Starting phenix.real_space_refine
on Fri Aug 22 13:44:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erc_28552/08_2025/8erc_28552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erc_28552/08_2025/8erc_28552.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8erc_28552/08_2025/8erc_28552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erc_28552/08_2025/8erc_28552.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erc_28552/08_2025/8erc_28552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erc_28552/08_2025/8erc_28552.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.715
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      24      5.16       5
     C    2332      2.51       5
     N     574      2.21       5
     O     580      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  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: 3510
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3510
          Classifications: {'peptide': 441}
          Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 408}
  Time building chain proxies: 1.24, per 1000 atoms: 0.35
  Number of scatterers: 3510
  At special positions: 0
  Unit cell: (80.025, 69.3, 80.025, 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      24     16.00
     O     580      8.00
     N     574      7.00
     C    2332      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: 0.33
  Conformation dependent library (CDL) restraints added in 112.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  822

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 1 sheets defined
      80.0% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 24
      removed outlier: 4.259A  pdb=" N   ILE A  16 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      Proline residue:  A  17  - end of helix
      removed outlier: 4.085A  pdb=" N   LYS A  24 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 47
    Processing helix  chain 'A' and resid 49 through 67
      removed outlier: 4.405A  pdb=" N   SER A  53 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 88
    Processing helix  chain 'A' and resid 88 through 93
    Processing helix  chain 'A' and resid 98 through 133
    Processing helix  chain 'A' and resid 148 through 157
    Processing helix  chain 'A' and resid 169 through 178
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 197 through 212
    Processing helix  chain 'A' and resid 213 through 225
      removed outlier: 3.709A  pdb=" N   ALA A 216 " --> pdb=" O   PRO A 213 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL A 217 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   ASP A 220 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ALA A 221 " --> pdb=" O   ARG A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 259
      removed outlier: 4.307A  pdb=" N   ILE A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
      Proline residue:  A 236  - end of helix
      removed outlier: 3.731A  pdb=" N   ALA A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 269
      No H-bonds generated for 'chain 'A' and resid 267 through 269'
    Processing helix  chain 'A' and resid 285 through 292
    Processing helix  chain 'A' and resid 303 through 309
    Processing helix  chain 'A' and resid 312 through 319
    Processing helix  chain 'A' and resid 321 through 332
    Processing helix  chain 'A' and resid 340 through 357
    Processing helix  chain 'A' and resid 359 through 384
      removed outlier: 3.876A  pdb=" N   TYR A 363 " --> pdb=" O   HIS A 359 " (cutoff:3.500A)
      Proline residue:  A 370  - end of helix
    Processing helix  chain 'A' and resid 388 through 417
      removed outlier: 3.868A  pdb=" N   GLY A 413 " --> pdb=" O   TYR A 409 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   LEU A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 429
    Processing helix  chain 'A' and resid 431 through 441
    Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 265

    248 hydrogen bonds defined for protein.
    723 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: 0.36

  Time building geometry restraints manager: 0.43 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: 1045
        1.34 -     1.46: 877
        1.46 -     1.58: 1676
        1.58 -     1.70: 0
        1.70 -     1.81: 36
  Bond restraints: 3634
  Sorted by residual:
  bond pdb=" CG  PRO A 166 "
       pdb=" CD  PRO A 166 "
    ideal  model  delta    sigma   weight residual
    1.512  1.479  0.033 2.70e-02 1.37e+03 1.48e+00
  bond pdb=" CA  PRO A 166 "
       pdb=" C   PRO A 166 "
    ideal  model  delta    sigma   weight residual
    1.524  1.504  0.020 2.00e-02 2.50e+03 9.91e-01
  bond pdb=" CB  PRO A 166 "
       pdb=" CG  PRO A 166 "
    ideal  model  delta    sigma   weight residual
    1.506  1.469  0.037 3.90e-02 6.57e+02 9.16e-01
  bond pdb=" C   TRP A 196 "
       pdb=" N   PRO A 197 "
    ideal  model  delta    sigma   weight residual
    1.332  1.340 -0.008 8.90e-03 1.26e+04 7.96e-01
  bond pdb=" CB  HIS A 399 "
       pdb=" CG  HIS A 399 "
    ideal  model  delta    sigma   weight residual
    1.497  1.485  0.012 1.40e-02 5.10e+03 7.12e-01
  ... (remaining 3629 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 4769
        1.43 -     2.86: 138
        2.86 -     4.29: 36
        4.29 -     5.72: 15
        5.72 -     7.15: 6
  Bond angle restraints: 4964
  Sorted by residual:
  angle pdb=" C   GLU A 129 "
        pdb=" N   MET A 130 "
        pdb=" CA  MET A 130 "
      ideal   model   delta    sigma   weight residual
     121.58  115.03    6.55 1.95e+00 2.63e-01 1.13e+01
  angle pdb=" CA  GLU A 376 "
        pdb=" CB  GLU A 376 "
        pdb=" CG  GLU A 376 "
      ideal   model   delta    sigma   weight residual
     114.10  108.79    5.31 2.00e+00 2.50e-01 7.06e+00
  angle pdb=" N   GLY A 357 "
        pdb=" CA  GLY A 357 "
        pdb=" C   GLY A 357 "
      ideal   model   delta    sigma   weight residual
     110.63  114.43   -3.80 1.45e+00 4.76e-01 6.87e+00
  angle pdb=" CA  MET A 130 "
        pdb=" CB  MET A 130 "
        pdb=" CG  MET A 130 "
      ideal   model   delta    sigma   weight residual
     114.10  119.08   -4.98 2.00e+00 2.50e-01 6.21e+00
  angle pdb=" N   MET A 130 "
        pdb=" CA  MET A 130 "
        pdb=" CB  MET A 130 "
      ideal   model   delta    sigma   weight residual
     110.41  114.52   -4.11 1.68e+00 3.54e-01 5.97e+00
  ... (remaining 4959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.59: 1873
       15.59 -    31.18: 169
       31.18 -    46.76: 45
       46.76 -    62.35: 3
       62.35 -    77.94: 3
  Dihedral angle restraints: 2093
    sinusoidal: 806
      harmonic: 1287
  Sorted by residual:
  dihedral pdb=" CG  ARG A 378 "
           pdb=" CD  ARG A 378 "
           pdb=" NE  ARG A 378 "
           pdb=" CZ  ARG A 378 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.70  -44.70     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CB  LYS A 111 "
           pdb=" CG  LYS A 111 "
           pdb=" CD  LYS A 111 "
           pdb=" CE  LYS A 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.97   50.97     3      1.50e+01 4.44e-03 8.96e+00
  dihedral pdb=" CA  GLU A 293 "
           pdb=" CB  GLU A 293 "
           pdb=" CG  GLU A 293 "
           pdb=" CD  GLU A 293 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  105.45  -45.45     3      1.50e+01 4.44e-03 8.17e+00
  ... (remaining 2090 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 312
       0.026 -    0.052: 139
       0.052 -    0.078: 49
       0.078 -    0.105: 28
       0.105 -    0.131: 9
  Chirality restraints: 537
  Sorted by residual:
  chirality pdb=" CA  TRP A 196 "
            pdb=" N   TRP A 196 "
            pdb=" C   TRP A 196 "
            pdb=" CB  TRP A 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.27e-01
  chirality pdb=" CA  GLN A  65 "
            pdb=" N   GLN A  65 "
            pdb=" C   GLN A  65 "
            pdb=" CB  GLN A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  PRO A 236 "
            pdb=" N   PRO A 236 "
            pdb=" C   PRO A 236 "
            pdb=" CB  PRO A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.43e-01
  ... (remaining 534 not shown)

  Planarity restraints: 612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 426 "   -0.011 2.00e-02 2.50e+03   9.86e-03 2.43e+00
        pdb=" CG  TRP A 426 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 426 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 426 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 426 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 426 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 426 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 426 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 426 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 426 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 165 "    0.024 5.00e-02 4.00e+02   3.76e-02 2.26e+00
        pdb=" N   PRO A 166 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 166 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 166 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 377 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.96e+00
        pdb=" C   GLY A 377 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   GLY A 377 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ARG A 378 "    0.008 2.00e-02 2.50e+03
  ... (remaining 609 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 29
        2.67 -     3.23: 3563
        3.23 -     3.79: 5816
        3.79 -     4.34: 7102
        4.34 -     4.90: 11674
  Nonbonded interactions: 28184
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 246 "
            pdb=" OG1 THR A 307 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" OD1 ASN A 301 "
            pdb=" OG1 THR A 323 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" NH2 ARG A 405 "
            pdb=" OD2 ASP A 408 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" O   TYR A 333 "
            pdb=" NH2 ARG A 344 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" O   PHE A 205 "
            pdb=" OG  SER A 209 "
     model   vdw
     2.334 3.040
  ... (remaining 28179 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:             0.990
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.320
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
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   0.037   3634  Z= 0.143
  Angle     :  0.671   7.145   4964  Z= 0.339
  Chirality :  0.038   0.131    537
  Planarity :  0.005   0.038    612
  Dihedral  : 12.915  77.940   1271
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.99 (0.41), residues: 439
  helix:  1.62 (0.29), residues: 309
  sheet:  None (None), residues: 0
  loop :  0.82 (0.61), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 300 
 TYR   0.015   0.001   TYR A 331 
 PHE   0.020   0.002   PHE A 245 
 TRP   0.026   0.002   TRP A 426 
 HIS   0.005   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 3634)
  covalent geometry    : angle       0.67142 ( 4964)
  hydrogen bonds       : bond        0.12756 (  248)
  hydrogen bonds       : angle       5.18933 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6651 (tmm) cc_final: 0.6375 (tmm)
REVERT: A  120 GLN cc_start: 0.6980 (tp40) cc_final: 0.6738 (tp-100)
REVERT: A  146 VAL cc_start: 0.9489 (p) cc_final: 0.9284 (t)
REVERT: A  160 VAL cc_start: 0.8703 (t) cc_final: 0.8377 (t)
REVERT: A  231 LEU cc_start: 0.8757 (mt) cc_final: 0.8542 (tp)
REVERT: A  254 CYS cc_start: 0.7844 (m) cc_final: 0.7420 (m)
REVERT: A  412 MET cc_start: 0.7759 (mpp) cc_final: 0.6958 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0618
  time to fit residues: 8.1288
Evaluate side-chains
  95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0000
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 123 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.185447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.156460 restraints weight = 6319.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.162699 restraints weight = 3730.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.166843 restraints weight = 2545.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.169471 restraints weight = 1916.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.171135 restraints weight = 1546.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6512
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3634  Z= 0.140
  Angle     :  0.631   7.649   4964  Z= 0.311
  Chirality :  0.039   0.198    537
  Planarity :  0.005   0.039    612
  Dihedral  :  3.463  11.891    490
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.05 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  2.07 (0.41), residues: 439
  helix:  1.72 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop :  0.60 (0.64), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 300 
 TYR   0.027   0.002   TYR A 425 
 PHE   0.040   0.002   PHE A  22 
 TRP   0.017   0.001   TRP A 426 
 HIS   0.005   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3634)
  covalent geometry    : angle       0.63057 ( 4964)
  hydrogen bonds       : bond        0.05019 (  248)
  hydrogen bonds       : angle       4.51468 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 GLN cc_start: 0.7023 (tp40) cc_final: 0.6682 (tp-100)
REVERT: A  146 VAL cc_start: 0.9511 (p) cc_final: 0.9305 (t)
REVERT: A  231 LEU cc_start: 0.8649 (mt) cc_final: 0.7935 (tp)
REVERT: A  234 MET cc_start: 0.6042 (ppp) cc_final: 0.5822 (ppp)
REVERT: A  254 CYS cc_start: 0.7925 (m) cc_final: 0.7511 (m)
REVERT: A  409 TYR cc_start: 0.8610 (t80) cc_final: 0.7993 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 103
  average time/residue: 0.0565
  time to fit residues: 7.1894
Evaluate side-chains
  100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  164 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    7.9990
   chunk 36 optimal weight:    0.4980
   chunk 9 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  52 HIS
A 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.184280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.155941 restraints weight = 6221.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.161641 restraints weight = 3673.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.165651 restraints weight = 2511.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.168362 restraints weight = 1888.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.170197 restraints weight = 1508.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3634  Z= 0.156
  Angle     :  0.607   7.981   4964  Z= 0.302
  Chirality :  0.038   0.131    537
  Planarity :  0.004   0.038    612
  Dihedral  :  3.482  11.528    490
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.92 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  2.05 (0.41), residues: 439
  helix:  1.74 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop :  0.48 (0.63), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 194 
 TYR   0.020   0.002   TYR A 159 
 PHE   0.037   0.002   PHE A 232 
 TRP   0.012   0.001   TRP A 176 
 HIS   0.005   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3634)
  covalent geometry    : angle       0.60721 ( 4964)
  hydrogen bonds       : bond        0.04747 (  248)
  hydrogen bonds       : angle       4.48258 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 VAL cc_start: 0.9516 (p) cc_final: 0.9308 (t)
REVERT: A  150 MET cc_start: 0.6695 (tmm) cc_final: 0.6409 (tpt)
REVERT: A  231 LEU cc_start: 0.8654 (mt) cc_final: 0.8447 (tp)
REVERT: A  254 CYS cc_start: 0.7821 (m) cc_final: 0.7406 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 102
  average time/residue: 0.0593
  time to fit residues: 7.3109
Evaluate side-chains
  104 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  164 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0670
   chunk 41 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0570
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A  52 HIS
A 120 GLN
A 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.184885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.157001 restraints weight = 6210.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.162639 restraints weight = 3675.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.166784 restraints weight = 2512.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.169456 restraints weight = 1882.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.170981 restraints weight = 1497.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3634  Z= 0.127
  Angle     :  0.600   8.097   4964  Z= 0.292
  Chirality :  0.038   0.218    537
  Planarity :  0.005   0.041    612
  Dihedral  :  3.431  11.686    490
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.40 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.41), residues: 439
  helix:  1.89 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop :  0.57 (0.64), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 230 
 TYR   0.024   0.002   TYR A 159 
 PHE   0.037   0.002   PHE A 232 
 TRP   0.014   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 3634)
  covalent geometry    : angle       0.60017 ( 4964)
  hydrogen bonds       : bond        0.04298 (  248)
  hydrogen bonds       : angle       4.31026 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6658 (m90) cc_final: 0.6451 (m90)
REVERT: A  120 GLN cc_start: 0.7170 (tp40) cc_final: 0.6728 (tp-100)
REVERT: A  130 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6555 (pmm)
REVERT: A  150 MET cc_start: 0.6737 (tmm) cc_final: 0.6526 (tpt)
REVERT: A  231 LEU cc_start: 0.8624 (mt) cc_final: 0.8050 (tp)
REVERT: A  254 CYS cc_start: 0.7833 (m) cc_final: 0.7418 (m)
  outliers start: 14
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0611
  time to fit residues: 7.8888
Evaluate side-chains
  102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 CYS
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  158 CYS
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  322 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0170
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.8024

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

Flipped N/Q/H residues before XYZ refinement:
A 123 HIS
A 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.185182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.156518 restraints weight = 6232.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.162114 restraints weight = 3842.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.166136 restraints weight = 2667.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.168978 restraints weight = 2011.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.170983 restraints weight = 1602.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3634  Z= 0.135
  Angle     :  0.625   8.283   4964  Z= 0.300
  Chirality :  0.039   0.273    537
  Planarity :  0.005   0.042    612
  Dihedral  :  3.419  11.748    490
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.51 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  2.19 (0.41), residues: 439
  helix:  1.81 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.62 (0.64), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 230 
 TYR   0.027   0.002   TYR A 409 
 PHE   0.039   0.002   PHE A 232 
 TRP   0.015   0.001   TRP A 196 
 HIS   0.002   0.000   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3634)
  covalent geometry    : angle       0.62523 ( 4964)
  hydrogen bonds       : bond        0.04245 (  248)
  hydrogen bonds       : angle       4.30215 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7955 (tttt) cc_final: 0.7682 (tttt)
REVERT: A   52 HIS cc_start: 0.6738 (m90) cc_final: 0.6455 (m90)
REVERT: A  120 GLN cc_start: 0.7120 (tp40) cc_final: 0.6693 (tp-100)
REVERT: A  130 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6497 (pmm)
REVERT: A  234 MET cc_start: 0.5610 (ppp) cc_final: 0.5380 (ppp)
REVERT: A  254 CYS cc_start: 0.7849 (m) cc_final: 0.7456 (m)
  outliers start: 13
  outliers final: 8
  residues processed: 101
  average time/residue: 0.0554
  time to fit residues: 6.9209
Evaluate side-chains
  102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  397 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.184857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.156017 restraints weight = 6270.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.161500 restraints weight = 3888.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.165484 restraints weight = 2734.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.168109 restraints weight = 2076.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.169604 restraints weight = 1683.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3634  Z= 0.150
  Angle     :  0.637   8.288   4964  Z= 0.306
  Chirality :  0.040   0.333    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.413  11.961    490
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 18.23 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  2.20 (0.41), residues: 439
  helix:  1.80 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.67 (0.65), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 230 
 TYR   0.024   0.002   TYR A 409 
 PHE   0.037   0.002   PHE A 232 
 TRP   0.016   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3634)
  covalent geometry    : angle       0.63654 ( 4964)
  hydrogen bonds       : bond        0.04294 (  248)
  hydrogen bonds       : angle       4.36735 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6699 (m90) cc_final: 0.6404 (m90)
REVERT: A  120 GLN cc_start: 0.7029 (tp40) cc_final: 0.6635 (tp-100)
REVERT: A  130 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6547 (pmm)
REVERT: A  234 MET cc_start: 0.5632 (ppp) cc_final: 0.5405 (ppp)
REVERT: A  254 CYS cc_start: 0.8011 (m) cc_final: 0.7636 (m)
REVERT: A  376 GLU cc_start: 0.8132 (tp30) cc_final: 0.7695 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0655
  time to fit residues: 8.6033
Evaluate side-chains
  108 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  397 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A 123 HIS
A 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.181607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.150920 restraints weight = 6271.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.156024 restraints weight = 4023.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.159850 restraints weight = 2900.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.162149 restraints weight = 2261.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.164421 restraints weight = 1900.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3634  Z= 0.229
  Angle     :  0.696   7.701   4964  Z= 0.351
  Chirality :  0.043   0.279    537
  Planarity :  0.005   0.044    612
  Dihedral  :  3.602  12.630    490
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.89 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.73 (0.41), residues: 439
  helix:  1.47 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop :  0.38 (0.68), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 230 
 TYR   0.031   0.002   TYR A 409 
 PHE   0.043   0.002   PHE A 232 
 TRP   0.020   0.002   TRP A 196 
 HIS   0.004   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 3634)
  covalent geometry    : angle       0.69650 ( 4964)
  hydrogen bonds       : bond        0.05045 (  248)
  hydrogen bonds       : angle       4.70664 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6921 (m90) cc_final: 0.6463 (m90)
REVERT: A  120 GLN cc_start: 0.7074 (tp40) cc_final: 0.6607 (tp-100)
REVERT: A  130 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6668 (pmm)
REVERT: A  234 MET cc_start: 0.5820 (ppp) cc_final: 0.5541 (ppp)
REVERT: A  243 MET cc_start: 0.7613 (tpp) cc_final: 0.7296 (tpp)
REVERT: A  254 CYS cc_start: 0.7944 (m) cc_final: 0.7585 (m)
  outliers start: 12
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0578
  time to fit residues: 7.0208
Evaluate side-chains
  100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 CYS
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  397 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 6 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0970
   chunk 36 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   overall best weight:    1.0380

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 399 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.184739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.154958 restraints weight = 6370.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.160369 restraints weight = 4049.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.164147 restraints weight = 2889.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.166282 restraints weight = 2250.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.168675 restraints weight = 1882.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3634  Z= 0.155
  Angle     :  0.675   8.340   4964  Z= 0.326
  Chirality :  0.044   0.329    537
  Planarity :  0.005   0.044    612
  Dihedral  :  3.546  12.525    490
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.17 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.90 (0.41), residues: 439
  helix:  1.58 (0.28), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.58 (0.65), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 242 
 TYR   0.030   0.002   TYR A 409 
 PHE   0.042   0.002   PHE A 232 
 TRP   0.012   0.002   TRP A   6 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3634)
  covalent geometry    : angle       0.67537 ( 4964)
  hydrogen bonds       : bond        0.04631 (  248)
  hydrogen bonds       : angle       4.46885 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7992 (tttt) cc_final: 0.7526 (tttm)
REVERT: A   52 HIS cc_start: 0.6712 (m90) cc_final: 0.6484 (m90)
REVERT: A  120 GLN cc_start: 0.6938 (tp40) cc_final: 0.6557 (tp-100)
REVERT: A  130 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6586 (pmm)
REVERT: A  234 MET cc_start: 0.5749 (ppp) cc_final: 0.5498 (ppp)
REVERT: A  254 CYS cc_start: 0.7870 (m) cc_final: 0.7477 (m)
REVERT: A  376 GLU cc_start: 0.8297 (tp30) cc_final: 0.7860 (tp30)
  outliers start: 11
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0423
  time to fit residues: 5.4489
Evaluate side-chains
  100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  179 GLN
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  397 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0980
   chunk 26 optimal weight:    0.0060
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.5198

-------------------------------------------------------------------------------
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 = 0.4306 r_free = 0.4306 target = 0.186180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.156840 restraints weight = 6339.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.162410 restraints weight = 3939.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.166480 restraints weight = 2783.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.169217 restraints weight = 2129.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.171202 restraints weight = 1727.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3634  Z= 0.134
  Angle     :  0.704   9.897   4964  Z= 0.329
  Chirality :  0.044   0.322    537
  Planarity :  0.005   0.044    612
  Dihedral  :  3.531  12.380    490
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.99 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.99 (0.41), residues: 439
  helix:  1.64 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop :  0.63 (0.65), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 242 
 TYR   0.028   0.002   TYR A 409 
 PHE   0.045   0.002   PHE A 232 
 TRP   0.012   0.001   TRP A   6 
 HIS   0.003   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3634)
  covalent geometry    : angle       0.70447 ( 4964)
  hydrogen bonds       : bond        0.04420 (  248)
  hydrogen bonds       : angle       4.38369 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6834 (m90) cc_final: 0.6498 (m90)
REVERT: A  120 GLN cc_start: 0.7055 (tp40) cc_final: 0.6653 (tp-100)
REVERT: A  130 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6471 (pmm)
REVERT: A  234 MET cc_start: 0.5712 (ppp) cc_final: 0.5463 (ppp)
REVERT: A  254 CYS cc_start: 0.7886 (m) cc_final: 0.7483 (m)
REVERT: A  376 GLU cc_start: 0.8272 (tp30) cc_final: 0.7849 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0571
  time to fit residues: 6.8068
Evaluate side-chains
  98 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  397 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0670
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0040
   chunk 38 optimal weight:    0.0370
   chunk 26 optimal weight:    0.0040
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.1420

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

Flipped N/Q/H residues before XYZ refinement:
A 123 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.189128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.161037 restraints weight = 6354.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.166878 restraints weight = 3878.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.170835 restraints weight = 2658.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.173793 restraints weight = 1994.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.175328 restraints weight = 1566.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6463
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3634  Z= 0.128
  Angle     :  0.689   9.905   4964  Z= 0.324
  Chirality :  0.043   0.343    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.468  11.978    490
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 21.82 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  2.00 (0.41), residues: 439
  helix:  1.70 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop :  0.40 (0.64), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 242 
 TYR   0.026   0.001   TYR A 409 
 PHE   0.043   0.002   PHE A 232 
 TRP   0.011   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3634)
  covalent geometry    : angle       0.68935 ( 4964)
  hydrogen bonds       : bond        0.04014 (  248)
  hydrogen bonds       : angle       4.33309 (  723)

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

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

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  878 Ramachandran restraints generated.
    439 Oldfield, 0 Emsley, 439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 GLN cc_start: 0.7075 (tp40) cc_final: 0.6800 (tp-100)
REVERT: A  130 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6196 (pmm)
REVERT: A  234 MET cc_start: 0.5684 (ppp) cc_final: 0.5433 (ppp)
REVERT: A  376 GLU cc_start: 0.8325 (tp30) cc_final: 0.7938 (tp30)
  outliers start: 8
  outliers final: 6
  residues processed: 93
  average time/residue: 0.0515
  time to fit residues: 6.0653
Evaluate side-chains
  95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  126 GLN
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  397 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0770
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
A 123 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.187467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.159069 restraints weight = 6181.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.164562 restraints weight = 3778.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.168652 restraints weight = 2619.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.171591 restraints weight = 1963.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.173381 restraints weight = 1556.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6510
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3634  Z= 0.145
  Angle     :  0.714  11.082   4964  Z= 0.342
  Chirality :  0.044   0.397    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.406  12.202    490
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.93 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.99 (0.41), residues: 439
  helix:  1.73 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop :  0.27 (0.64), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 242 
 TYR   0.024   0.001   TYR A 159 
 PHE   0.044   0.002   PHE A 232 
 TRP   0.025   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3634)
  covalent geometry    : angle       0.71434 ( 4964)
  hydrogen bonds       : bond        0.04228 (  248)
  hydrogen bonds       : angle       4.27576 (  723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 796.34 seconds
wall clock time: 14 minutes 19.86 seconds (859.86 seconds total)