Starting phenix.real_space_refine
on Wed Sep 17 11:17:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9avi_43902/09_2025/9avi_43902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9avi_43902/09_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_43902/09_2025/9avi_43902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9avi_43902/09_2025/9avi_43902.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9avi_43902/09_2025/9avi_43902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9avi_43902/09_2025/9avi_43902.cif"
  }
  resolution = 3.02
  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=   0.009
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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:
    B, C, D, E
  Time building chain proxies: 1.33, per 1000 atoms: 0.16
  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: 0.56
  Conformation dependent library (CDL) restraints added in 287.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.13
  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: 1.23

  Time building geometry restraints manager: 0.71 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: 0.01
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:             5.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.550
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.110
-------------------------------------------------------------------------------
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= 0.982
  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 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: -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
 ARG   0.003   0.001   ARG B 116 
 TYR   0.019   0.005   TYR C  47 
 PHE   0.031   0.007   PHE C 195 
 TRP   0.023   0.006   TRP C  62 
 HIS   0.006   0.003   HIS B  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.01285 ( 8535)
  covalent geometry    : angle       1.93652 (11555)
  hydrogen bonds       : bond        0.21174 (  665)
  hydrogen bonds       : angle       8.53968 ( 1995)

*********************** 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  : 0.295 
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: 0.1416
  time to fit residues: 32.8916
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  : 0.232 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.074519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.053092 restraints weight = 22186.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 2.88
r_work: 0.2779 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8535  Z= 0.152
  Angle     :  0.615   7.998  11555  Z= 0.321
  Chirality :  0.038   0.113   1340
  Planarity :  0.005   0.026   1450
  Dihedral  :  7.405  57.484   1207
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.89 %
    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 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:  0.09 (0.24), residues: 1070
  helix:  0.34 (0.15), residues: 985
  sheet:  None (None), residues: 0
  loop : -1.83 (0.57), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  51 
 TYR   0.014   0.002   TYR C 142 
 PHE   0.012   0.001   PHE B  87 
 TRP   0.004   0.001   TRP B 150 
 HIS   0.003   0.001   HIS E 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8535)
  covalent geometry    : angle       0.61490 (11555)
  hydrogen bonds       : bond        0.04262 (  665)
  hydrogen bonds       : angle       3.73593 ( 1995)

*********************** 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
  147 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9513 (mtp85) cc_final: 0.9287 (ttm110)
REVERT: A  113 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7889 (ttp-110)
REVERT: B  100 ARG cc_start: 0.9529 (mtp85) cc_final: 0.9300 (ttm-80)
REVERT: B  113 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7962 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9521 (mtp85) cc_final: 0.9195 (ttm110)
REVERT: C  113 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8313 (ttp-110)
REVERT: D  113 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8309 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9501 (mtp85) cc_final: 0.9206 (ttm110)
REVERT: E  113 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8066 (ttp-110)
  outliers start: 20
  outliers final: 12
  residues processed: 140
  average time/residue: 0.1413
  time to fit residues: 24.1689
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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  166 THR
Chi-restraints excluded: chain C residue  199 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  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 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 76 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.073431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.052583 restraints weight = 21831.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 2.88
r_work: 0.2775 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.3325

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= 0.134
  Angle     :  0.551   7.268  11555  Z= 0.279
  Chirality :  0.035   0.107   1340
  Planarity :  0.004   0.026   1450
  Dihedral  :  5.756  59.787   1174
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.60 %
    Favored  : 83.09 %
  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:  2.64 (0.25), residues: 1070
  helix:  1.94 (0.16), residues: 985
  sheet:  None (None), residues: 0
  loop : -0.35 (0.66), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  51 
 TYR   0.011   0.001   TYR A  38 
 PHE   0.009   0.001   PHE C  87 
 TRP   0.003   0.001   TRP C  62 
 HIS   0.003   0.001   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8535)
  covalent geometry    : angle       0.55114 (11555)
  hydrogen bonds       : bond        0.03704 (  665)
  hydrogen bonds       : angle       3.13046 ( 1995)

*********************** 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
  165 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9515 (mtp85) cc_final: 0.9280 (ttm110)
REVERT: A  113 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7940 (ttp-110)
REVERT: A  208 ASP cc_start: 0.8554 (t0) cc_final: 0.8320 (t0)
REVERT: B  100 ARG cc_start: 0.9536 (mtp85) cc_final: 0.9217 (ttm110)
REVERT: B  113 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8078 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9521 (mtp85) cc_final: 0.9172 (ttm110)
REVERT: C  113 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8112 (ttp-110)
REVERT: D  113 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8509 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9508 (mtp85) cc_final: 0.9174 (ttm110)
REVERT: E  113 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8106 (ttp-110)
  outliers start: 29
  outliers final: 15
  residues processed: 153
  average time/residue: 0.1426
  time to fit residues: 26.6545
Evaluate side-chains
  141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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   49 LYS
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  125 SER
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 62 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.076432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.054461 restraints weight = 21382.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 3.09
r_work: 0.2763 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3679

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= 0.133
  Angle     :  0.528   6.646  11555  Z= 0.264
  Chirality :  0.035   0.109   1340
  Planarity :  0.003   0.024   1450
  Dihedral  :  5.214  55.902   1170
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 13.49 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.59 (0.26), residues: 1070
  helix:  2.57 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -0.19 (0.61), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 121 
 TYR   0.010   0.001   TYR C 142 
 PHE   0.009   0.001   PHE D 195 
 TRP   0.005   0.001   TRP E  62 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8535)
  covalent geometry    : angle       0.52777 (11555)
  hydrogen bonds       : bond        0.03485 (  665)
  hydrogen bonds       : angle       2.92567 ( 1995)

*********************** 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
  162 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 126
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9480 (mtp85) cc_final: 0.9114 (ttm110)
REVERT: A  113 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7815 (ttp-110)
REVERT: A  153 MET cc_start: 0.9177 (ttp) cc_final: 0.8790 (ttp)
REVERT: B  100 ARG cc_start: 0.9526 (mtp85) cc_final: 0.9248 (ttm110)
REVERT: B  113 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7908 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9492 (mtp85) cc_final: 0.9160 (ttm110)
REVERT: C  113 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8011 (ttp-110)
REVERT: D  113 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8422 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9480 (mtp85) cc_final: 0.9192 (ttm110)
REVERT: E  113 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8029 (ttp-110)
  outliers start: 36
  outliers final: 19
  residues processed: 143
  average time/residue: 0.1488
  time to fit residues: 25.9139
Evaluate side-chains
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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  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  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  199 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 = 0.3430 r_free = 0.3430 target = 0.074528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.052150 restraints weight = 21517.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.12
r_work: 0.2710 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8535  Z= 0.193
  Angle     :  0.577   6.559  11555  Z= 0.286
  Chirality :  0.037   0.111   1340
  Planarity :  0.003   0.022   1450
  Dihedral  :  4.937  46.565   1170
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 13.94 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.56 (0.26), residues: 1070
  helix:  2.56 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop : -1.37 (0.57), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  51 
 TYR   0.011   0.002   TYR C 142 
 PHE   0.011   0.001   PHE E 195 
 TRP   0.005   0.001   TRP D  37 
 HIS   0.003   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 8535)
  covalent geometry    : angle       0.57693 (11555)
  hydrogen bonds       : bond        0.03731 (  665)
  hydrogen bonds       : angle       2.98591 ( 1995)

*********************** 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
  152 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 113
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9422 (mtp85) cc_final: 0.9099 (ttm110)
REVERT: A  113 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8003 (ttp-110)
REVERT: A  153 MET cc_start: 0.9148 (ttp) cc_final: 0.8843 (ttp)
REVERT: B   42 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8587 (ttmm)
REVERT: B  113 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7906 (ttp-110)
REVERT: B  153 MET cc_start: 0.9027 (ttp) cc_final: 0.8773 (ttm)
REVERT: C  100 ARG cc_start: 0.9464 (mtp85) cc_final: 0.9131 (ttm110)
REVERT: D  113 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8517 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9471 (mtp85) cc_final: 0.9139 (ttm110)
REVERT: E  113 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7899 (ttp-110)
  outliers start: 39
  outliers final: 24
  residues processed: 138
  average time/residue: 0.1423
  time to fit residues: 24.4727
Evaluate side-chains
  135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
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  199 THR
Chi-restraints excluded: chain B residue  108 ILE
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  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 D residue   60 MET
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  166 THR
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  113 ARG
Chi-restraints excluded: chain E residue  119 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.074293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.051906 restraints weight = 21239.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.10
r_work: 0.2706 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8535  Z= 0.186
  Angle     :  0.577   6.318  11555  Z= 0.284
  Chirality :  0.037   0.112   1340
  Planarity :  0.003   0.021   1450
  Dihedral  :  4.556  40.511   1166
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.00 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.66 (0.26), residues: 1070
  helix:  2.62 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop : -1.21 (0.59), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 121 
 TYR   0.012   0.001   TYR C 142 
 PHE   0.010   0.001   PHE C 195 
 TRP   0.005   0.001   TRP A  37 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 8535)
  covalent geometry    : angle       0.57653 (11555)
  hydrogen bonds       : bond        0.03688 (  665)
  hydrogen bonds       : angle       2.96057 ( 1995)

*********************** 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
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9118 (ttp) cc_final: 0.8831 (ttp)
REVERT: B  153 MET cc_start: 0.9025 (ttp) cc_final: 0.8788 (ttm)
REVERT: E  113 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8113 (ttp-110)
  outliers start: 29
  outliers final: 24
  residues processed: 126
  average time/residue: 0.1287
  time to fit residues: 20.5781
Evaluate side-chains
  126 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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  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  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  108 ILE
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  113 ARG
Chi-restraints excluded: chain E residue  119 LEU
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 18 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0050
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0370
   chunk 40 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.4472

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.076263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.054441 restraints weight = 21218.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 3.10
r_work: 0.2777 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.4210

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= 0.104
  Angle     :  0.505   6.925  11555  Z= 0.250
  Chirality :  0.033   0.107   1340
  Planarity :  0.003   0.025   1450
  Dihedral  :  3.529  34.322   1154
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.11 %
    Favored  : 81.71 %
  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:  4.22 (0.26), residues: 1070
  helix:  2.96 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop :  0.21 (0.63), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 121 
 TYR   0.014   0.001   TYR C 128 
 PHE   0.009   0.001   PHE B  87 
 TRP   0.004   0.001   TRP B 150 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8535)
  covalent geometry    : angle       0.50539 (11555)
  hydrogen bonds       : bond        0.03158 (  665)
  hydrogen bonds       : angle       2.72116 ( 1995)

*********************** 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: 19
    poor density    : 116
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9132 (ttp) cc_final: 0.8810 (ttp)
REVERT: B  153 MET cc_start: 0.8998 (ttp) cc_final: 0.8780 (ttm)
  outliers start: 19
  outliers final: 16
  residues processed: 129
  average time/residue: 0.1513
  time to fit residues: 24.3255
Evaluate side-chains
  118 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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  166 THR
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 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  119 LEU
Chi-restraints excluded: chain E residue  125 SER
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain E residue  166 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.073890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.051428 restraints weight = 21379.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 3.13
r_work: 0.2698 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8535  Z= 0.202
  Angle     :  0.609   7.703  11555  Z= 0.296
  Chirality :  0.037   0.113   1340
  Planarity :  0.003   0.024   1450
  Dihedral  :  3.336  13.110   1150
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.31 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.87 (0.26), residues: 1070
  helix:  2.74 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.95 (0.61), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  51 
 TYR   0.011   0.002   TYR A 142 
 PHE   0.011   0.001   PHE B  87 
 TRP   0.006   0.001   TRP D  37 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 8535)
  covalent geometry    : angle       0.60905 (11555)
  hydrogen bonds       : bond        0.03645 (  665)
  hydrogen bonds       : angle       2.93590 ( 1995)

*********************** 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
  131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9110 (ttp) cc_final: 0.8811 (ttp)
  outliers start: 24
  outliers final: 19
  residues processed: 122
  average time/residue: 0.1327
  time to fit residues: 20.7582
Evaluate side-chains
  121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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  108 ILE
Chi-restraints excluded: chain B residue  114 ILE
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 D residue   49 LYS
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  108 ILE
Chi-restraints excluded: chain E residue  119 LEU
Chi-restraints excluded: chain E residue  148 THR
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 44 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 87 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3445 r_free = 0.3445 target = 0.074944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.052752 restraints weight = 21243.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 3.12
r_work: 0.2736 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.4307

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= 0.129
  Angle     :  0.547   8.207  11555  Z= 0.267
  Chirality :  0.035   0.108   1340
  Planarity :  0.003   0.026   1450
  Dihedral  :  3.235  11.957   1150
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.69 %
    Favored  : 81.49 %
  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:  4.06 (0.26), residues: 1070
  helix:  2.86 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.93 (0.62), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  51 
 TYR   0.015   0.001   TYR C 128 
 PHE   0.007   0.001   PHE B  57 
 TRP   0.004   0.001   TRP A  37 
 HIS   0.005   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8535)
  covalent geometry    : angle       0.54716 (11555)
  hydrogen bonds       : bond        0.03337 (  665)
  hydrogen bonds       : angle       2.76726 ( 1995)

*********************** 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
  121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9107 (ttp) cc_final: 0.8789 (ttp)
  outliers start: 16
  outliers final: 13
  residues processed: 116
  average time/residue: 0.1205
  time to fit residues: 18.3908
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  : 0.369 
-------------------------------------------------------------------------------
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  114 ILE
Chi-restraints excluded: chain B residue  166 THR
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 D residue  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  119 LEU
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 63 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    0.4980
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.3413 r_free = 0.3413 target = 0.073181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.050756 restraints weight = 21554.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 3.13
r_work: 0.2678 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8535  Z= 0.227
  Angle     :  0.647   8.813  11555  Z= 0.315
  Chirality :  0.038   0.114   1340
  Planarity :  0.003   0.024   1450
  Dihedral  :  3.344  12.963   1150
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.80 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.88 (0.26), residues: 1070
  helix:  2.75 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -1.11 (0.59), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  51 
 TYR   0.016   0.002   TYR B 128 
 PHE   0.009   0.001   PHE D 195 
 TRP   0.007   0.001   TRP D  37 
 HIS   0.004   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 8535)
  covalent geometry    : angle       0.64651 (11555)
  hydrogen bonds       : bond        0.03764 (  665)
  hydrogen bonds       : angle       3.02767 ( 1995)

********************** 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
  119 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.348 
Fit side-chains
  outliers start: 17
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1217
  time to fit residues: 18.2353
Evaluate side-chains
  114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
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 B residue  108 ILE
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  166 THR
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 D residue  108 ILE
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain E residue  119 LEU
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 67 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0010
   chunk 69 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.5386

-------------------------------------------------------------------------------
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 = 0.3414 r_free = 0.3414 target = 0.071971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.050893 restraints weight = 21926.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 2.93
r_work: 0.2751 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.4410

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= 0.114
  Angle     :  0.540   8.580  11555  Z= 0.264
  Chirality :  0.034   0.107   1340
  Planarity :  0.003   0.030   1450
  Dihedral  :  3.192  11.393   1150
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.14 %
    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 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:  4.28 (0.26), residues: 1070
  helix:  3.01 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.93 (0.62), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  51 
 TYR   0.019   0.002   TYR C 128 
 PHE   0.006   0.001   PHE C  87 
 TRP   0.004   0.001   TRP D 150 
 HIS   0.005   0.001   HIS E  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8535)
  covalent geometry    : angle       0.54014 (11555)
  hydrogen bonds       : bond        0.03254 (  665)
  hydrogen bonds       : angle       2.73714 ( 1995)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1920.63 seconds
wall clock time: 33 minutes 41.82 seconds (2021.82 seconds total)