Starting phenix.real_space_refine
on Wed Feb 12 21:13:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9avi_43902/02_2025/9avi_43902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9avi_43902/02_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_43902/02_2025/9avi_43902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9avi_43902/02_2025/9avi_43902.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9avi_43902/02_2025/9avi_43902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9avi_43902/02_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-5592/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: 4.39, per 1000 atoms: 0.52
  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: 2.05
  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: 0.78
  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: 2.31

  Time building geometry restraints manager: 2.36 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: 0.07
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:             3.890
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     20.780
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.090
-------------------------------------------------------------------------------
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  : 1.052 
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: 0.3124
  time to fit residues: 72.7002
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  : 1.037 
-------------------------------------------------------------------------------
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 = 37)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.053898 restraints weight = 21559.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.86
r_work: 0.2792 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
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  : 0.996 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9509 (mtp85) cc_final: 0.9266 (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: 0.9309 (ttm-80)
REVERT: B  113 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7991 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9521 (mtp85) cc_final: 0.9201 (ttm110)
REVERT: C  113 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8292 (ttp-110)
REVERT: D  113 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8333 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9499 (mtp85) cc_final: 0.9213 (ttm110)
REVERT: E  113 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8161 (ttp-110)
  outliers start: 22
  outliers final: 13
  residues processed: 143
  average time/residue: 0.3343
  time to fit residues: 58.6669
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  : 0.996 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.072479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.051640 restraints weight = 22138.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 2.89
r_work: 0.2748 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8535  Z= 0.246
  Angle     :  0.580   7.284  11555  Z= 0.293
  Chirality :  0.037   0.110   1340
  Planarity :  0.004   0.027   1450
  Dihedral  :  5.766  59.787   1173
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 12.69 %
    Favored  : 83.66 %
  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:  2.61 (0.25), residues: 1070
  helix:  1.92 (0.16), residues: 985
  sheet:  None (None), residues: 0
  loop : -0.35 (0.66), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  37 
 HIS   0.003   0.001   HIS D 197 
 PHE   0.011   0.001   PHE B 195 
 TYR   0.012   0.001   TYR C 142 
 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
  163 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9504 (mtp85) cc_final: 0.9267 (ttm110)
REVERT: A  113 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8013 (ttp-110)
REVERT: B  100 ARG cc_start: 0.9526 (mtp85) cc_final: 0.9205 (ttm110)
REVERT: B  113 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8058 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9521 (mtp85) cc_final: 0.9177 (ttm110)
REVERT: C  113 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8152 (ttp-110)
REVERT: D  113 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8599 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9513 (mtp85) cc_final: 0.9185 (ttm110)
REVERT: E  113 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8119 (ttp-110)
  outliers start: 32
  outliers final: 15
  residues processed: 150
  average time/residue: 0.3260
  time to fit residues: 60.3434
Evaluate side-chains
  139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
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  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  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:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    0.4980
   chunk 13 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 74 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   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 = 0.3465 r_free = 0.3465 target = 0.076576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.054678 restraints weight = 21119.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 3.10
r_work: 0.2776 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8535  Z= 0.174
  Angle     :  0.513   6.590  11555  Z= 0.258
  Chirality :  0.035   0.109   1340
  Planarity :  0.003   0.025   1450
  Dihedral  :  5.206  54.537   1170
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 13.83 %
    Favored  : 82.63 %
  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:  3.57 (0.26), residues: 1070
  helix:  2.56 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -0.20 (0.62), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  62 
 HIS   0.004   0.001   HIS E  56 
 PHE   0.008   0.001   PHE C  87 
 TYR   0.011   0.001   TYR A  38 
 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
  159 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9474 (mtp85) cc_final: 0.9115 (ttm110)
REVERT: A  113 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7814 (ttp-110)
REVERT: A  153 MET cc_start: 0.9184 (ttp) cc_final: 0.8788 (ttp)
REVERT: B   42 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8557 (ttmm)
REVERT: B  100 ARG cc_start: 0.9511 (mtp85) cc_final: 0.9250 (ttm110)
REVERT: B  113 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7922 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9488 (mtp85) cc_final: 0.9162 (ttm110)
REVERT: C  113 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7999 (ttp-110)
REVERT: D  100 ARG cc_start: 0.9480 (ttm-80) cc_final: 0.9247 (ttm-80)
REVERT: D  113 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8417 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9474 (mtp85) cc_final: 0.8966 (ttm110)
REVERT: E  113 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8013 (ttp-110)
  outliers start: 31
  outliers final: 18
  residues processed: 144
  average time/residue: 0.3857
  time to fit residues: 66.9263
Evaluate side-chains
  138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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 E residue  113 ARG
Chi-restraints excluded: chain E residue  119 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 63 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 78 optimal weight:    9.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.076125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.053951 restraints weight = 20944.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 3.10
r_work: 0.2753 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3881

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= 0.192
  Angle     :  0.520   6.359  11555  Z= 0.258
  Chirality :  0.035   0.108   1340
  Planarity :  0.003   0.024   1450
  Dihedral  :  4.818  45.785   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 :  3.89 %
    Allowed  : 14.06 %
    Favored  : 82.06 %
  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:  3.92 (0.26), residues: 1070
  helix:  2.78 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -0.09 (0.65), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  62 
 HIS   0.004   0.001   HIS E  56 
 PHE   0.008   0.001   PHE D 195 
 TYR   0.010   0.001   TYR C 142 
 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
  149 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9419 (mtp85) cc_final: 0.9056 (ttm110)
REVERT: A  113 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7954 (ttp-110)
REVERT: A  153 MET cc_start: 0.9168 (ttp) cc_final: 0.8844 (ttp)
REVERT: B   42 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8587 (ttmm)
REVERT: B  100 ARG cc_start: 0.9496 (mtp85) cc_final: 0.9207 (ttm110)
REVERT: B  113 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7854 (ttp-110)
REVERT: C  100 ARG cc_start: 0.9473 (mtp85) cc_final: 0.9175 (ttm110)
REVERT: D  113 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8511 (ttp-110)
REVERT: E  100 ARG cc_start: 0.9416 (mtp85) cc_final: 0.9108 (ttm110)
REVERT: E  113 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7955 (ttp-110)
  outliers start: 34
  outliers final: 19
  residues processed: 139
  average time/residue: 0.3277
  time to fit residues: 56.3880
Evaluate side-chains
  131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
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  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  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  119 LEU
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 20 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0870
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.076722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.054668 restraints weight = 20811.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2955 rms_B_bonded: 3.10
r_work: 0.2772 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.4114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8535  Z= 0.162
  Angle     :  0.506   6.528  11555  Z= 0.250
  Chirality :  0.034   0.107   1340
  Planarity :  0.003   0.024   1450
  Dihedral  :  4.273  37.727   1166
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.20 %
    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:  4.18 (0.26), residues: 1070
  helix:  2.94 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop :  0.09 (0.65), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  62 
 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
  141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A  153 MET cc_start: 0.9175 (ttp) cc_final: 0.8887 (ttp)
REVERT: B   42 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8598 (ttmm)
REVERT: E   26 MET cc_start: 0.9039 (mtm) cc_final: 0.8616 (mtm)
REVERT: E  100 ARG cc_start: 0.9406 (mtp85) cc_final: 0.9171 (ttm-80)
  outliers start: 25
  outliers final: 21
  residues processed: 133
  average time/residue: 0.2992
  time to fit residues: 50.1131
Evaluate side-chains
  125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
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 B residue   60 MET
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  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  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
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:    0.9980
   chunk 80 optimal weight:    0.2980
   chunk 90 optimal weight:    5.9990
   chunk 104 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   chunk 49 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3474 r_free = 0.3474 target = 0.076696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.054671 restraints weight = 21066.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 3.11
r_work: 0.2777 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4250

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= 0.165
  Angle     :  0.512   7.102  11555  Z= 0.251
  Chirality :  0.034   0.107   1340
  Planarity :  0.003   0.026   1450
  Dihedral  :  3.151  11.850   1150
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.89 %
    Favored  : 81.37 %
  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:  4.31 (0.26), residues: 1070
  helix:  3.01 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop :  0.33 (0.64), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  62 
 HIS   0.005   0.001   HIS E  56 
 PHE   0.007   0.001   PHE B  57 
 TYR   0.010   0.001   TYR A  38 
 ARG   0.007   0.001   ARG B  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
  137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 1.012 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9368 (ttm-80) cc_final: 0.9167 (ttm110)
REVERT: A  153 MET cc_start: 0.9160 (ttp) cc_final: 0.8835 (ttp)
REVERT: B   42 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8606 (ttmm)
  outliers start: 24
  outliers final: 22
  residues processed: 130
  average time/residue: 0.2700
  time to fit residues: 45.1057
Evaluate side-chains
  127 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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 B residue   60 MET
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  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  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  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 101 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 102 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9980
   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 = 0.3422 r_free = 0.3422 target = 0.072425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.051427 restraints weight = 22068.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.91
r_work: 0.2760 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8535  Z= 0.187
  Angle     :  0.527   7.917  11555  Z= 0.257
  Chirality :  0.034   0.107   1340
  Planarity :  0.003   0.025   1450
  Dihedral  :  3.121  11.840   1150
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.38
  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 (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:  4.16 (0.26), residues: 1070
  helix:  2.92 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.71 (0.64), residues: 65

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   0.007   0.001   PHE B  57 
 TYR   0.010   0.001   TYR E  38 
 ARG   0.007   0.001   ARG E  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
  132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.9329 (ttm-80) cc_final: 0.9121 (ttm110)
REVERT: A  153 MET cc_start: 0.9248 (ttp) cc_final: 0.8896 (ttp)
  outliers start: 24
  outliers final: 22
  residues processed: 123
  average time/residue: 0.2596
  time to fit residues: 41.6236
Evaluate side-chains
  125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
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   60 MET
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 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  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  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:    2.9990
   chunk 43 optimal weight:    0.0010
   chunk 75 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.6386

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.072905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.051862 restraints weight = 22087.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.92
r_work: 0.2770 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.4429

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= 0.172
  Angle     :  0.522   8.238  11555  Z= 0.254
  Chirality :  0.034   0.107   1340
  Planarity :  0.003   0.024   1450
  Dihedral  :  3.050  10.946   1150
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.09 %
    Favored  : 82.29 %
  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:  4.30 (0.26), residues: 1070
  helix:  3.00 (0.17), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.58 (0.65), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  62 
 HIS   0.002   0.001   HIS E 197 
 PHE   0.007   0.001   PHE D  87 
 TYR   0.012   0.001   TYR B  38 
 ARG   0.006   0.001   ARG E  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
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A   73 ASN cc_start: 0.9547 (m-40) cc_final: 0.9338 (m-40)
REVERT: A  153 MET cc_start: 0.9230 (ttp) cc_final: 0.8845 (ttp)
  outliers start: 23
  outliers final: 23
  residues processed: 123
  average time/residue: 0.2639
  time to fit residues: 42.6304
Evaluate side-chains
  125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
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   60 MET
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 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  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain D residue  199 THR
Chi-restraints excluded: chain E residue  108 ILE
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 102 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 28 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.3426 r_free = 0.3426 target = 0.072557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.051181 restraints weight = 22423.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.94
r_work: 0.2762 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8535  Z= 0.179
  Angle     :  0.539   9.163  11555  Z= 0.262
  Chirality :  0.034   0.107   1340
  Planarity :  0.003   0.027   1450
  Dihedral  :  3.030  10.968   1150
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.50
  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 (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:  3.04 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.57 (0.64), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D 150 
 HIS   0.002   0.001   HIS E 197 
 PHE   0.007   0.001   PHE E  57 
 TYR   0.010   0.001   TYR A  38 
 ARG   0.007   0.001   ARG C  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
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A   73 ASN cc_start: 0.9551 (m-40) cc_final: 0.9342 (m-40)
REVERT: A  153 MET cc_start: 0.9216 (ttp) cc_final: 0.8831 (ttp)
REVERT: C  153 MET cc_start: 0.9049 (ttt) cc_final: 0.8765 (ttt)
  outliers start: 24
  outliers final: 22
  residues processed: 122
  average time/residue: 0.2455
  time to fit residues: 39.7760
Evaluate side-chains
  128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
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   60 MET
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 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  148 THR
Chi-restraints excluded: chain D residue  166 THR
Chi-restraints excluded: chain D residue  199 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 31 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0030
   chunk 91 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 43 optimal weight:    0.1980
   overall best weight:    0.4790

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.074826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.053070 restraints weight = 22414.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 3.05
r_work: 0.2802 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8535  Z= 0.156
  Angle     :  0.522   8.705  11555  Z= 0.253
  Chirality :  0.034   0.108   1340
  Planarity :  0.003   0.029   1450
  Dihedral  :  2.957  10.457   1150
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.66 %
    Favored  : 82.06 %
  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:  4.54 (0.26), residues: 1070
  helix:  3.16 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.49 (0.65), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  62 
 HIS   0.002   0.001   HIS D 197 
 PHE   0.008   0.001   PHE E  87 
 TYR   0.010   0.001   TYR A  38 
 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: 3766.57 seconds
wall clock time: 67 minutes 39.81 seconds (4059.81 seconds total)