Starting phenix.real_space_refine
on Fri Aug 22 12:39:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ol6_16952/08_2025/8ol6_16952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ol6_16952/08_2025/8ol6_16952.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ol6_16952/08_2025/8ol6_16952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ol6_16952/08_2025/8ol6_16952.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ol6_16952/08_2025/8ol6_16952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ol6_16952/08_2025/8ol6_16952.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.428 sd=   1.733
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1470      2.51       5
     N     390      2.21       5
     O     390      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2260
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 226
          Classifications: {'peptide': 31}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 30}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.60, per 1000 atoms: 0.27
  Number of scatterers: 2260
  At special positions: 0
  Unit cell: (73.528, 66.256, 40.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     390      8.00
     N     390      7.00
     C    1470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 145.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  520

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20
      removed outlier: 6.444A  pdb=" N   VAL A  18 " --> pdb=" O   PHE C  19 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   VAL C  18 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   VAL E  18 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL G  18 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 35
      removed outlier: 6.118A  pdb=" N   ILE A  31 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   LEU C  34 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   GLY A  33 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LEU E  34 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   MET C  35 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LEU G  34 " --> pdb=" O   GLY E  33 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   MET E  35 " --> pdb=" O   LEU G  34 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LEU I  34 " --> pdb=" O   GLY G  33 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   MET G  35 " --> pdb=" O   LEU I  34 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41
    Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20
      removed outlier: 6.364A  pdb=" N   VAL B  18 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL D  18 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   VAL F  18 " --> pdb=" O   PHE H  19 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   VAL H  18 " --> pdb=" O   PHE J  19 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 35
      removed outlier: 6.955A  pdb=" N   LEU D  34 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   MET B  35 " --> pdb=" O   LEU D  34 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LEU F  34 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   MET D  35 " --> pdb=" O   LEU F  34 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LEU H  34 " --> pdb=" O   GLY F  33 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   MET F  35 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LEU J  34 " --> pdb=" O   GLY H  33 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   MET H  35 " --> pdb=" O   LEU J  34 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 41

    29 hydrogen bonds defined for protein.
    87 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: 0.40

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 740
        1.34 -     1.46: 310
        1.46 -     1.57: 1220
        1.57 -     1.68: 0
        1.68 -     1.80: 20
  Bond restraints: 2290
  Sorted by residual:
  bond pdb=" C   VAL H  36 "
       pdb=" O   VAL H  36 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.19e-02 7.06e+03 5.62e-01
  bond pdb=" C   VAL B  36 "
       pdb=" O   VAL B  36 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.19e-02 7.06e+03 5.50e-01
  bond pdb=" C   VAL C  36 "
       pdb=" O   VAL C  36 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.19e-02 7.06e+03 5.46e-01
  bond pdb=" C   VAL E  36 "
       pdb=" O   VAL E  36 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.19e-02 7.06e+03 5.11e-01
  bond pdb=" C   VAL I  36 "
       pdb=" O   VAL I  36 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.008 1.19e-02 7.06e+03 5.08e-01
  ... (remaining 2285 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.78: 2726
        0.78 -     1.55: 314
        1.55 -     2.33: 10
        2.33 -     3.11: 10
        3.11 -     3.88: 20
  Bond angle restraints: 3080
  Sorted by residual:
  angle pdb=" C   VAL A  39 "
        pdb=" N   VAL A  40 "
        pdb=" CA  VAL A  40 "
      ideal   model   delta    sigma   weight residual
     122.90  120.00    2.90 1.28e+00 6.10e-01 5.14e+00
  angle pdb=" C   VAL D  39 "
        pdb=" N   VAL D  40 "
        pdb=" CA  VAL D  40 "
      ideal   model   delta    sigma   weight residual
     122.90  120.01    2.89 1.28e+00 6.10e-01 5.10e+00
  angle pdb=" C   VAL J  39 "
        pdb=" N   VAL J  40 "
        pdb=" CA  VAL J  40 "
      ideal   model   delta    sigma   weight residual
     122.90  120.01    2.89 1.28e+00 6.10e-01 5.10e+00
  angle pdb=" C   VAL I  39 "
        pdb=" N   VAL I  40 "
        pdb=" CA  VAL I  40 "
      ideal   model   delta    sigma   weight residual
     122.90  120.01    2.89 1.28e+00 6.10e-01 5.09e+00
  angle pdb=" C   VAL B  39 "
        pdb=" N   VAL B  40 "
        pdb=" CA  VAL B  40 "
      ideal   model   delta    sigma   weight residual
     122.90  120.02    2.88 1.28e+00 6.10e-01 5.06e+00
  ... (remaining 3075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.06: 1040
        7.06 -    14.12: 140
       14.12 -    21.18: 60
       21.18 -    28.23: 40
       28.23 -    35.29: 10
  Dihedral angle restraints: 1290
    sinusoidal: 470
      harmonic: 820
  Sorted by residual:
  dihedral pdb=" N   MET I  35 "
           pdb=" CA  MET I  35 "
           pdb=" CB  MET I  35 "
           pdb=" CG  MET I  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   86.58  -26.58     3      1.50e+01 4.44e-03 3.90e+00
  dihedral pdb=" N   MET D  35 "
           pdb=" CA  MET D  35 "
           pdb=" CB  MET D  35 "
           pdb=" CG  MET D  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   86.58  -26.58     3      1.50e+01 4.44e-03 3.90e+00
  dihedral pdb=" N   MET E  35 "
           pdb=" CA  MET E  35 "
           pdb=" CB  MET E  35 "
           pdb=" CG  MET E  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   86.56  -26.56     3      1.50e+01 4.44e-03 3.89e+00
  ... (remaining 1287 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.023: 189
       0.023 -    0.046: 71
       0.046 -    0.069: 51
       0.069 -    0.092: 17
       0.092 -    0.115: 42
  Chirality restraints: 370
  Sorted by residual:
  chirality pdb=" CA  ILE E  32 "
            pdb=" N   ILE E  32 "
            pdb=" C   ILE E  32 "
            pdb=" CB  ILE E  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.29e-01
  chirality pdb=" CA  ILE I  32 "
            pdb=" N   ILE I  32 "
            pdb=" C   ILE I  32 "
            pdb=" CB  ILE I  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.28e-01
  chirality pdb=" CA  ILE C  32 "
            pdb=" N   ILE C  32 "
            pdb=" C   ILE C  32 "
            pdb=" CB  ILE C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.28e-01
  ... (remaining 367 not shown)

  Planarity restraints: 390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  39 "    0.003 2.00e-02 2.50e+03   5.75e-03 3.30e-01
        pdb=" C   VAL A  39 "   -0.010 2.00e-02 2.50e+03
        pdb=" O   VAL A  39 "    0.004 2.00e-02 2.50e+03
        pdb=" N   VAL A  40 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  39 "   -0.003 2.00e-02 2.50e+03   5.68e-03 3.23e-01
        pdb=" C   VAL D  39 "    0.010 2.00e-02 2.50e+03
        pdb=" O   VAL D  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   VAL D  40 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL I  39 "    0.003 2.00e-02 2.50e+03   5.67e-03 3.21e-01
        pdb=" C   VAL I  39 "   -0.010 2.00e-02 2.50e+03
        pdb=" O   VAL I  39 "    0.004 2.00e-02 2.50e+03
        pdb=" N   VAL I  40 "    0.003 2.00e-02 2.50e+03
  ... (remaining 387 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 451
        2.78 -     3.31: 1967
        3.31 -     3.84: 3629
        3.84 -     4.37: 3971
        4.37 -     4.90: 7939
  Nonbonded interactions: 17957
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS E  28 "
            pdb=" OXT ALA H  42 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NZ  LYS C  28 "
            pdb=" OXT ALA F  42 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NZ  LYS G  28 "
            pdb=" OXT ALA J  42 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NZ  LYS H  28 "
            pdb=" OXT ALA I  42 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NZ  LYS D  28 "
            pdb=" OXT ALA E  42 "
     model   vdw
     2.257 3.120
  ... (remaining 17952 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.690
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
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      :  0.004   0.011   2290  Z= 0.189
  Angle     :  0.560   3.884   3080  Z= 0.354
  Chirality :  0.048   0.115    370
  Planarity :  0.001   0.006    390
  Dihedral  :  9.684  35.293    770
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.04 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.28 (0.45), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.34), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE F  20 
 HIS   0.002   0.001   HIS H  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 2290)
  covalent geometry    : angle       0.55970 ( 3080)
  hydrogen bonds       : bond        0.11596 (   29)
  hydrogen bonds       : angle       8.88995 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.086 
Fit side-chains
REVERT: B   18 VAL cc_start: 0.9485 (t) cc_final: 0.9190 (p)
REVERT: C   39 VAL cc_start: 0.9441 (t) cc_final: 0.9160 (t)
REVERT: D   15 GLN cc_start: 0.8563 (tt0) cc_final: 0.8330 (tm-30)
REVERT: E   22 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7935 (mm-30)
REVERT: F   15 GLN cc_start: 0.8632 (tt0) cc_final: 0.8378 (tm-30)
REVERT: G   22 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7723 (mm-30)
REVERT: H   15 GLN cc_start: 0.8679 (tt0) cc_final: 0.8357 (tm-30)
REVERT: I   22 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7677 (mm-30)
REVERT: I   40 VAL cc_start: 0.9100 (t) cc_final: 0.8892 (p)
REVERT: J   14 HIS cc_start: 0.8525 (m170) cc_final: 0.6693 (p-80)
REVERT: J   16 LYS cc_start: 0.8538 (mttp) cc_final: 0.8188 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0598
  time to fit residues: 8.6170
Evaluate side-chains
  81 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 12 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   overall best weight:    5.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  14 HIS ** 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 = 0.3554 r_free = 0.3554 target = 0.103327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.088848 restraints weight = 4946.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.091101 restraints weight = 2539.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.092908 restraints weight = 1629.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.094149 restraints weight = 1168.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.094910 restraints weight = 902.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036   2290  Z= 0.301
  Angle     :  0.649   6.755   3080  Z= 0.333
  Chirality :  0.052   0.116    370
  Planarity :  0.003   0.019    390
  Dihedral  : 10.523  70.751    310
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 27.39 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.27 (0.46), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE E  19 
 HIS   0.004   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 ( 2290)
  covalent geometry    : angle       0.64884 ( 3080)
  hydrogen bonds       : bond        0.03777 (   29)
  hydrogen bonds       : angle       6.55042 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.089 
Fit side-chains
REVERT: C   39 VAL cc_start: 0.9490 (t) cc_final: 0.9228 (t)
REVERT: D   22 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7731 (tp30)
REVERT: E   22 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7880 (mm-30)
REVERT: F   22 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8065 (tp30)
REVERT: G   16 LYS cc_start: 0.7915 (mttp) cc_final: 0.7708 (mtpp)
REVERT: G   22 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7738 (mm-30)
REVERT: I   15 GLN cc_start: 0.8207 (mt0) cc_final: 0.7998 (mt0)
REVERT: I   16 LYS cc_start: 0.8068 (mttp) cc_final: 0.7299 (mmtt)
REVERT: I   22 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7643 (mm-30)
REVERT: J   14 HIS cc_start: 0.8795 (m170) cc_final: 0.6786 (p-80)
REVERT: J   16 LYS cc_start: 0.8510 (mttp) cc_final: 0.8072 (mmtt)
  outliers start: 16
  outliers final: 4
  residues processed: 103
  average time/residue: 0.0413
  time to fit residues: 5.3646
Evaluate side-chains
  99 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain I residue   35 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  14 HIS ** 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 = 0.3676 r_free = 0.3676 target = 0.108544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.093598 restraints weight = 4846.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.096060 restraints weight = 2487.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.097969 restraints weight = 1593.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.099438 restraints weight = 1128.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.100478 restraints weight = 861.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2290  Z= 0.133
  Angle     :  0.516   5.219   3080  Z= 0.266
  Chirality :  0.053   0.118    370
  Planarity :  0.002   0.017    390
  Dihedral  : 10.726  81.128    310
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  9.57 %
    Allowed  : 28.26 %
    Favored  : 62.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.47), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.72 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE E  20 
 HIS   0.001   0.000   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2290)
  covalent geometry    : angle       0.51583 ( 3080)
  hydrogen bonds       : bond        0.02767 (   29)
  hydrogen bonds       : angle       6.24496 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9190 (t) cc_final: 0.8933 (t)
REVERT: G   22 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7689 (mm-30)
REVERT: G   39 VAL cc_start: 0.9401 (t) cc_final: 0.9139 (t)
REVERT: I   15 GLN cc_start: 0.8175 (mt0) cc_final: 0.7903 (mt0)
REVERT: I   16 LYS cc_start: 0.8071 (mttp) cc_final: 0.7283 (mmtt)
REVERT: I   22 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7569 (mm-30)
REVERT: J   14 HIS cc_start: 0.8766 (m170) cc_final: 0.6654 (p-80)
REVERT: J   15 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7945 (tm-30)
REVERT: J   16 LYS cc_start: 0.8469 (mttp) cc_final: 0.7847 (tptt)
  outliers start: 22
  outliers final: 3
  residues processed: 107
  average time/residue: 0.0379
  time to fit residues: 5.1827
Evaluate side-chains
  98 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain G residue   41 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 14 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.106063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.091234 restraints weight = 4991.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.093622 restraints weight = 2657.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.095477 restraints weight = 1744.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.096800 restraints weight = 1264.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.097528 restraints weight = 983.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2290  Z= 0.171
  Angle     :  0.513   4.905   3080  Z= 0.265
  Chirality :  0.052   0.116    370
  Planarity :  0.002   0.014    390
  Dihedral  : 10.908  89.234    310
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  8.26 %
    Allowed  : 30.87 %
    Favored  : 60.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.37 (0.47), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE E  20 
 HIS   0.002   0.001   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 2290)
  covalent geometry    : angle       0.51263 ( 3080)
  hydrogen bonds       : bond        0.03129 (   29)
  hydrogen bonds       : angle       6.12629 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9250 (t) cc_final: 0.8989 (t)
REVERT: G   22 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8024 (tp30)
REVERT: H   22 GLU cc_start: 0.8238 (tp30) cc_final: 0.7580 (tp30)
REVERT: I   15 GLN cc_start: 0.8183 (mt0) cc_final: 0.7840 (mt0)
REVERT: I   16 LYS cc_start: 0.8196 (mttp) cc_final: 0.7372 (mmtt)
REVERT: I   22 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: J   14 HIS cc_start: 0.8758 (m170) cc_final: 0.6587 (p-80)
REVERT: J   16 LYS cc_start: 0.8485 (mttp) cc_final: 0.8102 (mmtt)
  outliers start: 19
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0370
  time to fit residues: 4.9850
Evaluate side-chains
  103 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain G residue   41 ILE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   27 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  14 HIS ** 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 = 0.3650 r_free = 0.3650 target = 0.107128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.091144 restraints weight = 4896.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.093621 restraints weight = 2633.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.095538 restraints weight = 1739.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.097122 restraints weight = 1274.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.098172 restraints weight = 1000.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2290  Z= 0.152
  Angle     :  0.506   4.479   3080  Z= 0.266
  Chirality :  0.053   0.118    370
  Planarity :  0.002   0.021    390
  Dihedral  : 10.727  84.521    310
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  9.57 %
    Allowed  : 29.13 %
    Favored  : 61.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.47), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE C  19 
 HIS   0.002   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2290)
  covalent geometry    : angle       0.50650 ( 3080)
  hydrogen bonds       : bond        0.02995 (   29)
  hydrogen bonds       : angle       6.00869 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9245 (t) cc_final: 0.8985 (t)
REVERT: E   39 VAL cc_start: 0.9485 (t) cc_final: 0.9217 (t)
REVERT: F   22 GLU cc_start: 0.8405 (tp30) cc_final: 0.7796 (tp30)
REVERT: G   22 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8037 (tp30)
REVERT: H   22 GLU cc_start: 0.8245 (tp30) cc_final: 0.7510 (tp30)
REVERT: I   16 LYS cc_start: 0.8248 (mttp) cc_final: 0.7402 (mmtt)
REVERT: J   14 HIS cc_start: 0.8685 (m170) cc_final: 0.6519 (p-80)
REVERT: J   16 LYS cc_start: 0.8533 (mttp) cc_final: 0.8097 (mmtt)
  outliers start: 22
  outliers final: 9
  residues processed: 106
  average time/residue: 0.0375
  time to fit residues: 5.0879
Evaluate side-chains
  104 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain G residue   41 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 20 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.106525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.091490 restraints weight = 4836.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.093786 restraints weight = 2589.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.095552 restraints weight = 1706.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.096884 restraints weight = 1248.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.097799 restraints weight = 979.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.4640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2290  Z= 0.165
  Angle     :  0.512   4.298   3080  Z= 0.269
  Chirality :  0.053   0.116    370
  Planarity :  0.002   0.020    390
  Dihedral  : 10.386  75.270    310
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.86 %
    Favored  : 93.79 %
  Rotamer:
    Outliers : 10.87 %
    Allowed  : 27.83 %
    Favored  : 61.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.43 (0.47), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE C  19 
 HIS   0.002   0.001   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 2290)
  covalent geometry    : angle       0.51170 ( 3080)
  hydrogen bonds       : bond        0.02833 (   29)
  hydrogen bonds       : angle       5.85927 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9204 (t) cc_final: 0.8940 (t)
REVERT: C   39 VAL cc_start: 0.9443 (t) cc_final: 0.9170 (t)
REVERT: E   22 GLU cc_start: 0.8530 (tp30) cc_final: 0.7808 (tp30)
REVERT: E   39 VAL cc_start: 0.9486 (t) cc_final: 0.9201 (t)
REVERT: F   22 GLU cc_start: 0.8417 (tp30) cc_final: 0.7809 (tp30)
REVERT: G   22 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7922 (tp30)
REVERT: H   22 GLU cc_start: 0.8265 (tp30) cc_final: 0.7556 (tp30)
REVERT: I   16 LYS cc_start: 0.8202 (mttp) cc_final: 0.7341 (mmtt)
REVERT: J   14 HIS cc_start: 0.8690 (m170) cc_final: 0.6484 (p-80)
REVERT: J   15 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: J   16 LYS cc_start: 0.8365 (mttp) cc_final: 0.7790 (mmtt)
  outliers start: 25
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0344
  time to fit residues: 4.7588
Evaluate side-chains
  104 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   35 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 2 optimal weight:    0.2980
   overall best weight:    3.0588

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN
** H  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.107128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.091430 restraints weight = 4977.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.093903 restraints weight = 2647.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.095788 restraints weight = 1736.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.097095 restraints weight = 1273.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.098175 restraints weight = 1004.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2290  Z= 0.174
  Angle     :  0.528   5.654   3080  Z= 0.277
  Chirality :  0.053   0.122    370
  Planarity :  0.002   0.020    390
  Dihedral  : 10.006  65.017    310
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.17 %
    Favored  : 94.48 %
  Rotamer:
    Outliers : 11.74 %
    Allowed  : 27.83 %
    Favored  : 60.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.43 (0.47), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE A  20 
 HIS   0.002   0.001   HIS J  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 2290)
  covalent geometry    : angle       0.52759 ( 3080)
  hydrogen bonds       : bond        0.03227 (   29)
  hydrogen bonds       : angle       5.70379 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9203 (t) cc_final: 0.8944 (t)
REVERT: B   39 VAL cc_start: 0.9141 (t) cc_final: 0.8850 (t)
REVERT: C   39 VAL cc_start: 0.9475 (t) cc_final: 0.9203 (t)
REVERT: E   39 VAL cc_start: 0.9529 (t) cc_final: 0.9247 (t)
REVERT: G   39 VAL cc_start: 0.9470 (t) cc_final: 0.9167 (t)
REVERT: H   15 GLN cc_start: 0.8647 (tt0) cc_final: 0.8159 (tt0)
REVERT: H   22 GLU cc_start: 0.8294 (tp30) cc_final: 0.7647 (tp30)
REVERT: I   16 LYS cc_start: 0.8213 (mttp) cc_final: 0.7356 (mmtt)
REVERT: J   15 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7915 (tm-30)
REVERT: J   16 LYS cc_start: 0.8343 (mttp) cc_final: 0.7609 (tptt)
  outliers start: 27
  outliers final: 16
  residues processed: 109
  average time/residue: 0.0349
  time to fit residues: 4.9158
Evaluate side-chains
  111 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain G residue   41 ILE
Chi-restraints excluded: chain I residue   15 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN
** H  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.107239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.091563 restraints weight = 4865.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.093975 restraints weight = 2630.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.095722 restraints weight = 1749.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.097168 restraints weight = 1290.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.098206 restraints weight = 1014.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.4806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2290  Z= 0.152
  Angle     :  0.526   6.325   3080  Z= 0.279
  Chirality :  0.053   0.131    370
  Planarity :  0.002   0.018    390
  Dihedral  :  9.779  61.219    310
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.83 %
    Favored  : 94.83 %
  Rotamer:
    Outliers : 11.30 %
    Allowed  : 27.83 %
    Favored  : 60.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.47), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE A  20 
 HIS   0.003   0.001   HIS I  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 2290)
  covalent geometry    : angle       0.52577 ( 3080)
  hydrogen bonds       : bond        0.03139 (   29)
  hydrogen bonds       : angle       5.69744 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9202 (t) cc_final: 0.8940 (t)
REVERT: B   39 VAL cc_start: 0.9148 (t) cc_final: 0.8854 (t)
REVERT: C   39 VAL cc_start: 0.9469 (t) cc_final: 0.9200 (t)
REVERT: E   22 GLU cc_start: 0.8541 (tp30) cc_final: 0.7834 (tp30)
REVERT: E   39 VAL cc_start: 0.9519 (t) cc_final: 0.9248 (t)
REVERT: F   22 GLU cc_start: 0.8454 (tp30) cc_final: 0.7823 (tp30)
REVERT: G   22 GLU cc_start: 0.8236 (tp30) cc_final: 0.7572 (tp30)
REVERT: G   39 VAL cc_start: 0.9483 (t) cc_final: 0.9194 (t)
REVERT: H   15 GLN cc_start: 0.8552 (tt0) cc_final: 0.8105 (tt0)
REVERT: H   22 GLU cc_start: 0.8263 (tp30) cc_final: 0.7573 (tp30)
REVERT: I   16 LYS cc_start: 0.8225 (mttp) cc_final: 0.7358 (mmtt)
REVERT: J   15 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: J   16 LYS cc_start: 0.8348 (mttp) cc_final: 0.7640 (tptt)
  outliers start: 26
  outliers final: 17
  residues processed: 107
  average time/residue: 0.0345
  time to fit residues: 4.7903
Evaluate side-chains
  113 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   35 MET
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain G residue   41 ILE
Chi-restraints excluded: chain I residue   15 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  14 HIS ** 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 = 0.3703 r_free = 0.3703 target = 0.109355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.093797 restraints weight = 4973.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.096245 restraints weight = 2678.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.098037 restraints weight = 1776.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.099526 restraints weight = 1308.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.100596 restraints weight = 1025.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.4928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2290  Z= 0.126
  Angle     :  0.515   6.951   3080  Z= 0.273
  Chirality :  0.054   0.130    370
  Planarity :  0.002   0.016    390
  Dihedral  :  9.305  61.690    310
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.83 %
    Favored  : 94.83 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 30.00 %
    Favored  : 60.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.56 (0.46), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE A  20 
 HIS   0.001   0.000   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 2290)
  covalent geometry    : angle       0.51488 ( 3080)
  hydrogen bonds       : bond        0.03018 (   29)
  hydrogen bonds       : angle       5.67798 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9210 (t) cc_final: 0.8953 (t)
REVERT: B   39 VAL cc_start: 0.9158 (t) cc_final: 0.8885 (t)
REVERT: C   39 VAL cc_start: 0.9468 (t) cc_final: 0.9205 (t)
REVERT: F   22 GLU cc_start: 0.8449 (tp30) cc_final: 0.7811 (tp30)
REVERT: G   22 GLU cc_start: 0.8260 (tp30) cc_final: 0.7761 (tp30)
REVERT: G   39 VAL cc_start: 0.9467 (t) cc_final: 0.9212 (t)
REVERT: H   15 GLN cc_start: 0.8589 (tt0) cc_final: 0.8262 (tt0)
REVERT: I   16 LYS cc_start: 0.8256 (mttp) cc_final: 0.7411 (mmtt)
REVERT: I   23 ASP cc_start: 0.7194 (p0) cc_final: 0.6113 (m-30)
REVERT: J   15 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7903 (tm-30)
  outliers start: 23
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0324
  time to fit residues: 4.7478
Evaluate side-chains
  109 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain H residue   40 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  14 HIS ** 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 = 0.3688 r_free = 0.3688 target = 0.108138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.093240 restraints weight = 4940.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.095670 restraints weight = 2636.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.097524 restraints weight = 1713.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.098845 restraints weight = 1247.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.099849 restraints weight = 968.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.4973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2290  Z= 0.182
  Angle     :  0.551   7.532   3080  Z= 0.287
  Chirality :  0.054   0.142    370
  Planarity :  0.002   0.015    390
  Dihedral  :  9.113  58.662    310
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.62 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  9.13 %
    Allowed  : 31.74 %
    Favored  : 59.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.55 (0.46), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE F  20 
 HIS   0.002   0.001   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 2290)
  covalent geometry    : angle       0.55088 ( 3080)
  hydrogen bonds       : bond        0.03147 (   29)
  hydrogen bonds       : angle       5.59700 (   87)

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

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

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  580 Ramachandran restraints generated.
    290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 VAL cc_start: 0.9241 (t) cc_final: 0.8998 (t)
REVERT: B   39 VAL cc_start: 0.9200 (t) cc_final: 0.8926 (t)
REVERT: E   22 GLU cc_start: 0.8547 (tp30) cc_final: 0.7847 (tp30)
REVERT: E   39 VAL cc_start: 0.9530 (t) cc_final: 0.9289 (t)
REVERT: F   22 GLU cc_start: 0.8446 (tp30) cc_final: 0.7829 (tp30)
REVERT: F   39 VAL cc_start: 0.9526 (t) cc_final: 0.9275 (t)
REVERT: G   22 GLU cc_start: 0.8275 (tp30) cc_final: 0.7528 (tp30)
REVERT: H   22 GLU cc_start: 0.8246 (tp30) cc_final: 0.7620 (tp30)
REVERT: I   16 LYS cc_start: 0.8258 (mttp) cc_final: 0.7391 (mmtt)
REVERT: J   15 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7949 (tm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 106
  average time/residue: 0.0325
  time to fit residues: 4.4981
Evaluate side-chains
  110 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   35 MET
Chi-restraints excluded: chain D residue   41 ILE
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   26 SER
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain G residue   12 VAL
Chi-restraints excluded: chain G residue   41 ILE
Chi-restraints excluded: chain J residue   40 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0370
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0070
   chunk 9 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0570
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.4198

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  14 HIS ** 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 = 0.3720 r_free = 0.3720 target = 0.110074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.094289 restraints weight = 4875.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.096737 restraints weight = 2701.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.098589 restraints weight = 1816.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.100013 restraints weight = 1347.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.101038 restraints weight = 1062.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.5071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2290  Z= 0.113
  Angle     :  0.560   7.875   3080  Z= 0.285
  Chirality :  0.054   0.132    370
  Planarity :  0.002   0.015    390
  Dihedral  :  9.207  61.542    310
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  4.14 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  9.13 %
    Allowed  : 32.17 %
    Favored  : 58.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.58 (0.46), residues: 290
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE A  20 
 HIS   0.001   0.000   HIS F  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 2290)
  covalent geometry    : angle       0.56044 ( 3080)
  hydrogen bonds       : bond        0.03103 (   29)
  hydrogen bonds       : angle       5.61600 (   87)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 609.31 seconds
wall clock time: 11 minutes 47.88 seconds (707.88 seconds total)