Starting phenix.real_space_refine
on Fri Oct 10 10:17:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kf6_37200/10_2025/8kf6_37200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kf6_37200/10_2025/8kf6_37200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kf6_37200/10_2025/8kf6_37200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kf6_37200/10_2025/8kf6_37200.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kf6_37200/10_2025/8kf6_37200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kf6_37200/10_2025/8kf6_37200.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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       9      5.16       5
     C    1419      2.51       5
     N     369      2.21       5
     O     378      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2175
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "F"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 225
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
    Chain: "A"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "G"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "D"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 225
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
    Chain: "H"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "E"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 225
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
    Chain: "I"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "B"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "C"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 250
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
  Time building chain proxies: 0.94, per 1000 atoms: 0.43
  Number of scatterers: 2175
  At special positions: 0
  Unit cell: (64.74, 95.45, 38.18, 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       9     16.00
     O     378      8.00
     N     369      7.00
     C    1419      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: 0.14
  Conformation dependent library (CDL) restraints added in 128.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  492

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'F' and resid 39 through 41
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19
      removed outlier: 6.215A  pdb=" N   VAL A  18 " --> pdb=" O   PHE B  19 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   VAL B  18 " --> pdb=" O   PHE C  19 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 32
    Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 41
      removed outlier: 6.817A  pdb=" N   VAL A  40 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL B  40 " --> pdb=" O   ILE C  41 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 13
    Processing sheet with id=AA7, first strand: chain 'G' and resid 24 through 25
      removed outlier: 6.856A  pdb=" N   VAL G  24 " --> pdb=" O   GLY H  25 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   VAL H  24 " --> pdb=" O   GLY I  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    10 hydrogen bonds defined for protein.
    30 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: 0.31

  Time building geometry restraints manager: 0.21 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: 705
        1.34 -     1.45: 300
        1.45 -     1.57: 1185
        1.57 -     1.68: 0
        1.68 -     1.80: 18
  Bond restraints: 2208
  Sorted by residual:
  bond pdb=" CA  PHE B  20 "
       pdb=" C   PHE B  20 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.34e-02 5.57e+03 8.37e-01
  bond pdb=" CA  PHE C  20 "
       pdb=" C   PHE C  20 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.34e-02 5.57e+03 8.04e-01
  bond pdb=" CA  PHE A  20 "
       pdb=" C   PHE A  20 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.34e-02 5.57e+03 8.03e-01
  bond pdb=" CA  VAL I  36 "
       pdb=" C   VAL I  36 "
    ideal  model  delta    sigma   weight residual
    1.527  1.519  0.008 8.50e-03 1.38e+04 8.01e-01
  bond pdb=" CB  VAL A  18 "
       pdb=" CG2 VAL A  18 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.63e-01
  ... (remaining 2203 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.83: 2425
        0.83 -     1.66: 421
        1.66 -     2.49: 94
        2.49 -     3.32: 18
        3.32 -     4.15: 6
  Bond angle restraints: 2964
  Sorted by residual:
  angle pdb=" N   GLU H  22 "
        pdb=" CA  GLU H  22 "
        pdb=" C   GLU H  22 "
      ideal   model   delta    sigma   weight residual
     114.56  110.65    3.91 1.27e+00 6.20e-01 9.50e+00
  angle pdb=" N   GLY F  25 "
        pdb=" CA  GLY F  25 "
        pdb=" C   GLY F  25 "
      ideal   model   delta    sigma   weight residual
     112.73  115.89   -3.16 1.20e+00 6.94e-01 6.94e+00
  angle pdb=" CA  GLY I  37 "
        pdb=" C   GLY I  37 "
        pdb=" O   GLY I  37 "
      ideal   model   delta    sigma   weight residual
     122.39  120.13    2.26 9.30e-01 1.16e+00 5.93e+00
  angle pdb=" C   VAL H  12 "
        pdb=" N   HIS H  13 "
        pdb=" CA  HIS H  13 "
      ideal   model   delta    sigma   weight residual
     121.80  117.65    4.15 1.71e+00 3.42e-01 5.88e+00
  angle pdb=" C   VAL F  24 "
        pdb=" N   GLY F  25 "
        pdb=" CA  GLY F  25 "
      ideal   model   delta    sigma   weight residual
     119.98  122.37   -2.39 1.11e+00 8.12e-01 4.63e+00
  ... (remaining 2959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.41: 1089
       16.41 -    32.82: 123
       32.82 -    49.22: 10
       49.22 -    65.63: 4
       65.63 -    82.04: 4
  Dihedral angle restraints: 1230
    sinusoidal: 444
      harmonic: 786
  Sorted by residual:
  dihedral pdb=" CA  PHE C  20 "
           pdb=" C   PHE C  20 "
           pdb=" N   ALA C  21 "
           pdb=" CA  ALA C  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.44   28.56     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  PHE A  20 "
           pdb=" C   PHE A  20 "
           pdb=" N   ALA A  21 "
           pdb=" CA  ALA A  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.45   28.55     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  PHE B  20 "
           pdb=" C   PHE B  20 "
           pdb=" N   ALA B  21 "
           pdb=" CA  ALA B  21 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.45   28.55     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 1227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 163
       0.031 -    0.062: 100
       0.062 -    0.093: 18
       0.093 -    0.124: 53
       0.124 -    0.154: 11
  Chirality restraints: 345
  Sorted by residual:
  chirality pdb=" CA  VAL B  12 "
            pdb=" N   VAL B  12 "
            pdb=" C   VAL B  12 "
            pdb=" CB  VAL B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CA  VAL C  12 "
            pdb=" N   VAL C  12 "
            pdb=" C   VAL C  12 "
            pdb=" CB  VAL C  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.88e-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    2.59   -0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 342 not shown)

  Planarity restraints: 372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE G  20 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" C   PHE G  20 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   PHE G  20 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ALA G  21 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE H  20 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" C   PHE H  20 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   PHE H  20 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ALA H  21 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE I  20 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.81e+00
        pdb=" C   PHE I  20 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   PHE I  20 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ALA I  21 "    0.008 2.00e-02 2.50e+03
  ... (remaining 369 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 891
        2.91 -     3.41: 1959
        3.41 -     3.91: 3231
        3.91 -     4.40: 3503
        4.40 -     4.90: 6933
  Nonbonded interactions: 16517
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS I  16 "
            pdb=" OE2 GLU I  22 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" OG  SER F  26 "
            pdb=" N   ASN F  27 "
     model   vdw
     2.418 3.120
  nonbonded pdb=" OG  SER I  26 "
            pdb=" N   ASN I  27 "
     model   vdw
     2.465 3.120
  nonbonded pdb=" OG  SER H  26 "
            pdb=" N   ASN H  27 "
     model   vdw
     2.473 3.120
  nonbonded pdb=" CE1 PHE B  20 "
            pdb=" CE2 PHE C  20 "
     model   vdw
     2.493 3.640
  ... (remaining 16512 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' and resid 12 through 42)
  selection = (chain 'B' and resid 12 through 42)
  selection = (chain 'C' and resid 12 through 42)
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = (chain 'G' and resid 12 through 42)
  selection = (chain 'H' and resid 12 through 42)
  selection = (chain 'I' and resid 12 through 42)
}

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:             2.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.140
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
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   0.028   2208  Z= 0.214
  Angle     :  0.697   4.146   2964  Z= 0.423
  Chirality :  0.059   0.154    345
  Planarity :  0.003   0.014    372
  Dihedral  : 14.133  82.040    738
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 19.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.20 %
    Favored  : 82.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  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: -5.74 (0.32), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.37 (0.24), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR H  10 
 PHE   0.009   0.002   PHE G  20 
 HIS   0.006   0.001   HIS C  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 2208)
  covalent geometry    : angle       0.69702 ( 2964)
  hydrogen bonds       : bond        0.18596 (   10)
  hydrogen bonds       : angle       7.75350 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.086 
Fit side-chains
REVERT: F   22 GLU cc_start: 0.8574 (tp30) cc_final: 0.8367 (tp30)
REVERT: I   15 GLN cc_start: 0.8750 (mp10) cc_final: 0.8473 (mp10)
REVERT: B   15 GLN cc_start: 0.8911 (mp10) cc_final: 0.8463 (mp10)
REVERT: C   15 GLN cc_start: 0.8738 (mp10) cc_final: 0.8394 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0691
  time to fit residues: 2.0555
Evaluate side-chains
  25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 8 optimal weight:    0.1980
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    4.4388

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

Flipped N/Q/H residues before XYZ refinement:
F  14 HIS
F  15 GLN
A  13 HIS
G  13 HIS
H  13 HIS
E  13 HIS
E  15 GLN
I  13 HIS
B  13 HIS
C  13 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.153589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.113013 restraints weight = 2308.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.115843 restraints weight = 1435.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.117814 restraints weight = 1061.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.119071 restraints weight = 867.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.119908 restraints weight = 761.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   2208  Z= 0.290
  Angle     :  0.768   6.898   2964  Z= 0.425
  Chirality :  0.063   0.159    345
  Planarity :  0.003   0.015    372
  Dihedral  :  6.438  27.765    294
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 27.60 %
    Favored  : 72.40 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  9.59 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.47 (0.33), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.16 (0.25), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR H  10 
 PHE   0.016   0.003   PHE A  19 
 HIS   0.010   0.002   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 ( 2208)
  covalent geometry    : angle       0.76765 ( 2964)
  hydrogen bonds       : bond        0.04199 (   10)
  hydrogen bonds       : angle       6.07122 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.084 
Fit side-chains
REVERT: F   35 MET cc_start: 0.7849 (ttm) cc_final: 0.7589 (ttp)
REVERT: G   28 LYS cc_start: 0.8253 (mttt) cc_final: 0.7929 (mttp)
REVERT: H   28 LYS cc_start: 0.8373 (mttt) cc_final: 0.7981 (mttp)
REVERT: B   15 GLN cc_start: 0.8945 (mp10) cc_final: 0.8701 (mp10)
  outliers start: 6
  outliers final: 5
  residues processed: 35
  average time/residue: 0.0686
  time to fit residues: 2.8362
Evaluate side-chains
  35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 1 optimal weight:    0.0970
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0040
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.4196

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

Flipped N/Q/H residues before XYZ refinement:
F  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.166745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.124757 restraints weight = 2208.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.127892 restraints weight = 1330.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.129999 restraints weight = 975.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.131130 restraints weight = 797.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.132170 restraints weight = 711.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2208  Z= 0.127
  Angle     :  0.603   5.753   2964  Z= 0.333
  Chirality :  0.058   0.139    345
  Planarity :  0.002   0.015    372
  Dihedral  :  5.962  29.631    294
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.26 %
    Favored  : 86.74 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  8.68 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.08 (0.35), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.87 (0.27), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR H  10 
 PHE   0.010   0.001   PHE C  20 
 HIS   0.003   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 2208)
  covalent geometry    : angle       0.60300 ( 2964)
  hydrogen bonds       : bond        0.03536 (   10)
  hydrogen bonds       : angle       6.02640 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.087 
Fit side-chains
REVERT: F   35 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7308 (ttp)
REVERT: B   15 GLN cc_start: 0.8802 (mp10) cc_final: 0.8516 (mp10)
REVERT: B   22 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6841 (pp20)
  outliers start: 6
  outliers final: 4
  residues processed: 27
  average time/residue: 0.0574
  time to fit residues: 1.9288
Evaluate side-chains
  29 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   chunk 20 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 18 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    2.4786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.162128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.119599 restraints weight = 2223.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.122766 restraints weight = 1340.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.124896 restraints weight = 979.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.126217 restraints weight = 799.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.126925 restraints weight = 704.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2208  Z= 0.177
  Angle     :  0.619   5.799   2964  Z= 0.346
  Chirality :  0.059   0.151    345
  Planarity :  0.002   0.014    372
  Dihedral  :  5.920  30.257    294
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.85 %
    Favored  : 83.15 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.24 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.85 (0.36), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.69 (0.28), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR H  10 
 PHE   0.011   0.002   PHE B  20 
 HIS   0.004   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 2208)
  covalent geometry    : angle       0.61949 ( 2964)
  hydrogen bonds       : bond        0.03574 (   10)
  hydrogen bonds       : angle       6.14751 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.084 
Fit side-chains
REVERT: F   35 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7322 (ttm)
REVERT: D   35 MET cc_start: 0.8649 (mmm) cc_final: 0.8171 (ttm)
REVERT: B   15 GLN cc_start: 0.8821 (mp10) cc_final: 0.8557 (mp10)
  outliers start: 7
  outliers final: 5
  residues processed: 28
  average time/residue: 0.0653
  time to fit residues: 2.2273
Evaluate side-chains
  30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 24
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0170
   chunk 17 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:   20.0000
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.7224

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.155462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.113274 restraints weight = 2163.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.116437 restraints weight = 1279.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.118641 restraints weight = 928.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.120029 restraints weight = 754.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.120966 restraints weight = 659.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2208  Z= 0.134
  Angle     :  0.561   5.446   2964  Z= 0.313
  Chirality :  0.057   0.142    345
  Planarity :  0.002   0.014    372
  Dihedral  :  5.717  29.424    294
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.54 %
    Favored  : 87.46 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 13.24 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.47 (0.38), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.29), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR H  10 
 PHE   0.011   0.001   PHE B  20 
 HIS   0.004   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2208)
  covalent geometry    : angle       0.56076 ( 2964)
  hydrogen bonds       : bond        0.03362 (   10)
  hydrogen bonds       : angle       6.07441 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.087 
Fit side-chains
REVERT: F   35 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7243 (ttm)
REVERT: D   35 MET cc_start: 0.8559 (mmm) cc_final: 0.8273 (ttm)
REVERT: B   15 GLN cc_start: 0.8785 (mp10) cc_final: 0.8312 (mp10)
REVERT: B   22 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.6819 (pp20)
REVERT: C   15 GLN cc_start: 0.8708 (mp10) cc_final: 0.8425 (mp10)
  outliers start: 8
  outliers final: 6
  residues processed: 31
  average time/residue: 0.0481
  time to fit residues: 1.8793
Evaluate side-chains
  33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 MET
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0670
   overall best weight:    1.3324

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.162048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.121088 restraints weight = 2137.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.123876 restraints weight = 1365.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.125767 restraints weight = 1026.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.127020 restraints weight = 851.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.127843 restraints weight = 753.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2208  Z= 0.116
  Angle     :  0.530   5.166   2964  Z= 0.296
  Chirality :  0.056   0.141    345
  Planarity :  0.002   0.015    372
  Dihedral  :  5.537  29.436    294
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 13.24 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.07 (0.40), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.30), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR H  10 
 PHE   0.011   0.001   PHE B  20 
 HIS   0.004   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 2208)
  covalent geometry    : angle       0.52995 ( 2964)
  hydrogen bonds       : bond        0.03402 (   10)
  hydrogen bonds       : angle       5.97071 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.083 
Fit side-chains
REVERT: D   22 GLU cc_start: 0.8556 (tp30) cc_final: 0.7866 (mp0)
REVERT: B   15 GLN cc_start: 0.8771 (mp10) cc_final: 0.8462 (mp10)
REVERT: B   22 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6976 (pp20)
  outliers start: 8
  outliers final: 6
  residues processed: 30
  average time/residue: 0.0525
  time to fit residues: 1.9641
Evaluate side-chains
  31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    2.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.154056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.111306 restraints weight = 2185.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.114479 restraints weight = 1324.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.116573 restraints weight = 968.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.117982 restraints weight = 792.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.118709 restraints weight = 693.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2208  Z= 0.168
  Angle     :  0.590   5.923   2964  Z= 0.332
  Chirality :  0.058   0.147    345
  Planarity :  0.003   0.023    372
  Dihedral  :  5.704  30.606    294
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.54 %
    Favored  : 87.46 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.16 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.95 (0.41), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.31), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR H  10 
 PHE   0.012   0.002   PHE B  20 
 HIS   0.005   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 2208)
  covalent geometry    : angle       0.58956 ( 2964)
  hydrogen bonds       : bond        0.03595 (   10)
  hydrogen bonds       : angle       6.05754 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.080 
Fit side-chains
REVERT: D   22 GLU cc_start: 0.8515 (tp30) cc_final: 0.7841 (mp0)
REVERT: D   35 MET cc_start: 0.8403 (ttm) cc_final: 0.8171 (mtp)
REVERT: B   15 GLN cc_start: 0.8810 (mp10) cc_final: 0.8472 (mp10)
REVERT: B   22 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.6962 (pp20)
  outliers start: 7
  outliers final: 6
  residues processed: 31
  average time/residue: 0.0518
  time to fit residues: 2.0066
Evaluate side-chains
  32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    4.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.148177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.108137 restraints weight = 2302.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.110712 restraints weight = 1484.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.112400 restraints weight = 1125.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.113610 restraints weight = 941.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.114376 restraints weight = 832.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   2208  Z= 0.285
  Angle     :  0.723   6.908   2964  Z= 0.409
  Chirality :  0.062   0.162    345
  Planarity :  0.003   0.027    372
  Dihedral  :  6.188  30.836    294
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.30 %
    Favored  : 76.70 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.07 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.13 (0.41), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.31), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.001   TYR H  10 
 PHE   0.018   0.003   PHE A  19 
 HIS   0.006   0.002   HIS H  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 ( 2208)
  covalent geometry    : angle       0.72297 ( 2964)
  hydrogen bonds       : bond        0.03740 (   10)
  hydrogen bonds       : angle       6.14922 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7643 (pt0)
REVERT: G   28 LYS cc_start: 0.8178 (mttt) cc_final: 0.7814 (mttp)
REVERT: D   22 GLU cc_start: 0.8515 (tp30) cc_final: 0.7920 (mp0)
REVERT: H   28 LYS cc_start: 0.8305 (mttt) cc_final: 0.7913 (mttp)
  outliers start: 7
  outliers final: 5
  residues processed: 33
  average time/residue: 0.0532
  time to fit residues: 2.1240
Evaluate side-chains
  33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0470
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.7684

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

Flipped N/Q/H residues before XYZ refinement:
D  14 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.158630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.117215 restraints weight = 2202.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.119985 restraints weight = 1397.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.121886 restraints weight = 1049.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.123180 restraints weight = 868.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.124007 restraints weight = 764.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2208  Z= 0.152
  Angle     :  0.627   6.143   2964  Z= 0.350
  Chirality :  0.058   0.145    345
  Planarity :  0.003   0.031    372
  Dihedral  :  5.845  30.523    294
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.47 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 13.24 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.96 (0.41), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR H  10 
 PHE   0.015   0.001   PHE B  20 
 HIS   0.004   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 2208)
  covalent geometry    : angle       0.62665 ( 2964)
  hydrogen bonds       : bond        0.03431 (   10)
  hydrogen bonds       : angle       6.09814 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.084 
Fit side-chains
REVERT: D   22 GLU cc_start: 0.8528 (tp30) cc_final: 0.7934 (mp0)
REVERT: B   13 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.6931 (p90)
REVERT: B   22 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7021 (pp20)
  outliers start: 8
  outliers final: 6
  residues processed: 33
  average time/residue: 0.0498
  time to fit residues: 2.0732
Evaluate side-chains
  34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    4.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.146853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.106201 restraints weight = 2324.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.108709 restraints weight = 1504.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.110501 restraints weight = 1144.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.111523 restraints weight = 954.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.112338 restraints weight = 854.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   2208  Z= 0.334
  Angle     :  0.796   6.984   2964  Z= 0.451
  Chirality :  0.064   0.165    345
  Planarity :  0.004   0.031    372
  Dihedral  :  6.300  30.888    294
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.52 %
    Favored  : 73.48 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 13.70 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.28 (0.41), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.31), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.001   TYR H  10 
 PHE   0.026   0.004   PHE H  20 
 HIS   0.007   0.002   HIS H  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00744 ( 2208)
  covalent geometry    : angle       0.79573 ( 2964)
  hydrogen bonds       : bond        0.03564 (   10)
  hydrogen bonds       : angle       6.13945 (   30)

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

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

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  558 Ramachandran restraints generated.
    279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.083 
Fit side-chains
REVERT: F   28 LYS cc_start: 0.8686 (mttm) cc_final: 0.8399 (mttm)
REVERT: A   22 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7583 (pt0)
REVERT: G   28 LYS cc_start: 0.8269 (mttt) cc_final: 0.7898 (mttp)
REVERT: D   22 GLU cc_start: 0.8530 (tp30) cc_final: 0.7983 (mp0)
REVERT: H   28 LYS cc_start: 0.8340 (mttt) cc_final: 0.7968 (mttp)
REVERT: I   28 LYS cc_start: 0.8374 (mttt) cc_final: 0.8150 (mttp)
REVERT: B   13 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7324 (p90)
  outliers start: 8
  outliers final: 6
  residues processed: 38
  average time/residue: 0.0695
  time to fit residues: 3.0723
Evaluate side-chains
  40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain C residue   24 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0770
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    2.2146

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.157169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.115452 restraints weight = 2251.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.118361 restraints weight = 1432.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.120303 restraints weight = 1074.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.121489 restraints weight = 890.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.122324 restraints weight = 790.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2208  Z= 0.178
  Angle     :  0.681   6.442   2964  Z= 0.382
  Chirality :  0.059   0.151    345
  Planarity :  0.003   0.032    372
  Dihedral  :  5.997  30.374    294
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 13.70 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.13 (0.41), residues: 279
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.32), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR H  10 
 PHE   0.020   0.002   PHE H  20 
 HIS   0.004   0.001   HIS B  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 2208)
  covalent geometry    : angle       0.68112 ( 2964)
  hydrogen bonds       : bond        0.03049 (   10)
  hydrogen bonds       : angle       6.16048 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 645.25 seconds
wall clock time: 11 minutes 42.14 seconds (702.14 seconds total)