Starting phenix.real_space_refine
on Fri Aug 22 16:01:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nxp_49910/08_2025/9nxp_49910.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nxp_49910/08_2025/9nxp_49910.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nxp_49910/08_2025/9nxp_49910.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nxp_49910/08_2025/9nxp_49910.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nxp_49910/08_2025/9nxp_49910.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nxp_49910/08_2025/9nxp_49910.cif"
  }
  resolution = 4.5
  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=  -0.001 sd=   0.003
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      21      5.16       5
     C    3435      2.51       5
     N     855      2.21       5
     O     993      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  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: 5304
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1768
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 200}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.34, per 1000 atoms: 0.25
  Number of scatterers: 5304
  At special positions: 0
  Unit cell: (59.598, 60.544, 168.388, 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      21     16.00
     O     993      8.00
     N     855      7.00
     C    3435      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: 0.42
  Conformation dependent library (CDL) restraints added in 221.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1254

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      18.4% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 15
      No H-bonds generated for 'chain 'A' and resid 13 through 15'
    Processing helix  chain 'A' and resid 16 through 37
      removed outlier: 4.249A  pdb=" N   PHE A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 143
    Processing helix  chain 'A' and resid 174 through 185
    Processing helix  chain 'B' and resid 13 through 15
      No H-bonds generated for 'chain 'B' and resid 13 through 15'
    Processing helix  chain 'B' and resid 16 through 37
      removed outlier: 4.250A  pdb=" N   PHE B  20 " --> pdb=" O   GLU B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 143
    Processing helix  chain 'B' and resid 174 through 185
    Processing helix  chain 'C' and resid 13 through 15
      No H-bonds generated for 'chain 'C' and resid 13 through 15'
    Processing helix  chain 'C' and resid 16 through 37
      removed outlier: 4.250A  pdb=" N   PHE C  20 " --> pdb=" O   GLU C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 143
    Processing helix  chain 'C' and resid 174 through 185
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94
    Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 137
      removed outlier: 6.763A  pdb=" N   THR A 134 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ILE A 208 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A 136 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 164
    Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 94
    Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 94
    Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 137
      removed outlier: 6.764A  pdb=" N   THR B 134 " --> pdb=" O   ILE B 208 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ILE B 208 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LEU B 136 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 164
    Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 94
    Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 94
    Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 137
      removed outlier: 6.764A  pdb=" N   THR C 134 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ILE C 208 " --> pdb=" O   THR C 134 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LEU C 136 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 164

    204 hydrogen bonds defined for protein.
    486 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: 0.73

  Time building geometry restraints manager: 0.58 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: 1690
        1.34 -     1.46: 1070
        1.46 -     1.57: 2676
        1.57 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 5475
  Sorted by residual:
  bond pdb=" C   LEU B  18 "
       pdb=" N   PRO B  19 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.017 1.28e-02 6.10e+03 1.76e+00
  bond pdb=" C   LEU A  18 "
       pdb=" N   PRO A  19 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.017 1.28e-02 6.10e+03 1.74e+00
  bond pdb=" C   LEU C  18 "
       pdb=" N   PRO C  19 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.28e-02 6.10e+03 1.60e+00
  bond pdb=" CA  LEU C  18 "
       pdb=" C   LEU C  18 "
    ideal  model  delta    sigma   weight residual
    1.521  1.531 -0.010 1.08e-02 8.57e+03 8.36e-01
  bond pdb=" CA  LEU B  18 "
       pdb=" C   LEU B  18 "
    ideal  model  delta    sigma   weight residual
    1.521  1.531 -0.010 1.08e-02 8.57e+03 8.02e-01
  ... (remaining 5470 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 7202
        1.66 -     3.32: 265
        3.32 -     4.97: 36
        4.97 -     6.63: 6
        6.63 -     8.29: 6
  Bond angle restraints: 7515
  Sorted by residual:
  angle pdb=" C   PHE A  58 "
        pdb=" N   ALA A  59 "
        pdb=" CA  ALA A  59 "
      ideal   model   delta    sigma   weight residual
     121.80  130.09   -8.29 2.44e+00 1.68e-01 1.15e+01
  angle pdb=" C   PHE C  58 "
        pdb=" N   ALA C  59 "
        pdb=" CA  ALA C  59 "
      ideal   model   delta    sigma   weight residual
     121.80  130.09   -8.29 2.44e+00 1.68e-01 1.15e+01
  angle pdb=" C   PHE B  58 "
        pdb=" N   ALA B  59 "
        pdb=" CA  ALA B  59 "
      ideal   model   delta    sigma   weight residual
     121.80  130.02   -8.22 2.44e+00 1.68e-01 1.13e+01
  angle pdb=" N   GLY A  61 "
        pdb=" CA  GLY A  61 "
        pdb=" C   GLY A  61 "
      ideal   model   delta    sigma   weight residual
     113.18  120.55   -7.37 2.37e+00 1.78e-01 9.68e+00
  angle pdb=" N   GLY B  61 "
        pdb=" CA  GLY B  61 "
        pdb=" C   GLY B  61 "
      ideal   model   delta    sigma   weight residual
     113.18  120.55   -7.37 2.37e+00 1.78e-01 9.67e+00
  ... (remaining 7510 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 2986
       17.00 -    34.00: 227
       34.00 -    51.00: 33
       51.00 -    68.00: 6
       68.00 -    85.00: 9
  Dihedral angle restraints: 3261
    sinusoidal: 1296
      harmonic: 1965
  Sorted by residual:
  dihedral pdb=" CA  GLY A  61 "
           pdb=" C   GLY A  61 "
           pdb=" N   VAL A  62 "
           pdb=" CA  VAL A  62 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.22  -18.78     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLY C  61 "
           pdb=" C   GLY C  61 "
           pdb=" N   VAL C  62 "
           pdb=" CA  VAL C  62 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.23  -18.77     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLY B  61 "
           pdb=" C   GLY B  61 "
           pdb=" N   VAL B  62 "
           pdb=" CA  VAL B  62 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.24  -18.76     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 3258 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 447
       0.026 -    0.053: 221
       0.053 -    0.079: 59
       0.079 -    0.105: 58
       0.105 -    0.132: 34
  Chirality restraints: 819
  Sorted by residual:
  chirality pdb=" CA  ILE B 157 "
            pdb=" N   ILE B 157 "
            pdb=" C   ILE B 157 "
            pdb=" CB  ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  chirality pdb=" CA  ILE A 157 "
            pdb=" N   ILE A 157 "
            pdb=" C   ILE A 157 "
            pdb=" CB  ILE A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  ILE C 157 "
            pdb=" N   ILE C 157 "
            pdb=" C   ILE C 157 "
            pdb=" CB  ILE C 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 816 not shown)

  Planarity restraints: 996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  64 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.72e+00
        pdb=" N   PRO A  65 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A  65 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  65 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  64 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.70e+00
        pdb=" N   PRO B  65 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B  65 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  65 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C  64 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO C  65 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C  65 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  65 "    0.023 5.00e-02 4.00e+02
  ... (remaining 993 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 112
        2.66 -     3.22: 5011
        3.22 -     3.78: 8809
        3.78 -     4.34: 11401
        4.34 -     4.90: 18176
  Nonbonded interactions: 43509
  Sorted by model distance:
  nonbonded pdb=" O   GLY B  41 "
            pdb=" OH  TYR B  57 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" O   GLY A  41 "
            pdb=" OH  TYR A  57 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" O   GLY C  41 "
            pdb=" OH  TYR C  57 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" OG1 THR A 201 "
            pdb=" OD1 ASN A 203 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG1 THR C 201 "
            pdb=" OD1 ASN C 203 "
     model   vdw
     2.207 3.040
  ... (remaining 43504 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'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
Set refine NCS operators
  NCS operators will be refined.
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:             6.390
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.810
  Find NCS groups from input model:        0.020
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5475  Z= 0.137
  Angle     :  0.728   8.290   7515  Z= 0.376
  Chirality :  0.044   0.132    819
  Planarity :  0.005   0.041    996
  Dihedral  : 13.055  84.996   2007
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  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:  0.01 (0.34), residues: 678
  helix:  1.18 (0.55), residues: 102
  sheet:  0.50 (0.46), residues: 123
  loop : -0.40 (0.32), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 110 
 TYR   0.009   0.002   TYR B  72 
 PHE   0.013   0.001   PHE A  58 
 TRP   0.006   0.001   TRP A  78 
 HIS   0.001   0.000   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5475)
  covalent geometry    : angle       0.72808 ( 7515)
  hydrogen bonds       : bond        0.07197 (  180)
  hydrogen bonds       : angle       4.67264 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.0733 (ppp) cc_final: -0.0082 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0466
  time to fit residues: 1.4447
Evaluate side-chains
  18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:   50.0000
   chunk 5 optimal weight:    0.0470
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.0670
   chunk 61 optimal weight:   50.0000
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0970
   overall best weight:    0.2614
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.074568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.062878 restraints weight = 17063.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.064112 restraints weight = 10285.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.064958 restraints weight = 6800.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.065565 restraints weight = 4813.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.065981 restraints weight = 3645.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5475  Z= 0.109
  Angle     :  0.645   7.792   7515  Z= 0.316
  Chirality :  0.045   0.133    819
  Planarity :  0.005   0.037    996
  Dihedral  :  4.615  18.408    729
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  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: -0.02 (0.33), residues: 678
  helix:  1.34 (0.54), residues: 102
  sheet:  0.59 (0.44), residues: 123
  loop : -0.50 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 185 
 TYR   0.010   0.001   TYR A  72 
 PHE   0.015   0.001   PHE C  58 
 TRP   0.007   0.001   TRP C  40 
 HIS   0.003   0.001   HIS C  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5475)
  covalent geometry    : angle       0.64456 ( 7515)
  hydrogen bonds       : bond        0.03081 (  180)
  hydrogen bonds       : angle       3.88830 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8008 (mmt) cc_final: 0.7654 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0741
  time to fit residues: 2.1504
Evaluate side-chains
  17 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 56 optimal weight:    0.0570
   chunk 45 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   chunk 39 optimal weight:   50.0000
   chunk 58 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0030
   overall best weight:    0.9110
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.074328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.062590 restraints weight = 16886.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.063936 restraints weight = 10061.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.064826 restraints weight = 6551.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.065443 restraints weight = 4619.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.065795 restraints weight = 3473.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5475  Z= 0.101
  Angle     :  0.622   7.048   7515  Z= 0.302
  Chirality :  0.044   0.130    819
  Planarity :  0.005   0.040    996
  Dihedral  :  4.436  18.272    729
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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:  0.14 (0.33), residues: 678
  helix:  1.51 (0.54), residues: 102
  sheet:  0.86 (0.41), residues: 141
  loop : -0.52 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 205 
 TYR   0.007   0.001   TYR A 165 
 PHE   0.011   0.001   PHE B  58 
 TRP   0.004   0.001   TRP C  40 
 HIS   0.001   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 5475)
  covalent geometry    : angle       0.62228 ( 7515)
  hydrogen bonds       : bond        0.02872 (  180)
  hydrogen bonds       : angle       3.76845 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.2047 (tmm) cc_final: 0.0683 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0562
  time to fit residues: 1.7551
Evaluate side-chains
  18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 27 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 65 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0170
   chunk 55 optimal weight:    0.9990
   chunk 50 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5620
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.074332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.062840 restraints weight = 16802.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.064142 restraints weight = 10123.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.065017 restraints weight = 6686.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.065615 restraints weight = 4771.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.066018 restraints weight = 3644.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5475  Z= 0.098
  Angle     :  0.613   6.841   7515  Z= 0.299
  Chirality :  0.045   0.142    819
  Planarity :  0.005   0.043    996
  Dihedral  :  4.397  17.940    729
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  1.55 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.15 (0.34), residues: 678
  helix:  1.50 (0.54), residues: 102
  sheet:  0.91 (0.42), residues: 141
  loop : -0.52 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 185 
 TYR   0.013   0.002   TYR C  72 
 PHE   0.010   0.001   PHE C  58 
 TRP   0.005   0.001   TRP C  40 
 HIS   0.002   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 5475)
  covalent geometry    : angle       0.61307 ( 7515)
  hydrogen bonds       : bond        0.02684 (  180)
  hydrogen bonds       : angle       3.62138 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ASP cc_start: 0.8103 (t0) cc_final: 0.7898 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0704
  time to fit residues: 2.4875
Evaluate side-chains
  16 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 61 optimal weight:   30.0000
   chunk 24 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 54 optimal weight:   20.0000
   chunk 34 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0060
   chunk 13 optimal weight:   20.0000
   chunk 17 optimal weight:    0.6980
   chunk 59 optimal weight:   40.0000
   overall best weight:    2.1000
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.072748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.061141 restraints weight = 18030.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.062307 restraints weight = 11014.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.063043 restraints weight = 7401.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.063684 restraints weight = 5443.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.064077 restraints weight = 4197.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5475  Z= 0.107
  Angle     :  0.615   6.391   7515  Z= 0.299
  Chirality :  0.044   0.125    819
  Planarity :  0.005   0.042    996
  Dihedral  :  4.344  18.282    729
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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:  0.14 (0.34), residues: 678
  helix:  1.52 (0.54), residues: 102
  sheet:  0.84 (0.43), residues: 141
  loop : -0.52 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 110 
 TYR   0.009   0.001   TYR B 165 
 PHE   0.007   0.001   PHE B  58 
 TRP   0.003   0.001   TRP B 143 
 HIS   0.001   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5475)
  covalent geometry    : angle       0.61463 ( 7515)
  hydrogen bonds       : bond        0.02791 (  180)
  hydrogen bonds       : angle       3.58259 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.7745 (mmt) cc_final: 0.7291 (mmt)
REVERT: A  197 MET cc_start: 0.2157 (tmm) cc_final: 0.1162 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0615
  time to fit residues: 1.9013
Evaluate side-chains
  16 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    2.1388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.072079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.060564 restraints weight = 17883.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.061778 restraints weight = 10538.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.062625 restraints weight = 6899.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.063107 restraints weight = 4905.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.063501 restraints weight = 3821.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5475  Z= 0.103
  Angle     :  0.597   6.285   7515  Z= 0.293
  Chirality :  0.044   0.125    819
  Planarity :  0.005   0.041    996
  Dihedral  :  4.286  18.853    729
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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:  0.22 (0.34), residues: 678
  helix:  1.54 (0.54), residues: 102
  sheet:  0.96 (0.43), residues: 141
  loop : -0.48 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 205 
 TYR   0.010   0.002   TYR C  72 
 PHE   0.007   0.001   PHE A  58 
 TRP   0.003   0.001   TRP C 119 
 HIS   0.003   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 5475)
  covalent geometry    : angle       0.59662 ( 7515)
  hydrogen bonds       : bond        0.02792 (  180)
  hydrogen bonds       : angle       3.48260 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.7941 (mmt) cc_final: 0.7593 (mmt)
REVERT: A  197 MET cc_start: 0.1818 (tmm) cc_final: 0.0868 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0624
  time to fit residues: 1.8581
Evaluate side-chains
  14 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 62 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0870
   chunk 13 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.7160
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.073085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.061236 restraints weight = 17158.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.062426 restraints weight = 10651.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.063258 restraints weight = 7289.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.063816 restraints weight = 5342.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.064264 restraints weight = 4173.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5475  Z= 0.099
  Angle     :  0.614   6.432   7515  Z= 0.299
  Chirality :  0.044   0.125    819
  Planarity :  0.005   0.043    996
  Dihedral  :  4.128  18.105    729
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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:  0.18 (0.34), residues: 678
  helix:  1.64 (0.54), residues: 102
  sheet:  1.12 (0.44), residues: 141
  loop : -0.62 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 205 
 TYR   0.008   0.001   TYR A  57 
 PHE   0.008   0.001   PHE A  58 
 TRP   0.005   0.001   TRP C  78 
 HIS   0.002   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 5475)
  covalent geometry    : angle       0.61376 ( 7515)
  hydrogen bonds       : bond        0.02615 (  180)
  hydrogen bonds       : angle       3.42748 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.2125 (tmm) cc_final: 0.1136 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0636
  time to fit residues: 2.1623
Evaluate side-chains
  16 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 50 optimal weight:    0.0870
   chunk 52 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 55 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.3162
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.073080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.061299 restraints weight = 17882.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.062452 restraints weight = 11241.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.063224 restraints weight = 7696.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.063759 restraints weight = 5671.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.064180 restraints weight = 4438.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5475  Z= 0.100
  Angle     :  0.625   6.073   7515  Z= 0.308
  Chirality :  0.044   0.124    819
  Planarity :  0.005   0.043    996
  Dihedral  :  4.329  21.369    729
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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:  0.19 (0.34), residues: 678
  helix:  1.62 (0.54), residues: 102
  sheet:  0.59 (0.42), residues: 162
  loop : -0.43 (0.33), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 110 
 TYR   0.010   0.002   TYR A  72 
 PHE   0.006   0.001   PHE A  58 
 TRP   0.005   0.001   TRP B 143 
 HIS   0.002   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5475)
  covalent geometry    : angle       0.62482 ( 7515)
  hydrogen bonds       : bond        0.02592 (  180)
  hydrogen bonds       : angle       3.34840 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 ASP cc_start: 0.8165 (t0) cc_final: 0.7950 (t0)
REVERT: A  197 MET cc_start: 0.2180 (tmm) cc_final: 0.1223 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0661
  time to fit residues: 2.0793
Evaluate side-chains
  18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 60 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0670
   chunk 13 optimal weight:   20.0000
   chunk 21 optimal weight:   40.0000
   chunk 52 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0470
   overall best weight:    0.5818
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.073094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.061404 restraints weight = 18188.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.062533 restraints weight = 11280.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.063327 restraints weight = 7680.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.063878 restraints weight = 5605.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.064237 restraints weight = 4351.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   5475  Z= 0.101
  Angle     :  0.641   6.153   7515  Z= 0.316
  Chirality :  0.044   0.125    819
  Planarity :  0.005   0.045    996
  Dihedral  :  4.404  24.253    729
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  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:  0.32 (0.34), residues: 678
  helix:  1.68 (0.54), residues: 102
  sheet:  1.17 (0.44), residues: 141
  loop : -0.48 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 110 
 TYR   0.009   0.001   TYR C 142 
 PHE   0.007   0.001   PHE C  58 
 TRP   0.005   0.001   TRP A 119 
 HIS   0.002   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 5475)
  covalent geometry    : angle       0.64094 ( 7515)
  hydrogen bonds       : bond        0.02528 (  180)
  hydrogen bonds       : angle       3.39284 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 ASP cc_start: 0.8182 (t0) cc_final: 0.7965 (t0)
REVERT: A  197 MET cc_start: 0.2163 (tmm) cc_final: 0.1258 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0612
  time to fit residues: 1.8892
Evaluate side-chains
  18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 6 optimal weight:    0.1980
   chunk 25 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0570
   chunk 37 optimal weight:    0.0030
   chunk 44 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0030
   chunk 22 optimal weight:   10.0000
   overall best weight:    0.2118
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.073471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.061884 restraints weight = 18027.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.063033 restraints weight = 11383.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.063854 restraints weight = 7799.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.064400 restraints weight = 5733.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.064749 restraints weight = 4467.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5475  Z= 0.105
  Angle     :  0.664   5.976   7515  Z= 0.328
  Chirality :  0.044   0.125    819
  Planarity :  0.005   0.044    996
  Dihedral  :  4.507  27.144    729
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  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:  0.23 (0.34), residues: 678
  helix:  1.70 (0.54), residues: 102
  sheet:  0.78 (0.44), residues: 150
  loop : -0.46 (0.33), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 205 
 TYR   0.010   0.002   TYR B  57 
 PHE   0.007   0.001   PHE A 223 
 TRP   0.006   0.001   TRP C  40 
 HIS   0.002   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 5475)
  covalent geometry    : angle       0.66390 ( 7515)
  hydrogen bonds       : bond        0.02467 (  180)
  hydrogen bonds       : angle       3.40591 (  486)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.8637 (tmmt) cc_final: 0.8413 (tptt)
REVERT: A  197 MET cc_start: 0.2193 (tmm) cc_final: 0.1278 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0577
  time to fit residues: 1.8631
Evaluate side-chains
  16 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 65 optimal weight:    0.0270
   chunk 14 optimal weight:    0.0000
   chunk 45 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0010
   chunk 30 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 8 optimal weight:    0.4980
   chunk 57 optimal weight:   20.0000
   chunk 47 optimal weight:    8.9990
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.2048
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.074163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.063448 restraints weight = 18951.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.064552 restraints weight = 12273.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.065245 restraints weight = 8650.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.065863 restraints weight = 6632.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.066259 restraints weight = 5226.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5475  Z= 0.107
  Angle     :  0.654   6.207   7515  Z= 0.322
  Chirality :  0.044   0.123    819
  Planarity :  0.006   0.044    996
  Dihedral  :  4.419  26.998    729
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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:  0.16 (0.34), residues: 678
  helix:  1.74 (0.54), residues: 102
  sheet:  0.32 (0.41), residues: 165
  loop : -0.38 (0.33), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 205 
 TYR   0.007   0.001   TYR A 142 
 PHE   0.013   0.001   PHE B 223 
 TRP   0.006   0.001   TRP C  40 
 HIS   0.002   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5475)
  covalent geometry    : angle       0.65392 ( 7515)
  hydrogen bonds       : bond        0.02509 (  180)
  hydrogen bonds       : angle       3.34947 (  486)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 942.92 seconds
wall clock time: 17 minutes 7.64 seconds (1027.64 seconds total)