Starting phenix.real_space_refine
on Wed Mar 12 22:11:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9avi_43902/03_2025/9avi_43902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9avi_43902/03_2025/9avi_43902.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9avi_43902/03_2025/9avi_43902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9avi_43902/03_2025/9avi_43902.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9avi_43902/03_2025/9avi_43902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9avi_43902/03_2025/9avi_43902.cif"
  }
  resolution = 3.02
  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=   0.009
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      30      5.16       5
     C    5430      2.51       5
     N    1390      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8370
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1674
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 5, 'TRANS': 210}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 4.77, per 1000 atoms: 0.57
  Number of scatterers: 8370
  At special positions: 0
  Unit cell: (85.799, 84.966, 110.789, 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      30     16.00
     O    1520      8.00
     N    1390      7.00
     C    5430      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: 2.00
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2010

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      83.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 17
      removed outlier: 3.704A  pdb=" N   LEU A  14 " --> pdb=" O   HIS A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 63
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 82 through 99
    Processing helix  chain 'A' and resid 103 through 114
    Processing helix  chain 'A' and resid 129 through 153
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 155 through 160
    Processing helix  chain 'A' and resid 166 through 189
      removed outlier: 3.733A  pdb=" N   VAL A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      Proline residue:  A 172  - end of helix
      removed outlier: 3.801A  pdb=" N   GLU A 176 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA A 180 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 225
    Processing helix  chain 'B' and resid 11 through 17
    Processing helix  chain 'B' and resid 19 through 63
    Processing helix  chain 'B' and resid 66 through 77
    Processing helix  chain 'B' and resid 82 through 99
    Processing helix  chain 'B' and resid 103 through 114
    Processing helix  chain 'B' and resid 129 through 153
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 155 through 160
    Processing helix  chain 'B' and resid 166 through 189
      removed outlier: 3.733A  pdb=" N   VAL B 170 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      Proline residue:  B 172  - end of helix
      removed outlier: 3.801A  pdb=" N   GLU B 176 " --> pdb=" O   PRO B 172 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA B 177 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA B 180 " --> pdb=" O   GLU B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 225
    Processing helix  chain 'C' and resid 11 through 17
    Processing helix  chain 'C' and resid 19 through 63
    Processing helix  chain 'C' and resid 66 through 77
    Processing helix  chain 'C' and resid 82 through 99
    Processing helix  chain 'C' and resid 103 through 114
    Processing helix  chain 'C' and resid 129 through 153
      Proline residue:  C 141  - end of helix
    Processing helix  chain 'C' and resid 155 through 160
    Processing helix  chain 'C' and resid 166 through 189
      removed outlier: 3.733A  pdb=" N   VAL C 170 " --> pdb=" O   THR C 166 " (cutoff:3.500A)
      Proline residue:  C 172  - end of helix
      removed outlier: 3.801A  pdb=" N   GLU C 176 " --> pdb=" O   PRO C 172 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA C 177 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA C 180 " --> pdb=" O   GLU C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 225
    Processing helix  chain 'D' and resid 11 through 17
    Processing helix  chain 'D' and resid 19 through 63
    Processing helix  chain 'D' and resid 66 through 77
    Processing helix  chain 'D' and resid 82 through 99
    Processing helix  chain 'D' and resid 103 through 114
    Processing helix  chain 'D' and resid 129 through 153
      Proline residue:  D 141  - end of helix
    Processing helix  chain 'D' and resid 155 through 160
    Processing helix  chain 'D' and resid 166 through 189
      removed outlier: 3.733A  pdb=" N   VAL D 170 " --> pdb=" O   THR D 166 " (cutoff:3.500A)
      Proline residue:  D 172  - end of helix
      removed outlier: 3.801A  pdb=" N   GLU D 176 " --> pdb=" O   PRO D 172 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA D 177 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA D 180 " --> pdb=" O   GLU D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 225
    Processing helix  chain 'E' and resid 11 through 17
    Processing helix  chain 'E' and resid 19 through 63
    Processing helix  chain 'E' and resid 66 through 77
    Processing helix  chain 'E' and resid 82 through 99
    Processing helix  chain 'E' and resid 103 through 114
    Processing helix  chain 'E' and resid 129 through 153
      Proline residue:  E 141  - end of helix
    Processing helix  chain 'E' and resid 155 through 160
    Processing helix  chain 'E' and resid 166 through 189
      removed outlier: 3.732A  pdb=" N   VAL E 170 " --> pdb=" O   THR E 166 " (cutoff:3.500A)
      Proline residue:  E 172  - end of helix
      removed outlier: 3.801A  pdb=" N   GLU E 176 " --> pdb=" O   PRO E 172 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA E 177 " --> pdb=" O   GLY E 173 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ALA E 180 " --> pdb=" O   GLU E 176 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 225

    665 hydrogen bonds defined for protein.
    1995 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: 2.34

  Time building geometry restraints manager: 2.38 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1355
        1.31 -     1.44: 2268
        1.44 -     1.56: 4852
        1.56 -     1.69: 0
        1.69 -     1.82: 60
  Bond restraints: 8535
  Sorted by residual:
  bond pdb=" C   PRO A 190 "
       pdb=" O   PRO A 190 "
    ideal  model  delta    sigma   weight residual
    1.237  1.185  0.053 1.32e-02 5.74e+03 1.59e+01
  bond pdb=" C   PRO E 190 "
       pdb=" O   PRO E 190 "
    ideal  model  delta    sigma   weight residual
    1.237  1.185  0.053 1.32e-02 5.74e+03 1.59e+01
  bond pdb=" C   PRO C 190 "
       pdb=" O   PRO C 190 "
    ideal  model  delta    sigma   weight residual
    1.237  1.185  0.053 1.32e-02 5.74e+03 1.59e+01
  bond pdb=" C   PRO B 190 "
       pdb=" O   PRO B 190 "
    ideal  model  delta    sigma   weight residual
    1.237  1.185  0.052 1.32e-02 5.74e+03 1.58e+01
  bond pdb=" C   PRO D 190 "
       pdb=" O   PRO D 190 "
    ideal  model  delta    sigma   weight residual
    1.237  1.185  0.052 1.32e-02 5.74e+03 1.56e+01
  ... (remaining 8530 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 6497
        1.50 -     3.00: 3519
        3.00 -     4.50: 1346
        4.50 -     5.99: 188
        5.99 -     7.49: 5
  Bond angle restraints: 11555
  Sorted by residual:
  angle pdb=" N   ALA B 194 "
        pdb=" CA  ALA B 194 "
        pdb=" C   ALA B 194 "
      ideal   model   delta    sigma   weight residual
     114.62  108.64    5.98 1.14e+00 7.69e-01 2.75e+01
  angle pdb=" N   ALA C 194 "
        pdb=" CA  ALA C 194 "
        pdb=" C   ALA C 194 "
      ideal   model   delta    sigma   weight residual
     114.62  108.68    5.94 1.14e+00 7.69e-01 2.72e+01
  angle pdb=" N   ALA E 194 "
        pdb=" CA  ALA E 194 "
        pdb=" C   ALA E 194 "
      ideal   model   delta    sigma   weight residual
     114.62  108.68    5.94 1.14e+00 7.69e-01 2.71e+01
  angle pdb=" N   ALA A 194 "
        pdb=" CA  ALA A 194 "
        pdb=" C   ALA A 194 "
      ideal   model   delta    sigma   weight residual
     114.62  108.70    5.92 1.14e+00 7.69e-01 2.70e+01
  angle pdb=" N   ALA D 194 "
        pdb=" CA  ALA D 194 "
        pdb=" C   ALA D 194 "
      ideal   model   delta    sigma   weight residual
     114.62  108.70    5.92 1.14e+00 7.69e-01 2.70e+01
  ... (remaining 11550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.80: 4185
       12.80 -    25.61: 608
       25.61 -    38.41: 182
       38.41 -    51.21: 65
       51.21 -    64.02: 15
  Dihedral angle restraints: 5055
    sinusoidal: 1935
      harmonic: 3120
  Sorted by residual:
  dihedral pdb=" CA  LEU D 115 "
           pdb=" C   LEU D 115 "
           pdb=" N   ARG D 116 "
           pdb=" CA  ARG D 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.54   25.46     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  LEU B 115 "
           pdb=" C   LEU B 115 "
           pdb=" N   ARG B 116 "
           pdb=" CA  ARG B 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.54   25.46     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  LEU A 115 "
           pdb=" C   LEU A 115 "
           pdb=" N   ARG A 116 "
           pdb=" CA  ARG A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.56   25.44     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 5052 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 651
       0.049 -    0.097: 407
       0.097 -    0.146: 174
       0.146 -    0.195: 93
       0.195 -    0.244: 15
  Chirality restraints: 1340
  Sorted by residual:
  chirality pdb=" CA  VAL C 117 "
            pdb=" N   VAL C 117 "
            pdb=" C   VAL C 117 "
            pdb=" CB  VAL C 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  VAL D 117 "
            pdb=" N   VAL D 117 "
            pdb=" C   VAL D 117 "
            pdb=" CB  VAL D 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  VAL A 117 "
            pdb=" N   VAL A 117 "
            pdb=" C   VAL A 117 "
            pdb=" CB  VAL A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1337 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 167 "    0.013 2.00e-02 2.50e+03   2.60e-02 6.78e+00
        pdb=" C   LEU D 167 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LEU D 167 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA D 168 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 167 "    0.013 2.00e-02 2.50e+03   2.60e-02 6.76e+00
        pdb=" C   LEU E 167 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LEU E 167 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA E 168 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 167 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.75e+00
        pdb=" C   LEU C 167 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LEU C 167 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA C 168 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 3613
        2.92 -     3.42: 9250
        3.42 -     3.91: 13616
        3.91 -     4.41: 15445
        4.41 -     4.90: 25452
  Nonbonded interactions: 67376
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 220 "
            pdb=" OG  SER B 224 "
     model   vdw
     2.430 3.040
  nonbonded pdb=" O   LEU A 220 "
            pdb=" OG  SER A 224 "
     model   vdw
     2.430 3.040
  nonbonded pdb=" O   LEU E 220 "
            pdb=" OG  SER E 224 "
     model   vdw
     2.430 3.040
  nonbonded pdb=" O   LEU D 220 "
            pdb=" OG  SER D 224 "
     model   vdw
     2.430 3.040
  nonbonded pdb=" O   LEU C 220 "
            pdb=" OG  SER C 224 "
     model   vdw
     2.430 3.040
  ... (remaining 67371 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: 0.08
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:             59.690
  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:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.120
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   85.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
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      :  0.013   0.053   8535  Z= 0.845
  Angle     :  1.937   7.493  11555  Z= 1.484
  Chirality :  0.079   0.244   1340
  Planarity :  0.007   0.026   1450
  Dihedral  : 14.200  64.016   3045
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  :  8.57 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.11 (0.18), residues: 1070
  helix: -2.95 (0.12), residues: 970
  sheet:  None (None), residues: 0
  loop : -4.56 (0.33), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.006   TRP C  62 
 HIS   0.006   0.003   HIS B  56 
 PHE   0.031   0.007   PHE C 195 
 TYR   0.019   0.005   TYR C  47 
 ARG   0.003   0.001   ARG B 116 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 143
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A   17 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8965 (pp30)
REVERT: A  100 ARG cc_start: 0.9590 (mtp85) cc_final: 0.9345 (ttm110)
REVERT: B   17 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.9053 (pp30)
REVERT: B  100 ARG cc_start: 0.9603 (mtp85) cc_final: 0.9344 (ttm110)
REVERT: C   17 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8998 (pp30)
REVERT: C  100 ARG cc_start: 0.9607 (mtp85) cc_final: 0.9399 (ttm110)
REVERT: C  128 TYR cc_start: 0.9152 (t80) cc_final: 0.8922 (t80)
REVERT: D   17 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.9032 (pp30)
REVERT: E   17 GLN cc_start: 0.9329 (OUTLIER) cc_final: 0.9061 (pp30)
REVERT: E  100 ARG cc_start: 0.9593 (mtp85) cc_final: 0.9337 (ttm110)
REVERT: E  128 TYR cc_start: 0.9142 (t80) cc_final: 0.8927 (t80)
  outliers start: 55
  outliers final: 21
  residues processed: 188
  average time/residue: 0.3105
  time to fit residues: 72.1551
Evaluate side-chains
  140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLN
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  113 ARG
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  143 ILE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain D residue   17 GLN
Chi-restraints excluded: chain D residue  108 ILE
Chi-restraints excluded: chain D residue  113 ARG
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain E residue   17 GLN
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  113 ARG
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  199 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 95 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  23 GLN
A  52 GLN
A  72 ASN
A 221 GLN
B  23 GLN
B  52 GLN
B  72 ASN
B 221 GLN
C  23 GLN
C  52 GLN
C  72 ASN
C 221 GLN
D  23 GLN
D  52 GLN
D  72 ASN
D 221 GLN
E  23 GLN
E  52 GLN
E  72 ASN
E 221 GLN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.075011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.053896 restraints weight = 21559.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.86
r_work: 0.2791 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8535  Z= 0.211
  Angle     :  0.612   8.084  11555  Z= 0.320
  Chirality :  0.038   0.123   1340
  Planarity :  0.005   0.028   1450
  Dihedral  :  7.374  56.929   1207
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 11.66 %
    Favored  : 85.83 %
  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:  0.17 (0.24), residues: 1070
  helix:  0.38 (0.16), residues: 985
  sheet:  None (None), residues: 0
  loop : -1.79 (0.57), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 150 
 HIS   0.004   0.002   HIS E 197 
 PHE   0.013   0.002   PHE B  87 
 TYR   0.014   0.002   TYR D 142 
 ARG   0.006   0.001   ARG E  51 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.456 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9510 (mtp85) cc_final: 0.9267 (ttm110)
REVERT: A  113 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7914 (ttp-110)
REVERT: B  100 ARG cc_start: 0.9530 (mtp85) cc_final: 0.9308 (ttm-80)
REVERT: B  113 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7992 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9521 (mtp85) cc_final: 0.9201 (ttm110)
REVERT: C  113 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8292 (ttp-110)
REVERT: D  113 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8333 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9499 (mtp85) cc_final: 0.9212 (ttm110)
REVERT: E  113 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8161 (ttp-110)
  outliers start: 22
  outliers final: 13
  residues processed: 143
  average time/residue: 0.3694
  time to fit residues: 65.0088
Evaluate side-chains
  140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  113 ARG
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue  113 ARG
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain E residue  113 ARG
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  166 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 64 optimal weight:    0.3980
   chunk 3 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.073796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.053038 restraints weight = 21859.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 2.89
r_work: 0.2784 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8535  Z= 0.187
  Angle     :  0.543   7.008  11555  Z= 0.275
  Chirality :  0.035   0.108   1340
  Planarity :  0.004   0.027   1450
  Dihedral  :  5.687  59.683   1173
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.14 %
    Favored  : 84.00 %
  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:  2.77 (0.25), residues: 1070
  helix:  2.03 (0.16), residues: 985
  sheet:  None (None), residues: 0
  loop : -0.32 (0.65), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  62 
 HIS   0.003   0.001   HIS D 197 
 PHE   0.009   0.001   PHE B 195 
 TYR   0.011   0.001   TYR E  38 
 ARG   0.006   0.001   ARG A  51 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 1.082 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9502 (mtp85) cc_final: 0.9270 (ttm110)
REVERT: A  113 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7897 (ttp-110)
REVERT: A  208 ASP cc_start: 0.8571 (t0) cc_final: 0.8343 (t0)
REVERT: B  100 ARG cc_start: 0.9540 (mtp85) cc_final: 0.9225 (ttm110)
REVERT: B  113 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8117 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9519 (mtp85) cc_final: 0.9172 (ttm110)
REVERT: C  113 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8048 (ttp-110)
REVERT: D  113 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8581 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9506 (mtp85) cc_final: 0.9176 (ttm110)
REVERT: E  113 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8117 (ttp-110)
  outliers start: 25
  outliers final: 13
  residues processed: 153
  average time/residue: 0.3807
  time to fit residues: 71.4358
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue  113 ARG
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   60 MET
Chi-restraints excluded: chain D residue  113 ARG
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  113 ARG
Chi-restraints excluded: chain E residue  166 THR
Chi-restraints excluded: chain E residue  199 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 81 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.077178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.055443 restraints weight = 21200.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 3.09
r_work: 0.2785 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8535  Z= 0.168
  Angle     :  0.506   6.470  11555  Z= 0.254
  Chirality :  0.035   0.108   1340
  Planarity :  0.003   0.024   1450
  Dihedral  :  5.129  56.557   1170
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 13.83 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.80 (0.26), residues: 1070
  helix:  2.70 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -0.13 (0.62), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  62 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.008   0.001   PHE C 195 
 TYR   0.010   0.001   TYR D 142 
 ARG   0.006   0.001   ARG D 121 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 130
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9477 (mtp85) cc_final: 0.9117 (ttm110)
REVERT: A  113 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7862 (ttp-110)
REVERT: B   42 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8559 (ttmm)
REVERT: B  100 ARG cc_start: 0.9528 (mtp85) cc_final: 0.9255 (ttm110)
REVERT: B  113 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7856 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9496 (mtp85) cc_final: 0.9162 (ttm110)
REVERT: C  113 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7932 (ttp-110)
REVERT: D  100 ARG cc_start: 0.9478 (ttm-80) cc_final: 0.9265 (ttm-80)
REVERT: D  113 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8376 (ttp-110)
REVERT: E   26 MET cc_start: 0.9008 (mtm) cc_final: 0.8580 (mtm)
REVERT: E  100 ARG cc_start: 0.9484 (mtp85) cc_final: 0.8975 (ttm110)
REVERT: E  113 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8026 (ttp-110)
  outliers start: 35
  outliers final: 21
  residues processed: 145
  average time/residue: 0.3627
  time to fit residues: 63.6506
Evaluate side-chains
  143 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ARG
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue  113 ARG
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  179 ILE
Chi-restraints excluded: chain C residue  113 ARG
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   60 MET
Chi-restraints excluded: chain D residue  113 ARG
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain D residue  179 ILE
Chi-restraints excluded: chain E residue  113 ARG
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  166 THR
Chi-restraints excluded: chain E residue  179 ILE
Chi-restraints excluded: chain E residue  199 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 99 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 101 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.076713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.054795 restraints weight = 20867.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 3.07
r_work: 0.2773 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8535  Z= 0.183
  Angle     :  0.516   6.161  11555  Z= 0.256
  Chirality :  0.035   0.108   1340
  Planarity :  0.003   0.025   1450
  Dihedral  :  4.741  46.871   1170
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 15.20 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.09 (0.26), residues: 1070
  helix:  2.89 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -0.05 (0.65), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 150 
 HIS   0.004   0.001   HIS E  56 
 PHE   0.008   0.001   PHE D 195 
 TYR   0.010   0.001   TYR A  38 
 ARG   0.006   0.001   ARG B 121 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 1.010 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9421 (mtp85) cc_final: 0.9053 (ttm110)
REVERT: B   42 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8580 (ttmm)
REVERT: B  100 ARG cc_start: 0.9508 (mtp85) cc_final: 0.9246 (ttm-80)
REVERT: B  113 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7813 (ttp-110)
REVERT: B  153 MET cc_start: 0.9133 (ttp) cc_final: 0.8809 (ttp)
REVERT: C  100 ARG cc_start: 0.9479 (mtp85) cc_final: 0.9103 (ttm110)
REVERT: C  181 THR cc_start: 0.9010 (t) cc_final: 0.8798 (t)
REVERT: D  100 ARG cc_start: 0.9371 (ttm-80) cc_final: 0.9148 (ttm-80)
REVERT: D  113 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8480 (ttp-110)
REVERT: E   26 MET cc_start: 0.9032 (mtm) cc_final: 0.8720 (mtm)
REVERT: E  100 ARG cc_start: 0.9427 (mtp85) cc_final: 0.9065 (ttm110)
REVERT: E  113 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7960 (ttp-110)
  outliers start: 35
  outliers final: 20
  residues processed: 143
  average time/residue: 0.3348
  time to fit residues: 59.0772
Evaluate side-chains
  133 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue  113 ARG
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   60 MET
Chi-restraints excluded: chain D residue  113 ARG
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  113 ARG
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  166 THR
Chi-restraints excluded: chain E residue  179 ILE
Chi-restraints excluded: chain E residue  199 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.075928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.053852 restraints weight = 20945.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 3.07
r_work: 0.2754 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8535  Z= 0.207
  Angle     :  0.533   6.464  11555  Z= 0.263
  Chirality :  0.035   0.108   1340
  Planarity :  0.003   0.023   1450
  Dihedral  :  4.099  40.196   1162
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.31 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.22 (0.26), residues: 1070
  helix:  2.97 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop :  0.11 (0.66), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  37 
 HIS   0.004   0.001   HIS E  56 
 PHE   0.015   0.001   PHE B  87 
 TYR   0.010   0.001   TYR C 142 
 ARG   0.006   0.001   ARG A  51 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9410 (mtp85) cc_final: 0.9209 (ttm-80)
REVERT: A  153 MET cc_start: 0.9049 (ttp) cc_final: 0.8770 (ttp)
REVERT: B  153 MET cc_start: 0.9117 (ttp) cc_final: 0.8835 (ttp)
REVERT: C  181 THR cc_start: 0.9026 (t) cc_final: 0.8806 (t)
REVERT: E  100 ARG cc_start: 0.9417 (mtp85) cc_final: 0.9168 (ttm-80)
  outliers start: 31
  outliers final: 22
  residues processed: 133
  average time/residue: 0.2725
  time to fit residues: 46.4303
Evaluate side-chains
  126 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue   60 MET
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  166 THR
Chi-restraints excluded: chain E residue  199 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 80 optimal weight:    0.4980
   chunk 90 optimal weight:    5.9990
   chunk 104 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 49 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   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 = 0.3448 r_free = 0.3448 target = 0.075318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.053140 restraints weight = 21262.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 3.11
r_work: 0.2743 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8535  Z= 0.216
  Angle     :  0.539   6.927  11555  Z= 0.264
  Chirality :  0.035   0.109   1340
  Planarity :  0.003   0.023   1450
  Dihedral  :  3.251  12.465   1150
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.31 %
    Favored  : 81.83 %
  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:  4.13 (0.26), residues: 1070
  helix:  2.90 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.83 (0.64), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 150 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.009   0.001   PHE D 195 
 TYR   0.011   0.001   TYR B  38 
 ARG   0.006   0.001   ARG E  51 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9130 (ttp) cc_final: 0.8797 (ttp)
REVERT: C  153 MET cc_start: 0.9003 (ttp) cc_final: 0.8681 (ttp)
REVERT: C  181 THR cc_start: 0.9097 (t) cc_final: 0.8888 (t)
  outliers start: 25
  outliers final: 23
  residues processed: 128
  average time/residue: 0.3144
  time to fit residues: 51.4678
Evaluate side-chains
  127 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  179 ILE
Chi-restraints excluded: chain D residue   49 LYS
Chi-restraints excluded: chain D residue   60 MET
Chi-restraints excluded: chain D residue  108 ILE
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  166 THR
Chi-restraints excluded: chain E residue  199 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0000
   chunk 0 optimal weight:    6.9990
   chunk 102 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 91 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.5184

-------------------------------------------------------------------------------
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 = 0.3475 r_free = 0.3475 target = 0.076651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.054704 restraints weight = 21205.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 3.11
r_work: 0.2788 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.4398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8535  Z= 0.156
  Angle     :  0.510   7.823  11555  Z= 0.249
  Chirality :  0.034   0.108   1340
  Planarity :  0.003   0.027   1450
  Dihedral  :  3.097  11.103   1150
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.46 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.59 (0.26), residues: 1070
  helix:  3.19 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop :  0.50 (0.64), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 150 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.007   0.001   PHE B  57 
 TYR   0.009   0.001   TYR C 142 
 ARG   0.007   0.001   ARG D  51 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.051 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9150 (ttp) cc_final: 0.8818 (ttp)
REVERT: B  153 MET cc_start: 0.9085 (ttp) cc_final: 0.8773 (ttp)
REVERT: C  153 MET cc_start: 0.9009 (ttp) cc_final: 0.8666 (ttp)
REVERT: C  181 THR cc_start: 0.9027 (t) cc_final: 0.8786 (t)
  outliers start: 14
  outliers final: 13
  residues processed: 123
  average time/residue: 0.3458
  time to fit residues: 56.2001
Evaluate side-chains
  114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  179 ILE
Chi-restraints excluded: chain D residue   60 MET
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  166 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3460 r_free = 0.3460 target = 0.075812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.053619 restraints weight = 21503.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 3.14
r_work: 0.2757 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.4409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8535  Z= 0.199
  Angle     :  0.543   8.184  11555  Z= 0.263
  Chirality :  0.035   0.107   1340
  Planarity :  0.003   0.025   1450
  Dihedral  :  3.073  11.760   1150
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.77 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.36 (0.26), residues: 1070
  helix:  3.05 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.66 (0.64), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 150 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.007   0.001   PHE B  57 
 TYR   0.012   0.001   TYR C 128 
 ARG   0.007   0.001   ARG D  51 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.702 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9105 (ttp) cc_final: 0.8809 (ttp)
REVERT: B  153 MET cc_start: 0.9088 (ttp) cc_final: 0.8873 (ttt)
REVERT: C  153 MET cc_start: 0.9028 (ttp) cc_final: 0.8694 (ttp)
REVERT: C  181 THR cc_start: 0.9038 (t) cc_final: 0.8811 (t)
  outliers start: 20
  outliers final: 20
  residues processed: 121
  average time/residue: 0.3788
  time to fit residues: 61.8891
Evaluate side-chains
  123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 2.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  179 ILE
Chi-restraints excluded: chain D residue   60 MET
Chi-restraints excluded: chain D residue  108 ILE
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  166 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   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 = 0.3425 r_free = 0.3425 target = 0.072568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.051663 restraints weight = 21935.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.89
r_work: 0.2768 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.4467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8535  Z= 0.184
  Angle     :  0.538   8.655  11555  Z= 0.261
  Chirality :  0.034   0.108   1340
  Planarity :  0.003   0.027   1450
  Dihedral  :  3.052  11.476   1150
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.89 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.42 (0.26), residues: 1070
  helix:  3.03 (0.16), residues: 1015
  sheet:  None (None), residues: 0
  loop : -0.13 (0.73), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 150 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.007   0.001   PHE D  57 
 TYR   0.013   0.001   TYR C 128 
 ARG   0.007   0.001   ARG A  51 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9208 (ttp) cc_final: 0.8849 (ttp)
REVERT: B  153 MET cc_start: 0.9135 (ttp) cc_final: 0.8901 (ttt)
REVERT: C  153 MET cc_start: 0.9094 (ttp) cc_final: 0.8747 (ttp)
REVERT: C  181 THR cc_start: 0.9132 (t) cc_final: 0.8907 (t)
  outliers start: 19
  outliers final: 18
  residues processed: 120
  average time/residue: 0.2513
  time to fit residues: 39.6641
Evaluate side-chains
  122 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  179 ILE
Chi-restraints excluded: chain D residue   60 MET
Chi-restraints excluded: chain D residue  108 ILE
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  166 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 60 optimal weight:    0.1980
   chunk 91 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.073747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.052170 restraints weight = 22543.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 3.07
r_work: 0.2786 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8535  Z= 0.179
  Angle     :  0.544   8.820  11555  Z= 0.262
  Chirality :  0.034   0.107   1340
  Planarity :  0.003   0.029   1450
  Dihedral  :  3.017  10.826   1150
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.77 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  4.50 (0.26), residues: 1070
  helix:  3.08 (0.16), residues: 1015
  sheet:  None (None), residues: 0
  loop : -0.12 (0.72), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 150 
 HIS   0.003   0.001   HIS E  56 
 PHE   0.010   0.001   PHE D  87 
 TYR   0.014   0.001   TYR C 128 
 ARG   0.007   0.001   ARG C  51 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4176.21 seconds
wall clock time: 75 minutes 20.64 seconds (4520.64 seconds total)