002   TRP E  79 
 HIS   0.002   0.001   HIS E  90 

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

*********************** 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  : 0.144 
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: 0.1006
  time to fit residues: 5.9935
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  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0470
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.5236

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.123433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.095792 restraints weight = 4052.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.66
r_work: 0.3381 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.0983

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= 0.117
  Angle     :  0.566   5.260   4945  Z= 0.304
  Chirality :  0.049   0.165    580
  Planarity :  0.004   0.033    610
  Dihedral  :  5.151  15.198    490
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.77 %
    Favored  : 84.68 %
  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: -2.26 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 103 
 TYR   0.014   0.002   TYR C  78 
 PHE   0.006   0.001   PHE A  95 
 TRP   0.003   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3640)
  covalent geometry    : angle       0.56632 ( 4945)
  hydrogen bonds       : bond        0.04150 (   68)
  hydrogen bonds       : angle       6.00884 (  204)

*********************** 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
  57 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7855 (mtt-85)
REVERT: C  104 ARG cc_start: 0.8279 (mtt180) cc_final: 0.8044 (mtt-85)
REVERT: D   62 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7661 (tt0)
REVERT: D   80 LYS cc_start: 0.8490 (tttt) cc_final: 0.8242 (tttp)
REVERT: E   92 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7502 (tm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 53
  average time/residue: 0.1051
  time to fit residues: 6.4858
Evaluate side-chains
  52 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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   62 GLU
Chi-restraints excluded: chain D residue  112 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.113085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.084027 restraints weight = 3993.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.88
r_work: 0.3214 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.044   3640  Z= 0.325
  Angle     :  0.716   5.724   4945  Z= 0.391
  Chirality :  0.054   0.180    580
  Planarity :  0.004   0.036    610
  Dihedral  :  5.767  18.214    490
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.29 %
    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 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: -2.43 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  21 
 TYR   0.030   0.004   TYR A  78 
 PHE   0.019   0.003   PHE D  95 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.003   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00787 ( 3640)
  covalent geometry    : angle       0.71640 ( 4945)
  hydrogen bonds       : bond        0.05564 (   68)
  hydrogen bonds       : angle       5.71072 (  204)

*********************** 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
  62 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7499 (tt0) cc_final: 0.6968 (tt0)
REVERT: A  104 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7430 (mtt-85)
REVERT: C  104 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7616 (mtt-85)
REVERT: D   80 LYS cc_start: 0.8350 (tttt) cc_final: 0.8117 (tttm)
REVERT: E   92 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7424 (tm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 53
  average time/residue: 0.1098
  time to fit residues: 6.7975
Evaluate side-chains
  61 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0470
   chunk 0 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.3923 r_free = 0.3923 target = 0.123385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.094477 restraints weight = 3948.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.75
r_work: 0.3379 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3640  Z= 0.104
  Angle     :  0.543   5.141   4945  Z= 0.290
  Chirality :  0.049   0.163    580
  Planarity :  0.003   0.030    610
  Dihedral  :  5.178  14.552    490
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.62 %
    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 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: -2.26 (0.37), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 103 
 TYR   0.014   0.001   TYR B 114 
 PHE   0.005   0.001   PHE D  33 
 TRP   0.001   0.000   TRP A  79 
 HIS   0.004   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3640)
  covalent geometry    : angle       0.54315 ( 4945)
  hydrogen bonds       : bond        0.02779 (   68)
  hydrogen bonds       : angle       5.30836 (  204)

*********************** 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
  57 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7642 (tt0) cc_final: 0.7157 (tt0)
REVERT: A  104 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7782 (mtt-85)
REVERT: C   13 MET cc_start: 0.7353 (ttp) cc_final: 0.7141 (ttm)
REVERT: C   30 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7503 (tpp)
REVERT: D   35 LYS cc_start: 0.8136 (mttt) cc_final: 0.7905 (mttt)
REVERT: D   80 LYS cc_start: 0.8556 (tttt) cc_final: 0.8342 (tttp)
REVERT: E   92 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7586 (tm-30)
REVERT: E  104 ARG cc_start: 0.8375 (mtt180) cc_final: 0.8069 (mtt-85)
  outliers start: 5
  outliers final: 1
  residues processed: 53
  average time/residue: 0.1171
  time to fit residues: 7.1154
Evaluate side-chains
  54 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain D residue  112 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0570
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0270
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.5960

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.116648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.087201 restraints weight = 3909.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.83
r_work: 0.3294 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3640  Z= 0.199
  Angle     :  0.599   5.282   4945  Z= 0.325
  Chirality :  0.051   0.165    580
  Planarity :  0.003   0.031    610
  Dihedral  :  5.361  15.911    490
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.81 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.34 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.28), residues: 435

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 3640)
  covalent geometry    : angle       0.59949 ( 4945)
  hydrogen bonds       : bond        0.04041 (   68)
  hydrogen bonds       : angle       5.25205 (  204)

*********************** 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
  65 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7392 (tt0) cc_final: 0.6879 (tt0)
REVERT: A  104 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7657 (mtt-85)
REVERT: B   61 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7205 (mp0)
REVERT: D   35 LYS cc_start: 0.7959 (mttt) cc_final: 0.7751 (mmmt)
REVERT: D   80 LYS cc_start: 0.8404 (tttt) cc_final: 0.8187 (tttm)
REVERT: E   92 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7497 (tm-30)
REVERT: E  104 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7885 (mtt-85)
  outliers start: 11
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1085
  time to fit residues: 7.0279
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  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
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   13 MET
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 8 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 31 optimal weight:    0.1980
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.3986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.116631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.087646 restraints weight = 3887.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.82
r_work: 0.3313 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1780

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= 0.172
  Angle     :  0.580   5.300   4945  Z= 0.314
  Chirality :  0.050   0.161    580
  Planarity :  0.003   0.029    610
  Dihedral  :  5.387  15.540    490
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.06 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.39 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  21 
 TYR   0.019   0.002   TYR C  78 
 PHE   0.010   0.002   PHE E  95 
 TRP   0.002   0.000   TRP C  79 
 HIS   0.002   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 3640)
  covalent geometry    : angle       0.57951 ( 4945)
  hydrogen bonds       : bond        0.03619 (   68)
  hydrogen bonds       : angle       5.12642 (  204)

*********************** 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
  65 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7379 (tt0) cc_final: 0.6865 (tt0)
REVERT: A  104 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7640 (mtt-85)
REVERT: B   61 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7224 (mp0)
REVERT: D   35 LYS cc_start: 0.8036 (mttt) cc_final: 0.7701 (mmmt)
REVERT: D   80 LYS cc_start: 0.8428 (tttt) cc_final: 0.8200 (tttm)
REVERT: E   92 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7506 (tm-30)
REVERT: E  104 ARG cc_start: 0.8237 (mtt180) cc_final: 0.7913 (mtt-85)
  outliers start: 10
  outliers final: 9
  residues processed: 58
  average time/residue: 0.1056
  time to fit residues: 7.0791
Evaluate side-chains
  64 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
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   61 GLU
Chi-restraints excluded: chain D residue  100 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0270
   chunk 14 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.0042

-------------------------------------------------------------------------------
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 = 0.3907 r_free = 0.3907 target = 0.118685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.089740 restraints weight = 3934.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.82
r_work: 0.3340 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1860

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= 0.136
  Angle     :  0.556   5.133   4945  Z= 0.300
  Chirality :  0.050   0.170    580
  Planarity :  0.003   0.028    610
  Dihedral  :  5.189  15.405    490
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.58 %
    Favored  : 81.82 %
  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: -2.33 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  21 
 TYR   0.017   0.002   TYR C  78 
 PHE   0.008   0.001   PHE E  95 
 TRP   0.002   0.000   TRP D  79 
 HIS   0.002   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3640)
  covalent geometry    : angle       0.55633 ( 4945)
  hydrogen bonds       : bond        0.03156 (   68)
  hydrogen bonds       : angle       5.02980 (  204)

*********************** 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
  63 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7375 (tt0) cc_final: 0.6853 (tt0)
REVERT: A  104 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7422 (mtt-85)
REVERT: B   61 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7281 (mp0)
REVERT: D   35 LYS cc_start: 0.8103 (mttt) cc_final: 0.7823 (mmmt)
REVERT: D   80 LYS cc_start: 0.8394 (tttt) cc_final: 0.8166 (tttm)
REVERT: E   92 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7439 (tm-30)
REVERT: E  104 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7762 (mtt-85)
  outliers start: 10
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1006
  time to fit residues: 6.5612
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  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
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   13 MET
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 18 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.118304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.089149 restraints weight = 3915.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.81
r_work: 0.3337 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3640  Z= 0.149
  Angle     :  0.565   5.142   4945  Z= 0.305
  Chirality :  0.050   0.168    580
  Planarity :  0.003   0.027    610
  Dihedral  :  5.224  15.380    490
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.84 %
    Favored  : 81.82 %
  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: -2.38 (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
 ARG   0.002   0.000   ARG B 103 
 TYR   0.018   0.002   TYR C  78 
 PHE   0.009   0.002   PHE E  95 
 TRP   0.001   0.000   TRP C  79 
 HIS   0.002   0.000   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3640)
  covalent geometry    : angle       0.56488 ( 4945)
  hydrogen bonds       : bond        0.03332 (   68)
  hydrogen bonds       : angle       4.98464 (  204)

*********************** 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
  62 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7430 (tt0) cc_final: 0.6910 (tt0)
REVERT: A  104 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7485 (mtt-85)
REVERT: B   61 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7300 (mp0)
REVERT: D   35 LYS cc_start: 0.8114 (mttt) cc_final: 0.7844 (mmmt)
REVERT: D   80 LYS cc_start: 0.8414 (tttt) cc_final: 0.8189 (tttm)
REVERT: E   92 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7440 (tm-30)
REVERT: E  104 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7771 (mtt-85)
  outliers start: 9
  outliers final: 8
  residues processed: 56
  average time/residue: 0.1018
  time to fit residues: 6.6061
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  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 GLU
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0370
   chunk 2 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.3864

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.116782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.088096 restraints weight = 3892.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.78
r_work: 0.3321 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3640  Z= 0.172
  Angle     :  0.581   5.242   4945  Z= 0.315
  Chirality :  0.051   0.172    580
  Planarity :  0.003   0.025    610
  Dihedral  :  5.296  15.540    490
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.10 %
    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 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: -2.41 (0.36), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  21 
 TYR   0.019   0.002   TYR C  78 
 PHE   0.011   0.002   PHE E  95 
 TRP   0.001   0.000   TRP A  79 
 HIS   0.002   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 3640)
  covalent geometry    : angle       0.58125 ( 4945)
  hydrogen bonds       : bond        0.03588 (   68)
  hydrogen bonds       : angle       4.98937 (  204)

*********************** 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
  64 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7470 (tt0) cc_final: 0.6959 (tt0)
REVERT: A  104 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7677 (mtt-85)
REVERT: B   61 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7289 (mp0)
REVERT: D   35 LYS cc_start: 0.8148 (mttt) cc_final: 0.7889 (mmmt)
REVERT: D   80 LYS cc_start: 0.8476 (tttt) cc_final: 0.8262 (tttp)
REVERT: E   63 GLU cc_start: 0.8109 (tt0) cc_final: 0.7661 (mt-10)
REVERT: E   92 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7531 (tm-30)
REVERT: E  104 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7937 (mtt-85)
  outliers start: 11
  outliers final: 10
  residues processed: 56
  average time/residue: 0.1215
  time to fit residues: 7.8875
Evaluate side-chains
  64 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   61 GLU
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   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 19 optimal weight:    0.1980
   chunk 18 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0980
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3960 r_free = 0.3960 target = 0.123947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.096730 restraints weight = 3953.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.66
r_work: 0.3392 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3640  Z= 0.097
  Angle     :  0.525   4.980   4945  Z= 0.282
  Chirality :  0.049   0.165    580
  Planarity :  0.003   0.026    610
  Dihedral  :  5.005  15.447    490
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.14 %
    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 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: -2.28 (0.37), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 103 
 TYR   0.014   0.002   TYR C  78 
 PHE   0.005   0.001   PHE C  95 
 TRP   0.001   0.000   TRP C  79 
 HIS   0.002   0.000   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3640)
  covalent geometry    : angle       0.52538 ( 4945)
  hydrogen bonds       : bond        0.02468 (   68)
  hydrogen bonds       : angle       4.83684 (  204)

********************** 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
  60 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   62 GLU cc_start: 0.7505 (tt0) cc_final: 0.6999 (tt0)
REVERT: A  104 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7618 (mtt-85)
REVERT: C   30 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7538 (tpp)
REVERT: D   35 LYS cc_start: 0.8161 (mttt) cc_final: 0.7935 (mttt)
REVERT: D   80 LYS cc_start: 0.8511 (tttt) cc_final: 0.8298 (tttm)
REVERT: E   13 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6565 (tmm)
REVERT: E   63 GLU cc_start: 0.7956 (tt0) cc_final: 0.7526 (mt-10)
REVERT: E   92 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7559 (tm-30)
REVERT: E  104 ARG cc_start: 0.8315 (mtt180) cc_final: 0.8001 (mtt-85)
  outliers start: 7
  outliers final: 5
  residues processed: 55
  average time/residue: 0.1154
  time to fit residues: 7.2996
Evaluate side-chains
  60 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
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 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:    0.0770
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    0.4980
   chunk 22 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.8340

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.123857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.095703 restraints weight = 3894.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.76
r_work: 0.3371 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2091

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= 0.120
  Angle     :  0.537   4.965   4945  Z= 0.288
  Chirality :  0.049   0.164    580
  Planarity :  0.003   0.025    610
  Dihedral  :  4.995  15.442    490
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.88 %
    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 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: -2.25 (0.37), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 103 
 TYR   0.015   0.002   TYR C  78 
 PHE   0.008   0.001   PHE E  95 
 TRP   0.002   0.000   TRP D  79 
 HIS   0.002   0.000   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3640)
  covalent geometry    : angle       0.53689 ( 4945)
  hydrogen bonds       : bond        0.02875 (   68)
  hydrogen bonds       : angle       4.80579 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1051.15 seconds
wall clock time: 18 minutes 47.33 seconds (1127.33 seconds total)