Starting phenix.real_space_refine
on Mon Sep 23 12:26:02 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/09_2024/8olq_16961.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/09_2024/8olq_16961.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/09_2024/8olq_16961.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/09_2024/8olq_16961.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/09_2024/8olq_16961.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/09_2024/8olq_16961.cif"
  }
  resolution = 4.0
  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=   1.000
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
     C     800      2.51       5
     N     235      2.21       5
     O     225      1.98       5
     H    1185      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 2445
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 489
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 1.65, per 1000 atoms: 0.67
  Number of scatterers: 2445
  At special positions: 0
  Unit cell: (55.752, 43.632, 46.864, 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)
     O     225      8.00
     N     235      7.00
     C     800      6.00
     H    1185      1.00
    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: 0.65
  Conformation dependent library (CDL) restraints added in 170.9 milliseconds
  

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  280

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 5 sheets defined
      0.0% alpha, 34.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
      removed outlier: 6.755A  pdb=" N   GLU A   3 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   HIS B   6 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ARG A   5 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   GLU C   3 " --> pdb=" O   PHE D   4 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   HIS D   6 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG C   5 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13
      removed outlier: 6.701A  pdb=" N   VAL A  12 " --> pdb=" O   HIS B  13 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL B  12 " --> pdb=" O   HIS C  13 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL C  12 " --> pdb=" O   HIS D  13 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL D  12 " --> pdb=" O   HIS E  13 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 16 through 19
      removed outlier: 6.925A  pdb=" N   LEU A  17 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   LEU B  17 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   LEU C  17 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LEU D  17 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 27
      removed outlier: 5.899A  pdb=" N   GLY A  25 " --> pdb=" O   SER B  26 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   GLY B  25 " --> pdb=" O   SER C  26 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   GLY C  25 " --> pdb=" O   SER D  26 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   GLY D  25 " --> pdb=" O   SER E  26 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 31 through 32
      removed outlier: 6.446A  pdb=" N   ILE A  31 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ILE B  31 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE C  31 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ILE D  31 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    16 hydrogen bonds defined for protein.
    48 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.78

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        0.84 -     0.98: 1185
        0.98 -     1.12: 0
        1.12 -     1.26: 210
        1.26 -     1.40: 390
        1.40 -     1.54: 690
  Bond restraints: 2475
  Sorted by residual:
  bond pdb=" N   ALA B   2 "
       pdb=" CA  ALA B   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   ALA C   2 "
       pdb=" CA  ALA C   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   ALA E   2 "
       pdb=" CA  ALA E   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.89e+00
  bond pdb=" N   ALA D   2 "
       pdb=" CA  ALA D   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  bond pdb=" N   ALA A   2 "
       pdb=" CA  ALA A   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  ... (remaining 2470 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 4130
        0.91 -     1.81: 245
        1.81 -     2.72: 25
        2.72 -     3.63: 0
        3.63 -     4.53: 5
  Bond angle restraints: 4405
  Sorted by residual:
  angle pdb=" CA  ALA E   2 "
        pdb=" N   ALA E   2 "
        pdb=" H   ALA E   2 "
      ideal   model   delta    sigma   weight residual
     114.00  109.47    4.53 3.00e+00 1.11e-01 2.28e+00
  angle pdb=" CA  ALA A   2 "
        pdb=" N   ALA A   2 "
        pdb=" H   ALA A   2 "
      ideal   model   delta    sigma   weight residual
     114.00  109.49    4.51 3.00e+00 1.11e-01 2.26e+00
  angle pdb=" CA  SER A   8 "
        pdb=" C   SER A   8 "
        pdb=" N   GLY A   9 "
      ideal   model   delta    sigma   weight residual
     115.51  117.46   -1.95 1.30e+00 5.92e-01 2.26e+00
  angle pdb=" CA  ALA B   2 "
        pdb=" N   ALA B   2 "
        pdb=" H   ALA B   2 "
      ideal   model   delta    sigma   weight residual
     114.00  109.50    4.50 3.00e+00 1.11e-01 2.25e+00
  angle pdb=" CA  ALA C   2 "
        pdb=" N   ALA C   2 "
        pdb=" H   ALA C   2 "
      ideal   model   delta    sigma   weight residual
     114.00  109.50    4.50 3.00e+00 1.11e-01 2.25e+00
  ... (remaining 4400 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.99: 1060
       11.99 -    23.97: 75
       23.97 -    35.96: 5
       35.96 -    47.95: 15
       47.95 -    59.93: 10
  Dihedral angle restraints: 1165
    sinusoidal: 585
      harmonic: 580
  Sorted by residual:
  dihedral pdb=" CA  ASP A   7 "
           pdb=" C   ASP A   7 "
           pdb=" N   SER A   8 "
           pdb=" CA  SER A   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.64   10.36     0      5.00e+00 4.00e-02 4.29e+00
  dihedral pdb=" CA  ASP C   7 "
           pdb=" C   ASP C   7 "
           pdb=" N   SER C   8 "
           pdb=" CA  SER C   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.66   10.34     0      5.00e+00 4.00e-02 4.28e+00
  dihedral pdb=" CA  ASP B   7 "
           pdb=" C   ASP B   7 "
           pdb=" N   SER B   8 "
           pdb=" CA  SER B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  169.69   10.31     0      5.00e+00 4.00e-02 4.26e+00
  ... (remaining 1162 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.025: 99
       0.025 -    0.050: 36
       0.050 -    0.075: 15
       0.075 -    0.100: 5
       0.100 -    0.124: 15
  Chirality restraints: 170
  Sorted by residual:
  chirality pdb=" CA  VAL E  12 "
            pdb=" N   VAL E  12 "
            pdb=" C   VAL E  12 "
            pdb=" CB  VAL E  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  VAL A  12 "
            pdb=" N   VAL A  12 "
            pdb=" C   VAL A  12 "
            pdb=" CB  VAL A  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  ILE A  32 "
            pdb=" N   ILE A  32 "
            pdb=" C   ILE A  32 "
            pdb=" CB  ILE A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 167 not shown)

  Planarity restraints: 385
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  23 "    0.002 2.00e-02 2.50e+03   2.08e-03 6.47e-02
        pdb=" CG  ASN D  23 "   -0.004 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  23 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  23 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN D  23 "   -0.000 2.00e-02 2.50e+03
        pdb="HD22 ASN D  23 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C  23 "    0.002 2.00e-02 2.50e+03   2.00e-03 6.02e-02
        pdb=" CG  ASN C  23 "   -0.004 2.00e-02 2.50e+03
        pdb=" OD1 ASN C  23 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN C  23 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN C  23 "   -0.000 2.00e-02 2.50e+03
        pdb="HD22 ASN C  23 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  23 "   -0.001 2.00e-02 2.50e+03   1.84e-03 5.09e-02
        pdb=" CG  ASN B  23 "    0.004 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  23 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  23 "   -0.000 2.00e-02 2.50e+03
        pdb="HD21 ASN B  23 "   -0.000 2.00e-02 2.50e+03
        pdb="HD22 ASN B  23 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 382 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.24: 250
        2.24 -     2.81: 5059
        2.81 -     3.37: 5625
        3.37 -     3.94: 8026
        3.94 -     4.50: 11867
  Nonbonded interactions: 30827
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D  11 "
            pdb=" HG  SER E  26 "
     model   vdw
     1.677 2.450
  nonbonded pdb=" OE2 GLU B  11 "
            pdb=" HG  SER C  26 "
     model   vdw
     1.721 2.450
  nonbonded pdb=" O   GLN A  22 "
            pdb=" H   ASN B  23 "
     model   vdw
     1.749 2.450
  nonbonded pdb="HD21 ASN B  23 "
            pdb=" OD1 ASN B  27 "
     model   vdw
     1.756 2.450
  nonbonded pdb="HD21 ASN A  23 "
            pdb=" OD1 ASN A  27 "
     model   vdw
     1.756 2.450
  ... (remaining 30822 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: 0.00
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  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:             0.040
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.230
  Find NCS groups from input model:        0.050
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
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      :  0.003   0.033   1290  Z= 0.192
  Angle     :  0.489   2.040   1725  Z= 0.321
  Chirality :  0.048   0.124    170
  Planarity :  0.001   0.003    230
  Dihedral  :  7.644  23.346    440
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.70), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.38 (0.53), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B   6 
 PHE   0.003   0.001   PHE D  19 
 TYR   0.002   0.001   TYR B  10 
 ARG   0.000   0.000   ARG E   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.2260
  time to fit residues: 11.9481
Evaluate side-chains
  37 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   1290  Z= 0.146
  Angle     :  0.482   4.661   1725  Z= 0.273
  Chirality :  0.051   0.130    170
  Planarity :  0.002   0.020    230
  Dihedral  :  4.595  15.453    165
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.80 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.33 (0.58), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.00 (0.44), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A   6 
 PHE   0.012   0.002   PHE E  20 
 TYR   0.003   0.001   TYR C  10 
 ARG   0.002   0.000   ARG D   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 39
  average time/residue: 0.1362
  time to fit residues: 6.6049
Evaluate side-chains
  38 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 6 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 0 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   1290  Z= 0.105
  Angle     :  0.412   2.583   1725  Z= 0.246
  Chirality :  0.049   0.129    170
  Planarity :  0.002   0.009    230
  Dihedral  :  4.349  13.117    165
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 20.00 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.57), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.29 (0.43), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B   6 
 PHE   0.010   0.001   PHE E  20 
 TYR   0.004   0.001   TYR C  10 
 ARG   0.001   0.000   ARG D   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 41
  average time/residue: 0.1285
  time to fit residues: 6.5406
Evaluate side-chains
  40 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   1290  Z= 0.181
  Angle     :  0.439   2.299   1725  Z= 0.263
  Chirality :  0.050   0.126    170
  Planarity :  0.002   0.008    230
  Dihedral  :  4.671  13.740    165
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.20 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.02 (0.57), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.43), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C   6 
 PHE   0.006   0.001   PHE E  19 
 TYR   0.005   0.002   TYR E  10 
 ARG   0.001   0.000   ARG A   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 37
  average time/residue: 0.1186
  time to fit residues: 5.4369
Evaluate side-chains
  38 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.4619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1290  Z= 0.118
  Angle     :  0.396   1.859   1725  Z= 0.240
  Chirality :  0.050   0.127    170
  Planarity :  0.001   0.006    230
  Dihedral  :  4.417  13.302    165
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.00 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.08 (0.56), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.58 (0.43), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C   6 
 PHE   0.007   0.001   PHE E  20 
 TYR   0.004   0.001   TYR E  10 
 ARG   0.001   0.000   ARG E   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1277
  time to fit residues: 5.8568
Evaluate side-chains
  39 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0770
   chunk 12 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.9944

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.4998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1290  Z= 0.164
  Angle     :  0.426   1.983   1725  Z= 0.256
  Chirality :  0.051   0.127    170
  Planarity :  0.001   0.005    230
  Dihedral  :  4.541  13.846    165
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.40 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.14 (0.58), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.62 (0.44), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C   6 
 PHE   0.008   0.001   PHE E  19 
 TYR   0.005   0.002   TYR E  10 
 ARG   0.001   0.000   ARG A   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.7094 (m-80) cc_final: 0.6838 (m-80)
  outliers start: 4
  outliers final: 3
  residues processed: 37
  average time/residue: 0.1276
  time to fit residues: 5.8492
Evaluate side-chains
  39 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.5239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   1290  Z= 0.182
  Angle     :  0.427   2.031   1725  Z= 0.260
  Chirality :  0.050   0.125    170
  Planarity :  0.001   0.006    230
  Dihedral  :  4.656  14.880    165
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.00 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.57), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.43), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C   6 
 PHE   0.008   0.001   PHE E  19 
 TYR   0.005   0.002   TYR B  10 
 ARG   0.001   0.000   ARG E   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.7190 (m-80) cc_final: 0.6968 (m-80)
REVERT: C   11 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7630 (mt-10)
REVERT: D   19 PHE cc_start: 0.7253 (m-80) cc_final: 0.7003 (m-10)
  outliers start: 4
  outliers final: 3
  residues processed: 35
  average time/residue: 0.1286
  time to fit residues: 5.5867
Evaluate side-chains
  38 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 0 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.5263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1290  Z= 0.109
  Angle     :  0.389   1.860   1725  Z= 0.237
  Chirality :  0.050   0.127    170
  Planarity :  0.001   0.004    230
  Dihedral  :  4.289  13.456    165
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.80 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.59), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.45), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C   6 
 PHE   0.006   0.001   PHE E  19 
 TYR   0.005   0.001   TYR B  10 
 ARG   0.001   0.000   ARG D   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.7171 (m-80) cc_final: 0.6951 (m-80)
REVERT: C   11 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7635 (mt-10)
  outliers start: 4
  outliers final: 3
  residues processed: 35
  average time/residue: 0.1284
  time to fit residues: 5.6434
Evaluate side-chains
  38 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.5348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1290  Z= 0.112
  Angle     :  0.380   1.811   1725  Z= 0.231
  Chirality :  0.050   0.126    170
  Planarity :  0.001   0.004    230
  Dihedral  :  4.141  13.472    165
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.40 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.94 (0.61), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C   6 
 PHE   0.006   0.001   PHE E  19 
 TYR   0.004   0.001   TYR B  10 
 ARG   0.000   0.000   ARG D   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 PHE cc_start: 0.7056 (m-80) cc_final: 0.6829 (m-80)
REVERT: C   11 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7565 (mt-10)
  outliers start: 4
  outliers final: 3
  residues processed: 35
  average time/residue: 0.1297
  time to fit residues: 5.6161
Evaluate side-chains
  38 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0870
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.5556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   1290  Z= 0.237
  Angle     :  0.463   2.023   1725  Z= 0.280
  Chirality :  0.051   0.123    170
  Planarity :  0.002   0.006    230
  Dihedral  :  4.695  15.086    165
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.60 %
    Favored  : 79.20 %
  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: -2.35 (0.58), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.44), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C   6 
 PHE   0.007   0.001   PHE C  20 
 TYR   0.007   0.002   TYR B  10 
 ARG   0.001   0.000   ARG E   5 

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

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

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  300 Ramachandran restraints generated.
    150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 PHE cc_start: 0.7183 (m-80) cc_final: 0.6979 (m-80)
REVERT: C   11 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7649 (mt-10)
REVERT: D   19 PHE cc_start: 0.7263 (m-80) cc_final: 0.6964 (m-10)
  outliers start: 4
  outliers final: 3
  residues processed: 34
  average time/residue: 0.1351
  time to fit residues: 5.6854
Evaluate side-chains
  37 residues out of total 125 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain C residue   11 GLU
Chi-restraints excluded: chain D residue   31 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** C  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.151965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.131229 restraints weight = 6072.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.135901 restraints weight = 3087.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.139392 restraints weight = 1881.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.5516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   1290  Z= 0.110
  Angle     :  0.383   1.925   1725  Z= 0.233
  Chirality :  0.050   0.128    170
  Planarity :  0.001   0.004    230
  Dihedral  :  4.232  14.500    165
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.60 %
    Favored  : 79.20 %
  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: -2.19 (0.60), residues: 150
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C   6 
 PHE   0.005   0.001   PHE E  19 
 TYR   0.004   0.001   TYR B  10 
 ARG   0.001   0.000   ARG E   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1973.73 seconds
wall clock time: 34 minutes 56.32 seconds (2096.32 seconds total)