Starting phenix.real_space_refine
on Wed Sep 17 02:59:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ve7_43167/09_2025/8ve7_43167.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ve7_43167/09_2025/8ve7_43167.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ve7_43167/09_2025/8ve7_43167.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ve7_43167/09_2025/8ve7_43167.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ve7_43167/09_2025/8ve7_43167.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ve7_43167/09_2025/8ve7_43167.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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       6      5.16       5
     C    1434      2.51       5
     N     387      2.21       5
     O     437      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2264
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2264
          Classifications: {'peptide': 294}
          Link IDs: {'PTRANS': 6, 'TRANS': 287}
  Time building chain proxies: 0.96, per 1000 atoms: 0.42
  Number of scatterers: 2264
  At special positions: 0
  Unit cell: (53.71, 57.64, 115.28, 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       6     16.00
     O     437      8.00
     N     387      7.00
     C    1434      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: 0.25
  Conformation dependent library (CDL) restraints added in 114.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  538

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      75.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 45
    Processing helix  chain 'A' and resid 49 through 72
    Processing helix  chain 'A' and resid 80 through 97
      removed outlier: 3.887A  pdb=" N   ILE A  84 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   MET A  97 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 137
    Processing helix  chain 'A' and resid 139 through 175
    Processing helix  chain 'A' and resid 176 through 186
      removed outlier: 4.533A  pdb=" N   VAL A 180 " --> pdb=" O   GLN A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 208
    Processing helix  chain 'A' and resid 209 through 219
      removed outlier: 3.672A  pdb=" N   VAL A 213 " --> pdb=" O   HIS A 209 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   HIS A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 240
    Processing helix  chain 'A' and resid 242 through 252
    Processing helix  chain 'A' and resid 265 through 273
      removed outlier: 3.654A  pdb=" N   LEU A 269 " --> pdb=" O   THR A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 285
    Processing helix  chain 'A' and resid 298 through 307
      removed outlier: 3.532A  pdb=" N   GLY A 307 " --> pdb=" O   SER A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 316
      removed outlier: 3.930A  pdb=" N   ALA A 312 " --> pdb=" O   ASN A 308 " (cutoff:3.500A)

    157 hydrogen bonds defined for protein.
    471 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: 0.44

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 776
        1.34 -     1.46: 222
        1.46 -     1.57: 1288
        1.57 -     1.69: 0
        1.69 -     1.80: 11
  Bond restraints: 2297
  Sorted by residual:
  bond pdb=" CG  GLU A 214 "
       pdb=" CD  GLU A 214 "
    ideal  model  delta    sigma   weight residual
    1.516  1.493  0.023 2.50e-02 1.60e+03 8.43e-01
  bond pdb=" CD  GLU A 214 "
       pdb=" OE1 GLU A 214 "
    ideal  model  delta    sigma   weight residual
    1.249  1.233  0.016 1.90e-02 2.77e+03 7.19e-01
  bond pdb=" CB  GLN A  60 "
       pdb=" CG  GLN A  60 "
    ideal  model  delta    sigma   weight residual
    1.520  1.499  0.021 3.00e-02 1.11e+03 4.72e-01
  bond pdb=" CA  GLN A  60 "
       pdb=" C   GLN A  60 "
    ideal  model  delta    sigma   weight residual
    1.523  1.515  0.009 1.30e-02 5.92e+03 4.55e-01
  bond pdb=" CB  ARG A 123 "
       pdb=" CG  ARG A 123 "
    ideal  model  delta    sigma   weight residual
    1.520  1.501  0.019 3.00e-02 1.11e+03 4.04e-01
  ... (remaining 2292 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 2867
        0.98 -     1.95: 191
        1.95 -     2.93: 30
        2.93 -     3.90: 10
        3.90 -     4.88: 10
  Bond angle restraints: 3108
  Sorted by residual:
  angle pdb=" C   GLN A 176 "
        pdb=" CA  GLN A 176 "
        pdb=" CB  GLN A 176 "
      ideal   model   delta    sigma   weight residual
     110.19  115.07   -4.88 1.62e+00 3.81e-01 9.07e+00
  angle pdb=" C   ASN A 308 "
        pdb=" CA  ASN A 308 "
        pdb=" CB  ASN A 308 "
      ideal   model   delta    sigma   weight residual
     110.22  114.17   -3.95 1.67e+00 3.59e-01 5.59e+00
  angle pdb=" N   GLU A 214 "
        pdb=" CA  GLU A 214 "
        pdb=" CB  GLU A 214 "
      ideal   model   delta    sigma   weight residual
     110.01  113.37   -3.36 1.45e+00 4.76e-01 5.37e+00
  angle pdb=" CA  GLN A 176 "
        pdb=" CB  GLN A 176 "
        pdb=" CG  GLN A 176 "
      ideal   model   delta    sigma   weight residual
     114.10  118.14   -4.04 2.00e+00 2.50e-01 4.09e+00
  angle pdb=" CA  GLN A 196 "
        pdb=" CB  GLN A 196 "
        pdb=" CG  GLN A 196 "
      ideal   model   delta    sigma   weight residual
     114.10  117.84   -3.74 2.00e+00 2.50e-01 3.50e+00
  ... (remaining 3103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 1303
       17.80 -    35.59: 73
       35.59 -    53.38: 4
       53.38 -    71.18: 2
       71.18 -    88.97: 2
  Dihedral angle restraints: 1384
    sinusoidal: 547
      harmonic: 837
  Sorted by residual:
  dihedral pdb=" CA  GLN A 176 "
           pdb=" C   GLN A 176 "
           pdb=" N   ASP A 177 "
           pdb=" CA  ASP A 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.04  -33.96     0      5.00e+00 4.00e-02 4.61e+01
  dihedral pdb=" CB  GLU A 163 "
           pdb=" CG  GLU A 163 "
           pdb=" CD  GLU A 163 "
           pdb=" OE1 GLU A 163 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -81.63   81.63     1      3.00e+01 1.11e-03 9.11e+00
  dihedral pdb=" CG  LYS A  53 "
           pdb=" CD  LYS A  53 "
           pdb=" CE  LYS A  53 "
           pdb=" NZ  LYS A  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  105.56  -45.56     3      1.50e+01 4.44e-03 8.19e+00
  ... (remaining 1381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 194
       0.022 -    0.044: 82
       0.044 -    0.066: 52
       0.066 -    0.087: 30
       0.087 -    0.109: 5
  Chirality restraints: 363
  Sorted by residual:
  chirality pdb=" CA  ILE A  76 "
            pdb=" N   ILE A  76 "
            pdb=" C   ILE A  76 "
            pdb=" CB  ILE A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.98e-01
  chirality pdb=" CA  VAL A  98 "
            pdb=" N   VAL A  98 "
            pdb=" C   VAL A  98 "
            pdb=" CB  VAL A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.86e-01
  chirality pdb=" CG  LEU A 234 "
            pdb=" CB  LEU A 234 "
            pdb=" CD1 LEU A 234 "
            pdb=" CD2 LEU A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.49   -0.10 2.00e-01 2.50e+01 2.65e-01
  ... (remaining 360 not shown)

  Planarity restraints: 403
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 206 "   -0.005 2.00e-02 2.50e+03   6.60e-03 1.09e+00
        pdb=" CG  TRP A 206 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 206 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 206 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 206 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 206 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 206 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 206 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 308 "    0.005 2.00e-02 2.50e+03   9.04e-03 8.17e-01
        pdb=" C   ASN A 308 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   ASN A 308 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLU A 309 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  38 "    0.004 2.00e-02 2.50e+03   8.16e-03 6.65e-01
        pdb=" C   THR A  38 "   -0.014 2.00e-02 2.50e+03
        pdb=" O   THR A  38 "    0.005 2.00e-02 2.50e+03
        pdb=" N   SER A  39 "    0.005 2.00e-02 2.50e+03
  ... (remaining 400 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 53
        2.69 -     3.24: 2431
        3.24 -     3.80: 3727
        3.80 -     4.35: 4670
        4.35 -     4.90: 7332
  Nonbonded interactions: 18213
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  38 "
            pdb=" OE1 GLN A  60 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OG1 THR A 232 "
            pdb=" ND1 HIS A 235 "
     model   vdw
     2.141 3.120
  nonbonded pdb=" O   GLN A 196 "
            pdb=" OG1 THR A 228 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   PRO A 210 "
            pdb=" N   VAL A 213 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" O   ASP A 239 "
            pdb=" NH1 ARG A 273 "
     model   vdw
     2.345 3.120
  ... (remaining 18208 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.160
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
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   0.023   2297  Z= 0.167
  Angle     :  0.606   4.878   3108  Z= 0.345
  Chirality :  0.037   0.109    363
  Planarity :  0.003   0.020    403
  Dihedral  : 11.541  88.973    846
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  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 : 0.35 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.80 (0.49), residues: 292
  helix:  2.03 (0.34), residues: 217
  sheet:  None (None), residues: 0
  loop :  1.61 (0.76), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 226 
 TYR   0.009   0.001   TYR A  64 
 PHE   0.004   0.001   PHE A 154 
 TRP   0.018   0.002   TRP A 206 
 HIS   0.006   0.001   HIS A 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 2297)
  covalent geometry    : angle       0.60614 ( 3108)
  hydrogen bonds       : bond        0.11179 (  157)
  hydrogen bonds       : angle       4.96979 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: A  193 HIS cc_start: 0.8980 (p90) cc_final: 0.8692 (p90)
REVERT: A  257 ASN cc_start: 0.7832 (m-40) cc_final: 0.7593 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0762
  time to fit residues: 5.3658
Evaluate side-chains
  35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.127922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.087623 restraints weight = 6052.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.089823 restraints weight = 2981.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.091157 restraints weight = 1872.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.091726 restraints weight = 1424.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.092226 restraints weight = 1253.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2297  Z= 0.135
  Angle     :  0.547   5.946   3108  Z= 0.286
  Chirality :  0.038   0.119    363
  Planarity :  0.003   0.019    403
  Dihedral  :  4.013  24.837    311
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  :  6.78 %
    Favored  : 90.25 %
  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:  3.12 (0.47), residues: 292
  helix:  2.46 (0.33), residues: 216
  sheet:  None (None), residues: 0
  loop :  1.02 (0.72), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 273 
 TYR   0.005   0.001   TYR A 252 
 PHE   0.018   0.001   PHE A 103 
 TRP   0.006   0.001   TRP A  86 
 HIS   0.005   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 2297)
  covalent geometry    : angle       0.54688 ( 3108)
  hydrogen bonds       : bond        0.04447 (  157)
  hydrogen bonds       : angle       3.89364 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 TRP cc_start: 0.8349 (t60) cc_final: 0.8139 (t60)
REVERT: A  235 HIS cc_start: 0.7038 (m170) cc_final: 0.6780 (m90)
REVERT: A  257 ASN cc_start: 0.7921 (m-40) cc_final: 0.7711 (m110)
  outliers start: 7
  outliers final: 3
  residues processed: 40
  average time/residue: 0.0467
  time to fit residues: 2.3549
Evaluate side-chains
  36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  133 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 193 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.127664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.086961 restraints weight = 6120.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.089236 restraints weight = 2969.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.090519 restraints weight = 1854.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.091334 restraints weight = 1411.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.091612 restraints weight = 1217.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2297  Z= 0.122
  Angle     :  0.501   5.961   3108  Z= 0.268
  Chirality :  0.037   0.112    363
  Planarity :  0.003   0.022    403
  Dihedral  :  3.856  25.684    311
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.14 %
    Favored  : 85.59 %
  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:  3.18 (0.47), residues: 292
  helix:  2.54 (0.34), residues: 216
  sheet:  None (None), residues: 0
  loop :  0.91 (0.71), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 226 
 TYR   0.004   0.001   TYR A 145 
 PHE   0.014   0.001   PHE A 103 
 TRP   0.005   0.001   TRP A  86 
 HIS   0.004   0.001   HIS A 268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 2297)
  covalent geometry    : angle       0.50123 ( 3108)
  hydrogen bonds       : bond        0.04227 (  157)
  hydrogen bonds       : angle       3.76016 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8615 (ptp90) cc_final: 0.8359 (ptp90)
REVERT: A  257 ASN cc_start: 0.7907 (m-40) cc_final: 0.7700 (m110)
  outliers start: 3
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0494
  time to fit residues: 2.3556
Evaluate side-chains
  34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   chunk 14 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.127940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.086757 restraints weight = 6122.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.088942 restraints weight = 2888.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.090237 restraints weight = 1794.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.090886 restraints weight = 1368.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.091362 restraints weight = 1198.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2297  Z= 0.122
  Angle     :  0.511   5.920   3108  Z= 0.277
  Chirality :  0.037   0.114    363
  Planarity :  0.003   0.024    403
  Dihedral  :  3.942  26.272    311
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.83 %
    Favored  : 83.90 %
  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:  3.23 (0.48), residues: 292
  helix:  2.61 (0.34), residues: 216
  sheet:  None (None), residues: 0
  loop :  0.83 (0.71), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 226 
 TYR   0.007   0.001   TYR A  64 
 PHE   0.012   0.001   PHE A 103 
 TRP   0.010   0.001   TRP A 206 
 HIS   0.003   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 2297)
  covalent geometry    : angle       0.51052 ( 3108)
  hydrogen bonds       : bond        0.04137 (  157)
  hydrogen bonds       : angle       3.71246 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.8589 (ptp90) cc_final: 0.8320 (ptp90)
REVERT: A  257 ASN cc_start: 0.8073 (m-40) cc_final: 0.7831 (m110)
  outliers start: 3
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0490
  time to fit residues: 2.2283
Evaluate side-chains
  30 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.126246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.085503 restraints weight = 6116.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.087612 restraints weight = 2898.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.088860 restraints weight = 1809.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.089461 restraints weight = 1384.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.089461 restraints weight = 1217.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2297  Z= 0.152
  Angle     :  0.545   5.894   3108  Z= 0.283
  Chirality :  0.039   0.135    363
  Planarity :  0.003   0.021    403
  Dihedral  :  3.879  25.202    311
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.53 %
    Favored  : 81.78 %
  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:  3.06 (0.48), residues: 292
  helix:  2.50 (0.34), residues: 215
  sheet:  None (None), residues: 0
  loop :  0.75 (0.69), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 124 
 TYR   0.006   0.001   TYR A  94 
 PHE   0.011   0.001   PHE A 103 
 TRP   0.009   0.001   TRP A 206 
 HIS   0.006   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 2297)
  covalent geometry    : angle       0.54460 ( 3108)
  hydrogen bonds       : bond        0.04578 (  157)
  hydrogen bonds       : angle       3.82925 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  181 ARG cc_start: 0.8641 (ptp90) cc_final: 0.8380 (ptp90)
REVERT: A  235 HIS cc_start: 0.7295 (m170) cc_final: 0.6823 (m90)
  outliers start: 4
  outliers final: 2
  residues processed: 34
  average time/residue: 0.0486
  time to fit residues: 2.0848
Evaluate side-chains
  32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ASN
Chi-restraints excluded: chain A residue  133 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 209 HIS
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.127905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.087513 restraints weight = 6014.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.089708 restraints weight = 2895.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.090972 restraints weight = 1801.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.091681 restraints weight = 1376.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.092013 restraints weight = 1195.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2297  Z= 0.116
  Angle     :  0.505   5.821   3108  Z= 0.266
  Chirality :  0.038   0.110    363
  Planarity :  0.003   0.022    403
  Dihedral  :  3.908  26.126    311
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 18.22 %
    Favored  : 80.93 %
  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:  3.15 (0.48), residues: 292
  helix:  2.62 (0.34), residues: 216
  sheet:  None (None), residues: 0
  loop :  0.56 (0.70), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.007   0.001   TYR A  64 
 PHE   0.010   0.001   PHE A 103 
 TRP   0.012   0.001   TRP A 206 
 HIS   0.009   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 2297)
  covalent geometry    : angle       0.50502 ( 3108)
  hydrogen bonds       : bond        0.04112 (  157)
  hydrogen bonds       : angle       3.61462 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6899 (tm-30)
REVERT: A  181 ARG cc_start: 0.8544 (ptp90) cc_final: 0.8265 (ptp90)
  outliers start: 2
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0502
  time to fit residues: 2.1493
Evaluate side-chains
  32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0000
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.128381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.087996 restraints weight = 6187.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.090131 restraints weight = 3025.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.091426 restraints weight = 1885.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.092137 restraints weight = 1441.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.092402 restraints weight = 1252.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2297  Z= 0.112
  Angle     :  0.544  11.181   3108  Z= 0.271
  Chirality :  0.038   0.110    363
  Planarity :  0.003   0.024    403
  Dihedral  :  3.844  25.760    311
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 17.37 %
    Favored  : 80.51 %
  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:  3.05 (0.48), residues: 292
  helix:  2.57 (0.34), residues: 216
  sheet:  None (None), residues: 0
  loop :  0.44 (0.70), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.004   0.001   TYR A 145 
 PHE   0.010   0.001   PHE A 103 
 TRP   0.012   0.001   TRP A 206 
 HIS   0.010   0.002   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 2297)
  covalent geometry    : angle       0.54445 ( 3108)
  hydrogen bonds       : bond        0.04026 (  157)
  hydrogen bonds       : angle       3.57907 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6872 (tm-30)
REVERT: A   77 GLU cc_start: 0.8067 (tp30) cc_final: 0.7753 (tm-30)
REVERT: A  181 ARG cc_start: 0.8532 (ptp90) cc_final: 0.8246 (ptp90)
  outliers start: 5
  outliers final: 2
  residues processed: 40
  average time/residue: 0.0556
  time to fit residues: 2.7379
Evaluate side-chains
  36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  214 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 21 optimal weight:   20.0000
   chunk 20 optimal weight:   20.0000
   chunk 4 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.128139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.088109 restraints weight = 6049.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.090226 restraints weight = 2972.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.091335 restraints weight = 1873.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.092068 restraints weight = 1459.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.092068 restraints weight = 1274.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2297  Z= 0.126
  Angle     :  0.596  10.306   3108  Z= 0.306
  Chirality :  0.039   0.158    363
  Planarity :  0.003   0.024    403
  Dihedral  :  3.870  25.181    311
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.49 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.96 (0.48), residues: 292
  helix:  2.56 (0.34), residues: 215
  sheet:  None (None), residues: 0
  loop :  0.23 (0.68), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.005   0.001   TYR A 252 
 PHE   0.010   0.001   PHE A 103 
 TRP   0.013   0.002   TRP A 206 
 HIS   0.011   0.002   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 2297)
  covalent geometry    : angle       0.59562 ( 3108)
  hydrogen bonds       : bond        0.04293 (  157)
  hydrogen bonds       : angle       3.65134 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6757 (tm-30)
REVERT: A   77 GLU cc_start: 0.8136 (tp30) cc_final: 0.7836 (tm-30)
REVERT: A  181 ARG cc_start: 0.8511 (ptp90) cc_final: 0.8220 (ptp90)
  outliers start: 4
  outliers final: 3
  residues processed: 36
  average time/residue: 0.0491
  time to fit residues: 2.2473
Evaluate side-chains
  35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  214 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.128614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.088694 restraints weight = 6150.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.090806 restraints weight = 3008.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.092002 restraints weight = 1881.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.092701 restraints weight = 1443.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.092701 restraints weight = 1265.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2297  Z= 0.121
  Angle     :  0.593   9.772   3108  Z= 0.309
  Chirality :  0.040   0.185    363
  Planarity :  0.003   0.025    403
  Dihedral  :  3.872  25.429    311
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.34 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.82 (0.48), residues: 292
  helix:  2.44 (0.34), residues: 217
  sheet:  None (None), residues: 0
  loop :  0.21 (0.69), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.007   0.001   TYR A  64 
 PHE   0.009   0.001   PHE A 103 
 TRP   0.015   0.002   TRP A 206 
 HIS   0.011   0.002   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 2297)
  covalent geometry    : angle       0.59308 ( 3108)
  hydrogen bonds       : bond        0.04216 (  157)
  hydrogen bonds       : angle       3.63139 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6857 (tm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 36
  average time/residue: 0.0466
  time to fit residues: 2.1171
Evaluate side-chains
  35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   91 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    0.2980
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.128043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.087604 restraints weight = 6167.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.089716 restraints weight = 2992.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.090856 restraints weight = 1878.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.091569 restraints weight = 1445.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.091931 restraints weight = 1270.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   2297  Z= 0.157
  Angle     :  0.666   9.503   3108  Z= 0.353
  Chirality :  0.041   0.176    363
  Planarity :  0.003   0.024    403
  Dihedral  :  3.892  25.069    311
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 21.19 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.76 (0.48), residues: 292
  helix:  2.40 (0.34), residues: 217
  sheet:  None (None), residues: 0
  loop :  0.16 (0.69), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 124 
 TYR   0.006   0.001   TYR A 252 
 PHE   0.009   0.001   PHE A 103 
 TRP   0.013   0.002   TRP A 206 
 HIS   0.011   0.002   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 2297)
  covalent geometry    : angle       0.66592 ( 3108)
  hydrogen bonds       : bond        0.04529 (  157)
  hydrogen bonds       : angle       3.88897 (  471)

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

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

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.080 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 34
  average time/residue: 0.0468
  time to fit residues: 1.9812
Evaluate side-chains
  33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   91 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 17 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.127821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.087516 restraints weight = 6183.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.089558 restraints weight = 2990.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.090746 restraints weight = 1886.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.091395 restraints weight = 1449.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.091764 restraints weight = 1267.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2297  Z= 0.156
  Angle     :  0.688  10.048   3108  Z= 0.360
  Chirality :  0.044   0.249    363
  Planarity :  0.003   0.024    403
  Dihedral  :  3.943  25.229    311
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.76 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.76 (0.48), residues: 292
  helix:  2.41 (0.34), residues: 217
  sheet:  None (None), residues: 0
  loop :  0.12 (0.69), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 124 
 TYR   0.007   0.001   TYR A 252 
 PHE   0.010   0.001   PHE A 103 
 TRP   0.013   0.002   TRP A 206 
 HIS   0.012   0.002   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2297)
  covalent geometry    : angle       0.68804 ( 3108)
  hydrogen bonds       : bond        0.04579 (  157)
  hydrogen bonds       : angle       3.92295 (  471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 620.28 seconds
wall clock time: 11 minutes 55.24 seconds (715.24 seconds total)