Starting phenix.real_space_refine
on Wed Mar  5 20:14:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erc_28552/03_2025/8erc_28552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erc_28552/03_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_28552/03_2025/8erc_28552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erc_28552/03_2025/8erc_28552.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erc_28552/03_2025/8erc_28552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erc_28552/03_2025/8erc_28552.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.80, per 1000 atoms: 0.80
  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: 0.89
  Conformation dependent library (CDL) restraints added in 436.6 milliseconds
  

  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: 0.36
  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: 0.96

  Time building geometry restraints manager: 1.07 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.580
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.020
-------------------------------------------------------------------------------
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= 0.180
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.026   0.002   TRP A 426 
 HIS   0.005   0.001   HIS A 399 
 PHE   0.020   0.002   PHE A 245 
 TYR   0.015   0.001   TYR A 331 
 ARG   0.003   0.000   ARG A 300 

*********************** 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  : 0.406 
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: 0.1727
  time to fit residues: 22.7766
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  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0000
   chunk 17 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 = 0.4285 r_free = 0.4285 target = 0.183811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.154227 restraints weight = 6182.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.160222 restraints weight = 3714.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.164302 restraints weight = 2570.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6648
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3634  Z= 0.219
  Angle     :  0.648   7.911   4964  Z= 0.323
  Chirality :  0.040   0.214    537
  Planarity :  0.005   0.038    612
  Dihedral  :  3.453  11.598    490
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 11.60 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.41), residues: 439
  helix:  1.66 (0.28), residues: 319
  sheet:  None (None), residues: 0
  loop :  0.57 (0.64), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 426 
 HIS   0.005   0.001   HIS A 399 
 PHE   0.037   0.002   PHE A  22 
 TYR   0.028   0.002   TYR A 425 
 ARG   0.003   0.000   ARG A 230 

*********************** 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
  109 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 VAL cc_start: 0.9511 (p) cc_final: 0.9292 (t)
REVERT: A  254 CYS cc_start: 0.7953 (m) cc_final: 0.7555 (m)
REVERT: A  409 TYR cc_start: 0.8697 (t80) cc_final: 0.8052 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 102
  average time/residue: 0.1629
  time to fit residues: 20.3696
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  : 0.386 
-------------------------------------------------------------------------------
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 23 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 28 optimal weight:    0.3980
   chunk 34 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.185260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.156684 restraints weight = 6219.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.162195 restraints weight = 3810.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.166222 restraints weight = 2605.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6613
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   0.052   3634  Z= 0.191
  Angle     :  0.621   8.399   4964  Z= 0.307
  Chirality :  0.038   0.133    537
  Planarity :  0.005   0.039    612
  Dihedral  :  3.533  11.523    490
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.75 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.41), residues: 439
  helix:  1.71 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop :  0.51 (0.64), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 196 
 HIS   0.004   0.001   HIS A 399 
 PHE   0.038   0.002   PHE A 232 
 TYR   0.021   0.002   TYR A 159 
 ARG   0.006   0.001   ARG A 194 

*********************** 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
  105 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.7054 (mt) cc_final: 0.6849 (mm)
REVERT: A  120 GLN cc_start: 0.7239 (tp40) cc_final: 0.6867 (tp-100)
REVERT: A  146 VAL cc_start: 0.9503 (p) cc_final: 0.9294 (t)
REVERT: A  150 MET cc_start: 0.6740 (tmm) cc_final: 0.6465 (tpt)
REVERT: A  254 CYS cc_start: 0.7984 (m) cc_final: 0.7581 (m)
REVERT: A  409 TYR cc_start: 0.8699 (t80) cc_final: 0.7925 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1444
  time to fit residues: 17.8634
Evaluate side-chains
  100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 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 21 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 13 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 ** 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 = 0.4273 r_free = 0.4273 target = 0.182624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.153351 restraints weight = 6279.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.158997 restraints weight = 3849.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.163005 restraints weight = 2673.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.2252

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= 0.219
  Angle     :  0.629   7.805   4964  Z= 0.313
  Chirality :  0.040   0.208    537
  Planarity :  0.005   0.041    612
  Dihedral  :  3.472  12.108    490
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.13 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.41), residues: 439
  helix:  1.68 (0.28), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.61 (0.65), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 196 
 HIS   0.002   0.001   HIS A  72 
 PHE   0.036   0.002   PHE A 232 
 TYR   0.019   0.002   TYR A   8 
 ARG   0.003   0.000   ARG A 230 

*********************** 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
  112 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6787 (m90) cc_final: 0.6518 (m90)
REVERT: A  120 GLN cc_start: 0.7283 (tp40) cc_final: 0.6800 (tp-100)
REVERT: A  130 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.7003 (pmm)
REVERT: A  150 MET cc_start: 0.6751 (tmm) cc_final: 0.6492 (tpt)
REVERT: A  243 MET cc_start: 0.7639 (tpp) cc_final: 0.7318 (tpp)
REVERT: A  254 CYS cc_start: 0.7992 (m) cc_final: 0.7594 (m)
REVERT: A  409 TYR cc_start: 0.8745 (t80) cc_final: 0.8054 (t80)
REVERT: A  412 MET cc_start: 0.7705 (mpp) cc_final: 0.7455 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1467
  time to fit residues: 18.4344
Evaluate side-chains
  104 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0970
   chunk 43 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.4303 r_free = 0.4303 target = 0.185517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.157399 restraints weight = 6290.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.162983 restraints weight = 3829.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.166895 restraints weight = 2663.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6605
moved from start:          0.2485

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= 0.172
  Angle     :  0.624   8.692   4964  Z= 0.300
  Chirality :  0.039   0.275    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.440  12.123    490
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.34 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.41), residues: 439
  helix:  1.78 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.65 (0.65), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.040   0.002   PHE A 232 
 TYR   0.025   0.002   TYR A 159 
 ARG   0.002   0.000   ARG A 230 

*********************** 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
  110 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7897 (tttt) cc_final: 0.7635 (tttt)
REVERT: A   52 HIS cc_start: 0.6633 (m90) cc_final: 0.6364 (m90)
REVERT: A  120 GLN cc_start: 0.7260 (tp40) cc_final: 0.6776 (tp-100)
REVERT: A  130 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6504 (pmm)
REVERT: A  243 MET cc_start: 0.7532 (tpp) cc_final: 0.7290 (tpp)
REVERT: A  254 CYS cc_start: 0.7983 (m) cc_final: 0.7595 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 103
  average time/residue: 0.1534
  time to fit residues: 19.4676
Evaluate side-chains
  102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 21 optimal weight:    0.4980
   chunk 39 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** 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 = 0.4299 r_free = 0.4299 target = 0.185356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.156598 restraints weight = 6341.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.162251 restraints weight = 3869.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.166418 restraints weight = 2691.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6619
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3634  Z= 0.174
  Angle     :  0.641   8.783   4964  Z= 0.308
  Chirality :  0.040   0.306    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.441  12.107    490
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.78 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.41), residues: 439
  helix:  1.79 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.67 (0.65), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 196 
 HIS   0.005   0.001   HIS A 123 
 PHE   0.041   0.002   PHE A 232 
 TYR   0.028   0.001   TYR A 159 
 ARG   0.002   0.000   ARG A 230 

*********************** 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
  108 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6651 (m90) cc_final: 0.6344 (m90)
REVERT: A  120 GLN cc_start: 0.7162 (tp40) cc_final: 0.6726 (tp-100)
REVERT: A  130 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6481 (pmm)
REVERT: A  243 MET cc_start: 0.7546 (tpp) cc_final: 0.7262 (tpp)
REVERT: A  254 CYS cc_start: 0.8014 (m) cc_final: 0.7627 (m)
REVERT: A  376 GLU cc_start: 0.8125 (tp30) cc_final: 0.7658 (tp30)
REVERT: A  409 TYR cc_start: 0.8755 (t80) cc_final: 0.8535 (t80)
  outliers start: 11
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1542
  time to fit residues: 18.8488
Evaluate side-chains
  104 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    0.2980
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 ** 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 = 0.4291 r_free = 0.4291 target = 0.184470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.154997 restraints weight = 6241.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.160405 restraints weight = 3875.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.164540 restraints weight = 2755.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6676
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3634  Z= 0.203
  Angle     :  0.656   8.735   4964  Z= 0.320
  Chirality :  0.041   0.292    537
  Planarity :  0.005   0.044    612
  Dihedral  :  3.399  12.444    490
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.34 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.41), residues: 439
  helix:  1.76 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.74 (0.66), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 249 
 HIS   0.002   0.001   HIS A 123 
 PHE   0.042   0.002   PHE A 232 
 TYR   0.023   0.002   TYR A 159 
 ARG   0.003   0.000   ARG A 230 

*********************** 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
  109 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7972 (tttt) cc_final: 0.7740 (tttt)
REVERT: A   52 HIS cc_start: 0.6700 (m90) cc_final: 0.6333 (m90)
REVERT: A  120 GLN cc_start: 0.7258 (tp40) cc_final: 0.6738 (tp-100)
REVERT: A  130 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6468 (pmm)
REVERT: A  243 MET cc_start: 0.7609 (tpp) cc_final: 0.7267 (tpp)
REVERT: A  254 CYS cc_start: 0.7996 (m) cc_final: 0.7643 (m)
REVERT: A  376 GLU cc_start: 0.8194 (tp30) cc_final: 0.7717 (tp30)
  outliers start: 11
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1613
  time to fit residues: 20.4690
Evaluate side-chains
  105 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0970
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.185278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.155990 restraints weight = 6295.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.161836 restraints weight = 3867.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.165842 restraints weight = 2702.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6652
moved from start:          0.2884

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= 0.192
  Angle     :  0.676   9.596   4964  Z= 0.325
  Chirality :  0.041   0.344    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.414  12.534    490
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.44 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.41), residues: 439
  helix:  1.74 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.72 (0.66), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 426 
 HIS   0.003   0.001   HIS A 123 
 PHE   0.045   0.002   PHE A 232 
 TYR   0.019   0.002   TYR A 159 
 ARG   0.006   0.000   ARG A 242 

*********************** 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
  110 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7953 (tttt) cc_final: 0.7721 (tttt)
REVERT: A   52 HIS cc_start: 0.6733 (m90) cc_final: 0.6312 (m90)
REVERT: A  120 GLN cc_start: 0.7118 (tp40) cc_final: 0.6878 (tp-100)
REVERT: A  130 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6478 (pmm)
REVERT: A  243 MET cc_start: 0.7585 (tpp) cc_final: 0.7222 (tpp)
REVERT: A  254 CYS cc_start: 0.7962 (m) cc_final: 0.7582 (m)
REVERT: A  376 GLU cc_start: 0.8216 (tp30) cc_final: 0.7778 (tp30)
  outliers start: 11
  outliers final: 8
  residues processed: 103
  average time/residue: 0.1452
  time to fit residues: 18.9137
Evaluate side-chains
  105 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0030
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.7992

-------------------------------------------------------------------------------
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 = 0.4303 r_free = 0.4303 target = 0.185891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.158057 restraints weight = 6090.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.163385 restraints weight = 3747.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.167253 restraints weight = 2627.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6625
moved from start:          0.2958

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= 0.182
  Angle     :  0.673   9.458   4964  Z= 0.321
  Chirality :  0.041   0.354    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.380  12.516    490
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.34 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.41), residues: 439
  helix:  1.79 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop :  0.79 (0.65), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A   6 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.043   0.002   PHE A 232 
 TYR   0.026   0.002   TYR A 409 
 ARG   0.009   0.000   ARG A 242 

*********************** 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
  103 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7924 (tttt) cc_final: 0.7630 (tttt)
REVERT: A   52 HIS cc_start: 0.6714 (m90) cc_final: 0.6398 (m90)
REVERT: A  120 GLN cc_start: 0.7206 (tp40) cc_final: 0.6731 (tp-100)
REVERT: A  130 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6358 (pmm)
REVERT: A  243 MET cc_start: 0.7608 (tpp) cc_final: 0.7232 (tpp)
REVERT: A  376 GLU cc_start: 0.8293 (tp30) cc_final: 0.7865 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1452
  time to fit residues: 17.2532
Evaluate side-chains
  100 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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 23 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0010
   chunk 6 optimal weight:    0.0040
   chunk 22 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0770
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.2956

-------------------------------------------------------------------------------
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 = 0.4324 r_free = 0.4324 target = 0.187918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.159983 restraints weight = 6314.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.165964 restraints weight = 3799.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.169884 restraints weight = 2627.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3634  Z= 0.169
  Angle     :  0.697  10.956   4964  Z= 0.331
  Chirality :  0.042   0.390    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.406  12.440    490
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.41), residues: 439
  helix:  1.79 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop :  0.51 (0.65), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A   6 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.045   0.002   PHE A 232 
 TYR   0.030   0.002   TYR A 409 
 ARG   0.009   0.000   ARG A 242 

********************** 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
  99 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A   30 LYS cc_start: 0.7816 (tttt) cc_final: 0.7482 (tttt)
REVERT: A  120 GLN cc_start: 0.7121 (tp40) cc_final: 0.6708 (tp-100)
REVERT: A  126 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7461 (pp30)
REVERT: A  130 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.5911 (pmm)
REVERT: A  243 MET cc_start: 0.7518 (tpp) cc_final: 0.7129 (tpp)
REVERT: A  376 GLU cc_start: 0.8286 (tp30) cc_final: 0.7911 (tp30)
  outliers start: 10
  outliers final: 6
  residues processed: 94
  average time/residue: 0.1393
  time to fit residues: 16.5021
Evaluate side-chains
  98 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
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 19 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 43 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0570
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   overall best weight:    1.2900

-------------------------------------------------------------------------------
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 = 0.4299 r_free = 0.4299 target = 0.185004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.156398 restraints weight = 6171.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.161904 restraints weight = 3826.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.166021 restraints weight = 2666.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.3103

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= 0.216
  Angle     :  0.703  10.595   4964  Z= 0.340
  Chirality :  0.043   0.393    537
  Planarity :  0.005   0.044    612
  Dihedral  :  3.404  12.703    490
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 21.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.41), residues: 439
  helix:  1.76 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop :  0.39 (0.65), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 196 
 HIS   0.002   0.001   HIS A  72 
 PHE   0.045   0.002   PHE A 232 
 TYR   0.031   0.002   TYR A 409 
 ARG   0.010   0.001   ARG A 242 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1621.90 seconds
wall clock time: 28 minutes 41.60 seconds (1721.60 seconds total)