Starting phenix.real_space_refine
on Fri Aug 22 12:37:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8olg_16957/08_2025/8olg_16957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8olg_16957/08_2025/8olg_16957.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8olg_16957/08_2025/8olg_16957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8olg_16957/08_2025/8olg_16957.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8olg_16957/08_2025/8olg_16957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8olg_16957/08_2025/8olg_16957.map"
  }
  resolution = 4.2
  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=   1.001
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       5      5.16       5
     C     945      2.51       5
     N     270      2.21       5
     O     270      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: 1490
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 298
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 0.52, per 1000 atoms: 0.35
  Number of scatterers: 1490
  At special positions: 0
  Unit cell: (53.328, 57.368, 45.248, 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       5     16.00
     O     270      8.00
     N     270      7.00
     C     945      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: 0.07
  Conformation dependent library (CDL) restraints added in 44.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  330

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 5 sheets defined
      0.0% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 6.132A  pdb=" N   ALA A   2 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ALA B   2 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA C   2 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    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 23 through 27
      removed outlier: 6.841A  pdb=" N   VAL B  24 " --> pdb=" O   ASN A  23 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLY A  25 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   SER B  26 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ASN C  27 " --> pdb=" O   SER B  26 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   VAL C  24 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   ASN D  27 " --> pdb=" O   VAL C  24 " (cutoff:3.500A)
      removed outlier: 9.220A  pdb=" N   SER C  26 " --> pdb=" O   ASN D  27 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   PHE D  20 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   ASN E  23 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   GLN D  22 " --> pdb=" O   ASN E  23 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   GLY E  25 " --> pdb=" O   GLN D  22 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   VAL D  24 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   ASN E  27 " --> pdb=" O   VAL D  24 " (cutoff:3.500A)
      removed outlier: 9.365A  pdb=" N   SER D  26 " --> pdb=" O   ASN E  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 31
    Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 35
      removed outlier: 5.916A  pdb=" N   LEU A  34 " --> pdb=" O   MET B  35 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   LEU B  34 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   LEU C  34 " --> pdb=" O   MET D  35 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    11 hydrogen bonds defined for protein.
    33 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: 0.22

  Time building geometry restraints manager: 0.10 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: 510
        1.34 -     1.46: 350
        1.46 -     1.57: 650
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 1520
  Sorted by residual:
  bond pdb=" N   ASP C   1 "
       pdb=" CA  ASP C   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.12e+00
  bond pdb=" N   ASP A   1 "
       pdb=" CA  ASP A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.10e+00
  bond pdb=" N   ASP D   1 "
       pdb=" CA  ASP D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.04e+00
  bond pdb=" N   ASP B   1 "
       pdb=" CA  ASP B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" N   ASP E   1 "
       pdb=" CA  ASP E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  ... (remaining 1515 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.41: 1620
        0.41 -     0.82: 287
        0.82 -     1.23: 74
        1.23 -     1.64: 39
        1.64 -     2.04: 15
  Bond angle restraints: 2035
  Sorted by residual:
  angle pdb=" N   HIS C  13 "
        pdb=" CA  HIS C  13 "
        pdb=" C   HIS C  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.94   -2.04 1.63e+00 3.76e-01 1.57e+00
  angle pdb=" N   HIS D  13 "
        pdb=" CA  HIS D  13 "
        pdb=" C   HIS D  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.92   -2.02 1.63e+00 3.76e-01 1.53e+00
  angle pdb=" N   HIS B  13 "
        pdb=" CA  HIS B  13 "
        pdb=" C   HIS B  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.91   -2.01 1.63e+00 3.76e-01 1.52e+00
  angle pdb=" N   HIS E  13 "
        pdb=" CA  HIS E  13 "
        pdb=" C   HIS E  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.91   -2.01 1.63e+00 3.76e-01 1.52e+00
  angle pdb=" N   HIS A  13 "
        pdb=" CA  HIS A  13 "
        pdb=" C   HIS A  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.90   -2.00 1.63e+00 3.76e-01 1.50e+00
  ... (remaining 2030 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.81: 725
        8.81 -    17.61: 95
       17.61 -    26.42: 20
       26.42 -    35.22: 0
       35.22 -    44.03: 10
  Dihedral angle restraints: 850
    sinusoidal: 325
      harmonic: 525
  Sorted by residual:
  dihedral pdb=" N   HIS C   6 "
           pdb=" CA  HIS C   6 "
           pdb=" CB  HIS C   6 "
           pdb=" CG  HIS C   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.14  -38.86     3      1.50e+01 4.44e-03 6.86e+00
  dihedral pdb=" N   HIS A   6 "
           pdb=" CA  HIS A   6 "
           pdb=" CB  HIS A   6 "
           pdb=" CG  HIS A   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.16  -38.84     3      1.50e+01 4.44e-03 6.86e+00
  dihedral pdb=" N   HIS E   6 "
           pdb=" CA  HIS E   6 "
           pdb=" CB  HIS E   6 "
           pdb=" CG  HIS E   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.16  -38.84     3      1.50e+01 4.44e-03 6.86e+00
  ... (remaining 847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 89
       0.025 -    0.050: 81
       0.050 -    0.074: 12
       0.074 -    0.099: 8
       0.099 -    0.124: 20
  Chirality restraints: 210
  Sorted by residual:
  chirality pdb=" CA  ILE E  31 "
            pdb=" N   ILE E  31 "
            pdb=" C   ILE E  31 "
            pdb=" CB  ILE E  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  chirality pdb=" CA  ILE A  31 "
            pdb=" N   ILE A  31 "
            pdb=" C   ILE A  31 "
            pdb=" CB  ILE A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CA  ILE D  31 "
            pdb=" N   ILE D  31 "
            pdb=" C   ILE D  31 "
            pdb=" CB  ILE D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  ... (remaining 207 not shown)

  Planarity restraints: 270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  18 "    0.001 2.00e-02 2.50e+03   2.89e-03 8.38e-02
        pdb=" C   VAL A  18 "   -0.005 2.00e-02 2.50e+03
        pdb=" O   VAL A  18 "    0.002 2.00e-02 2.50e+03
        pdb=" N   PHE A  19 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  18 "    0.001 2.00e-02 2.50e+03   2.88e-03 8.31e-02
        pdb=" C   VAL C  18 "   -0.005 2.00e-02 2.50e+03
        pdb=" O   VAL C  18 "    0.002 2.00e-02 2.50e+03
        pdb=" N   PHE C  19 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  18 "    0.001 2.00e-02 2.50e+03   2.86e-03 8.17e-02
        pdb=" C   VAL B  18 "   -0.005 2.00e-02 2.50e+03
        pdb=" O   VAL B  18 "    0.002 2.00e-02 2.50e+03
        pdb=" N   PHE B  19 "    0.002 2.00e-02 2.50e+03
  ... (remaining 267 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 342
        2.79 -     3.32: 1347
        3.32 -     3.84: 2220
        3.84 -     4.37: 2700
        4.37 -     4.90: 5547
  Nonbonded interactions: 12156
  Sorted by model distance:
  nonbonded pdb=" O   HIS D  14 "
            pdb=" O   GLN E  15 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OD1 ASP D   7 "
            pdb=" N   SER D   8 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" OD1 ASP E   7 "
            pdb=" N   SER E   8 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" OD1 ASP A   7 "
            pdb=" N   SER A   8 "
     model   vdw
     2.396 3.120
  nonbonded pdb=" OD1 ASP C   7 "
            pdb=" N   SER C   8 "
     model   vdw
     2.396 3.120
  ... (remaining 12151 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.840
  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:          0.020
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.140
  Find NCS groups from input model:        0.010
  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:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
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      :  0.002   0.034   1520  Z= 0.134
  Angle     :  0.408   2.045   2035  Z= 0.240
  Chirality :  0.048   0.124    210
  Planarity :  0.001   0.005    270
  Dihedral  :  9.550  44.027    520
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.51 %
    Favored  : 86.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  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: -4.82 (0.39), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.67 (0.30), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.003   0.001   TYR C  10 
 PHE   0.004   0.001   PHE B   4 
 HIS   0.001   0.000   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 1520)
  covalent geometry    : angle       0.40770 ( 2035)
  hydrogen bonds       : bond        0.14620 (   11)
  hydrogen bonds       : angle       7.77797 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.049 
Fit side-chains
REVERT: A    7 ASP cc_start: 0.6200 (t0) cc_final: 0.5913 (p0)
REVERT: A   10 TYR cc_start: 0.7200 (t80) cc_final: 0.6832 (p90)
REVERT: A   20 PHE cc_start: 0.7185 (m-80) cc_final: 0.6907 (m-80)
REVERT: B   20 PHE cc_start: 0.6862 (m-80) cc_final: 0.6647 (m-80)
REVERT: C   10 TYR cc_start: 0.8033 (t80) cc_final: 0.7814 (t80)
REVERT: C   23 ASN cc_start: 0.8467 (m-40) cc_final: 0.8186 (p0)
REVERT: C   34 LEU cc_start: 0.7478 (tt) cc_final: 0.7188 (tt)
REVERT: D    7 ASP cc_start: 0.5072 (t0) cc_final: 0.4089 (m-30)
REVERT: D   23 ASN cc_start: 0.8371 (m-40) cc_final: 0.8019 (p0)
REVERT: E   13 HIS cc_start: 0.7125 (t-90) cc_final: 0.6918 (p90)
REVERT: E   23 ASN cc_start: 0.7074 (m-40) cc_final: 0.5711 (p0)
REVERT: E   35 MET cc_start: 0.4910 (ttp) cc_final: 0.4476 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0294
  time to fit residues: 2.9584
Evaluate side-chains
  55 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 6 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:    9.9990
   chunk 8 optimal weight:    0.5980
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   overall best weight:    3.7188

-------------------------------------------------------------------------------
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 = 0.4300 r_free = 0.4300 target = 0.156748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.139140 restraints weight = 2931.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.142878 restraints weight = 1468.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.145211 restraints weight = 884.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.146796 restraints weight = 607.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.147750 restraints weight = 456.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   1520  Z= 0.187
  Angle     :  0.672   4.541   2035  Z= 0.369
  Chirality :  0.050   0.145    210
  Planarity :  0.003   0.015    270
  Dihedral  :  5.188  17.165    200
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.14 %
    Favored  : 84.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  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: -4.20 (0.46), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.35), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.010   0.002   TYR C  10 
 PHE   0.011   0.002   PHE A   4 
 HIS   0.008   0.003   HIS C  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 1520)
  covalent geometry    : angle       0.67206 ( 2035)
  hydrogen bonds       : bond        0.03670 (   11)
  hydrogen bonds       : angle       6.30878 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.036 
Fit side-chains
REVERT: A    7 ASP cc_start: 0.5675 (t0) cc_final: 0.5056 (m-30)
REVERT: B    7 ASP cc_start: 0.6237 (t0) cc_final: 0.5983 (t0)
REVERT: C   22 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8741 (mm-40)
REVERT: C   31 ILE cc_start: 0.8960 (mm) cc_final: 0.8721 (tp)
REVERT: D    7 ASP cc_start: 0.5685 (t0) cc_final: 0.4934 (m-30)
REVERT: E   12 VAL cc_start: 0.8876 (t) cc_final: 0.8529 (m)
REVERT: E   35 MET cc_start: 0.5878 (ttp) cc_final: 0.5157 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0172
  time to fit residues: 1.4424
Evaluate side-chains
  54 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 2 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 12 optimal weight:    0.0270
   chunk 9 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    5.0046

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

Flipped N/Q/H residues before XYZ refinement:
E   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.156585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.138753 restraints weight = 2998.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.142188 restraints weight = 1557.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.144639 restraints weight = 961.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.146039 restraints weight = 662.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.147142 restraints weight = 513.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.5336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   1520  Z= 0.218
  Angle     :  0.735   5.335   2035  Z= 0.396
  Chirality :  0.051   0.138    210
  Planarity :  0.004   0.016    270
  Dihedral  :  5.539  18.296    200
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.84 %
    Favored  : 82.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  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: -4.58 (0.43), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.33), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.013   0.003   TYR D  10 
 PHE   0.015   0.002   PHE A   4 
 HIS   0.008   0.003   HIS C  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 1520)
  covalent geometry    : angle       0.73495 ( 2035)
  hydrogen bonds       : bond        0.05463 (   11)
  hydrogen bonds       : angle       6.47244 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 ASP cc_start: 0.6157 (t0) cc_final: 0.5950 (t0)
REVERT: B   10 TYR cc_start: 0.7649 (t80) cc_final: 0.7226 (t80)
REVERT: C   31 ILE cc_start: 0.9016 (mm) cc_final: 0.8785 (mm)
REVERT: D    7 ASP cc_start: 0.6002 (t0) cc_final: 0.5304 (m-30)
REVERT: E   35 MET cc_start: 0.6571 (ttp) cc_final: 0.4753 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0374
  time to fit residues: 2.6047
Evaluate side-chains
  53 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 0 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 9 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
E   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.157029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.138626 restraints weight = 3273.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.141773 restraints weight = 1881.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.143839 restraints weight = 1255.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.145416 restraints weight = 927.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.146559 restraints weight = 730.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.6299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   1520  Z= 0.272
  Angle     :  0.865   7.874   2035  Z= 0.465
  Chirality :  0.054   0.177    210
  Planarity :  0.004   0.018    270
  Dihedral  :  6.300  23.261    200
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.84 %
    Favored  : 82.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  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: -4.72 (0.40), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.30), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E   5 
 TYR   0.022   0.006   TYR C  10 
 PHE   0.020   0.003   PHE A   4 
 HIS   0.011   0.003   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 1520)
  covalent geometry    : angle       0.86524 ( 2035)
  hydrogen bonds       : bond        0.05746 (   11)
  hydrogen bonds       : angle       7.21327 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.056 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 ASN cc_start: 0.8199 (t0) cc_final: 0.7980 (t0)
REVERT: E   10 TYR cc_start: 0.7733 (t80) cc_final: 0.7401 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0224
  time to fit residues: 1.5986
Evaluate side-chains
  50 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.4365 r_free = 0.4365 target = 0.158100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.139972 restraints weight = 3010.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.143285 restraints weight = 1665.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.145428 restraints weight = 1080.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.146913 restraints weight = 782.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.147956 restraints weight = 617.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.6441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   1520  Z= 0.157
  Angle     :  0.665   6.481   2035  Z= 0.348
  Chirality :  0.047   0.139    210
  Planarity :  0.002   0.010    270
  Dihedral  :  5.507  20.321    200
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.68 %
    Favored  : 84.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  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: -4.63 (0.41), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.53 (0.32), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C   5 
 TYR   0.010   0.002   TYR D  10 
 PHE   0.011   0.002   PHE A   4 
 HIS   0.004   0.002   HIS C  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 1520)
  covalent geometry    : angle       0.66526 ( 2035)
  hydrogen bonds       : bond        0.05743 (   11)
  hydrogen bonds       : angle       6.81088 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.062 
Fit side-chains
REVERT: E    7 ASP cc_start: 0.6279 (t0) cc_final: 0.5855 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0241
  time to fit residues: 1.7435
Evaluate side-chains
  51 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 13 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   overall best weight:    2.2184

-------------------------------------------------------------------------------
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 = 0.4445 r_free = 0.4445 target = 0.160823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.143589 restraints weight = 2874.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.146992 restraints weight = 1556.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.149116 restraints weight = 983.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.150719 restraints weight = 699.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.151869 restraints weight = 533.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.6634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   1520  Z= 0.129
  Angle     :  0.625   6.486   2035  Z= 0.325
  Chirality :  0.047   0.136    210
  Planarity :  0.002   0.015    270
  Dihedral  :  5.209  18.155    200
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.22 %
    Favored  : 83.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  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: -4.47 (0.43), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.33), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.014   0.002   TYR C  10 
 PHE   0.008   0.001   PHE B   4 
 HIS   0.004   0.001   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 1520)
  covalent geometry    : angle       0.62545 ( 2035)
  hydrogen bonds       : bond        0.05540 (   11)
  hydrogen bonds       : angle       6.63839 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.101 
Fit side-chains
REVERT: E    7 ASP cc_start: 0.6247 (t0) cc_final: 0.5854 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0239
  time to fit residues: 1.7547
Evaluate side-chains
  53 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    5.1990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.156508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.138816 restraints weight = 2991.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.141963 restraints weight = 1630.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.144075 restraints weight = 1048.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.145536 restraints weight = 758.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.146672 restraints weight = 596.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.7011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   1520  Z= 0.218
  Angle     :  0.781   7.018   2035  Z= 0.407
  Chirality :  0.050   0.145    210
  Planarity :  0.003   0.014    270
  Dihedral  :  5.916  22.273    200
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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: -4.66 (0.41), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.31), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D   5 
 TYR   0.022   0.004   TYR C  10 
 PHE   0.014   0.002   PHE B   4 
 HIS   0.007   0.003   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 1520)
  covalent geometry    : angle       0.78054 ( 2035)
  hydrogen bonds       : bond        0.05425 (   11)
  hydrogen bonds       : angle       7.46299 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.072 
Fit side-chains
REVERT: B   10 TYR cc_start: 0.7404 (t80) cc_final: 0.6969 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0238
  time to fit residues: 1.7589
Evaluate side-chains
  52 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0870
   chunk 10 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.5962

-------------------------------------------------------------------------------
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 = 0.4487 r_free = 0.4487 target = 0.161845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.143510 restraints weight = 2897.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.146840 restraints weight = 1477.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.148889 restraints weight = 926.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.150488 restraints weight = 673.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.151486 restraints weight = 527.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.4379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.7192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1520  Z= 0.140
  Angle     :  0.715   6.849   2035  Z= 0.356
  Chirality :  0.047   0.141    210
  Planarity :  0.002   0.011    270
  Dihedral  :  5.629  19.395    200
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.22 %
    Favored  : 83.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -4.42 (0.44), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.33), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E   5 
 TYR   0.019   0.003   TYR C  10 
 PHE   0.009   0.001   PHE B   4 
 HIS   0.004   0.001   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 1520)
  covalent geometry    : angle       0.71537 ( 2035)
  hydrogen bonds       : bond        0.05288 (   11)
  hydrogen bonds       : angle       7.15458 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A   22 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6881 (mp10)
REVERT: B   10 TYR cc_start: 0.7122 (t80) cc_final: 0.6827 (t80)
REVERT: E   10 TYR cc_start: 0.7299 (t80) cc_final: 0.6924 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0269
  time to fit residues: 1.9282
Evaluate side-chains
  52 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    0.0770
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.9944

-------------------------------------------------------------------------------
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 = 0.4526 r_free = 0.4526 target = 0.165681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.147406 restraints weight = 2806.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.150668 restraints weight = 1458.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.152762 restraints weight = 924.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.154204 restraints weight = 673.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.155150 restraints weight = 532.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.7360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   1520  Z= 0.122
  Angle     :  0.645   7.087   2035  Z= 0.328
  Chirality :  0.045   0.139    210
  Planarity :  0.002   0.011    270
  Dihedral  :  5.337  18.049    200
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.22 %
    Favored  : 83.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  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: -4.31 (0.46), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.35), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E   5 
 TYR   0.015   0.002   TYR C  10 
 PHE   0.007   0.001   PHE B   4 
 HIS   0.003   0.001   HIS A  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 1520)
  covalent geometry    : angle       0.64528 ( 2035)
  hydrogen bonds       : bond        0.05136 (   11)
  hydrogen bonds       : angle       6.85395 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.060 
Fit side-chains
REVERT: B   35 MET cc_start: 0.5278 (mtt) cc_final: 0.4950 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0239
  time to fit residues: 1.6635
Evaluate side-chains
  49 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 5 optimal weight:    0.0980
   chunk 11 optimal weight:    0.0670
   chunk 1 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0770
   chunk 10 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.8480

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.169615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.152191 restraints weight = 2719.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.155770 restraints weight = 1348.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.158111 restraints weight = 815.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.159715 restraints weight = 566.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.160690 restraints weight = 428.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.4457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6601
moved from start:          0.7498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   1520  Z= 0.099
  Angle     :  0.605   6.897   2035  Z= 0.309
  Chirality :  0.045   0.137    210
  Planarity :  0.002   0.011    270
  Dihedral  :  5.228  18.226    200
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.51 %
    Favored  : 86.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  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: -4.19 (0.47), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.36), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E   5 
 TYR   0.012   0.002   TYR E  10 
 PHE   0.004   0.001   PHE E   4 
 HIS   0.001   0.000   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 1520)
  covalent geometry    : angle       0.60473 ( 2035)
  hydrogen bonds       : bond        0.04965 (   11)
  hydrogen bonds       : angle       6.75615 (   33)

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A   22 GLN cc_start: 0.6771 (mm-40) cc_final: 0.6297 (mm-40)
REVERT: E   10 TYR cc_start: 0.7591 (t80) cc_final: 0.7043 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0232
  time to fit residues: 1.6226
Evaluate side-chains
  47 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0870
   chunk 4 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0370
   chunk 6 optimal weight:   30.0000
   chunk 10 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    3.2242

-------------------------------------------------------------------------------
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 = 0.4480 r_free = 0.4480 target = 0.163829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.145847 restraints weight = 2846.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.149124 restraints weight = 1531.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.151215 restraints weight = 958.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.152827 restraints weight = 689.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.153607 restraints weight = 530.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.7560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   1520  Z= 0.154
  Angle     :  0.678   6.660   2035  Z= 0.358
  Chirality :  0.047   0.143    210
  Planarity :  0.002   0.011    270
  Dihedral  :  5.493  18.259    200
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.22 %
    Favored  : 83.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  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: -4.31 (0.46), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.35), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D   5 
 TYR   0.011   0.002   TYR E  10 
 PHE   0.009   0.002   PHE B   4 
 HIS   0.005   0.002   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 1520)
  covalent geometry    : angle       0.67790 ( 2035)
  hydrogen bonds       : bond        0.05003 (   11)
  hydrogen bonds       : angle       6.96742 (   33)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 535.06 seconds
wall clock time: 10 minutes 13.97 seconds (613.97 seconds total)