Starting phenix.real_space_refine
on Fri May  9 19:04:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8erc_28552/05_2025/8erc_28552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8erc_28552/05_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_28552/05_2025/8erc_28552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8erc_28552/05_2025/8erc_28552.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8erc_28552/05_2025/8erc_28552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8erc_28552/05_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-5687/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: 3.03, per 1000 atoms: 0.86
  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: 0.91
  Conformation dependent library (CDL) restraints added in 428.2 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: 0.95

  Time building geometry restraints manager: 1.08 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:             0.630
  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:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.310
  Find NCS groups from input model:        0.050
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.280
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.397 
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: 0.1640
  time to fit residues: 21.4903
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  : 0.377 
-------------------------------------------------------------------------------
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 = 0.154223 restraints weight = 6182.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.160119 restraints weight = 3712.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.164265 restraints weight = 2581.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
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= 0.170
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05268 (  248)
  hydrogen bonds       : angle       4.67667 (  723)
  covalent geometry    : bond        0.00342 ( 3634)
  covalent geometry    : angle       0.64818 ( 4964)

*********************** 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  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 VAL cc_start: 0.9509 (p) cc_final: 0.9289 (t)
REVERT: A  254 CYS cc_start: 0.7955 (m) cc_final: 0.7556 (m)
REVERT: A  409 TYR cc_start: 0.8693 (t80) cc_final: 0.8047 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 102
  average time/residue: 0.1679
  time to fit residues: 20.9248
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  : 0.408 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   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:    3.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.185425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.156874 restraints weight = 6226.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.162538 restraints weight = 3728.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.166593 restraints weight = 2569.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3634  Z= 0.139
  Angle     :  0.621   8.375   4964  Z= 0.307
  Chirality :  0.038   0.134    537
  Planarity :  0.005   0.039    612
  Dihedral  :  3.541  11.529    490
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.97
  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:  2.02 (0.41), residues: 439
  helix:  1.71 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop :  0.50 (0.64), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 196 
 HIS   0.005   0.001   HIS A 399 
 PHE   0.038   0.002   PHE A 232 
 TYR   0.020   0.002   TYR A 159 
 ARG   0.006   0.001   ARG A 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04719 (  248)
  hydrogen bonds       : angle       4.50919 (  723)
  covalent geometry    : bond        0.00282 ( 3634)
  covalent geometry    : angle       0.62133 ( 4964)

*********************** 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  : 0.367 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.7051 (mt) cc_final: 0.6837 (mm)
REVERT: A  120 GLN cc_start: 0.7235 (tp40) cc_final: 0.6862 (tp-100)
REVERT: A  146 VAL cc_start: 0.9502 (p) cc_final: 0.9295 (t)
REVERT: A  150 MET cc_start: 0.6720 (tmm) cc_final: 0.6425 (tpt)
REVERT: A  254 CYS cc_start: 0.7986 (m) cc_final: 0.7580 (m)
REVERT: A  409 TYR cc_start: 0.8704 (t80) cc_final: 0.7938 (t80)
  outliers start: 7
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1486
  time to fit residues: 18.2159
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  : 0.338 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0980
   chunk 15 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 13 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.181381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.151659 restraints weight = 6192.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.157005 restraints weight = 3863.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.160973 restraints weight = 2695.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3634  Z= 0.208
  Angle     :  0.651   7.693   4964  Z= 0.329
  Chirality :  0.040   0.226    537
  Planarity :  0.005   0.042    612
  Dihedral  :  3.522  12.219    490
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  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:  1.76 (0.41), residues: 439
  helix:  1.49 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop :  0.39 (0.68), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 176 
 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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04975 (  248)
  hydrogen bonds       : angle       4.73427 (  723)
  covalent geometry    : bond        0.00401 ( 3634)
  covalent geometry    : angle       0.65143 ( 4964)

*********************** 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
  109 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6792 (m90) cc_final: 0.6471 (m90)
REVERT: A  120 GLN cc_start: 0.7294 (tp40) cc_final: 0.6809 (tp-100)
REVERT: A  130 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6972 (pmm)
REVERT: A  146 VAL cc_start: 0.9504 (p) cc_final: 0.9302 (t)
REVERT: A  150 MET cc_start: 0.6825 (tmm) cc_final: 0.6578 (tpt)
REVERT: A  254 CYS cc_start: 0.8012 (m) cc_final: 0.7623 (m)
REVERT: A  409 TYR cc_start: 0.8748 (t80) cc_final: 0.8068 (t80)
REVERT: A  412 MET cc_start: 0.7735 (mpp) cc_final: 0.7499 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 99
  average time/residue: 0.1486
  time to fit residues: 18.0505
Evaluate side-chains
  101 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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  158 CYS
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:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0670
   chunk 23 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6918

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.185210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.156412 restraints weight = 6283.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.161802 restraints weight = 3875.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.165948 restraints weight = 2710.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.2469

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= 0.136
  Angle     :  0.632   8.885   4964  Z= 0.304
  Chirality :  0.039   0.264    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.465  12.402    490
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.61 %
    Favored  : 77.07 %
  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:  2.13 (0.41), residues: 439
  helix:  1.75 (0.28), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.62 (0.65), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 327 
 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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04441 (  248)
  hydrogen bonds       : angle       4.46098 (  723)
  covalent geometry    : bond        0.00272 ( 3634)
  covalent geometry    : angle       0.63210 ( 4964)

*********************** 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  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7972 (tttt) cc_final: 0.7713 (tttt)
REVERT: A   52 HIS cc_start: 0.6666 (m90) cc_final: 0.6375 (m90)
REVERT: A  120 GLN cc_start: 0.7280 (tp40) cc_final: 0.6777 (tp-100)
REVERT: A  130 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6528 (pmm)
REVERT: A  146 VAL cc_start: 0.9469 (p) cc_final: 0.9265 (t)
REVERT: A  254 CYS cc_start: 0.7977 (m) cc_final: 0.7582 (m)
REVERT: A  308 ASP cc_start: 0.8306 (t70) cc_final: 0.8037 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1522
  time to fit residues: 19.2104
Evaluate side-chains
  108 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
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  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:    6.9990
   chunk 21 optimal weight:    0.0470
   chunk 39 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5680

-------------------------------------------------------------------------------
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**
** A 279 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 = 0.4308 r_free = 0.4308 target = 0.186166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.157335 restraints weight = 6336.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.162841 restraints weight = 3830.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.166982 restraints weight = 2686.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6617
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3634  Z= 0.132
  Angle     :  0.667   8.952   4964  Z= 0.318
  Chirality :  0.040   0.319    537
  Planarity :  0.005   0.044    612
  Dihedral  :  3.462  12.284    490
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.89 %
    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:  2.13 (0.41), residues: 439
  helix:  1.75 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.64 (0.66), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 327 
 HIS   0.005   0.001   HIS A 123 
 PHE   0.042   0.002   PHE A 232 
 TYR   0.030   0.002   TYR A 159 
 ARG   0.002   0.000   ARG A 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04318 (  248)
  hydrogen bonds       : angle       4.45648 (  723)
  covalent geometry    : bond        0.00273 ( 3634)
  covalent geometry    : angle       0.66733 ( 4964)

*********************** 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
  112 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 HIS cc_start: 0.6624 (m90) cc_final: 0.6331 (m90)
REVERT: A  120 GLN cc_start: 0.7183 (tp40) cc_final: 0.6759 (tp-100)
REVERT: A  130 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6493 (pmm)
REVERT: A  254 CYS cc_start: 0.7989 (m) cc_final: 0.7615 (m)
REVERT: A  308 ASP cc_start: 0.8338 (t70) cc_final: 0.7703 (t0)
REVERT: A  376 GLU cc_start: 0.8141 (tp30) cc_final: 0.7673 (tp30)
REVERT: A  409 TYR cc_start: 0.8779 (t80) cc_final: 0.8481 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 102
  average time/residue: 0.1510
  time to fit residues: 18.9177
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  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   64 ILE
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  206 LEU
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:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 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 = 0.4308 r_free = 0.4308 target = 0.186258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.157530 restraints weight = 6235.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.162904 restraints weight = 3807.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.167035 restraints weight = 2666.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6624
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3634  Z= 0.138
  Angle     :  0.671   8.865   4964  Z= 0.320
  Chirality :  0.041   0.361    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.420  12.383    490
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.78 %
    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:  2.17 (0.41), residues: 439
  helix:  1.78 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.66 (0.66), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.041   0.002   PHE A 232 
 TYR   0.029   0.002   TYR A 159 
 ARG   0.002   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04335 (  248)
  hydrogen bonds       : angle       4.42846 (  723)
  covalent geometry    : bond        0.00283 ( 3634)
  covalent geometry    : angle       0.67072 ( 4964)

*********************** 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
  113 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7875 (tttt) cc_final: 0.7662 (tttt)
REVERT: A   52 HIS cc_start: 0.6642 (m90) cc_final: 0.6309 (m90)
REVERT: A  120 GLN cc_start: 0.7258 (tp40) cc_final: 0.6800 (tp-100)
REVERT: A  130 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6472 (pmm)
REVERT: A  254 CYS cc_start: 0.7990 (m) cc_final: 0.7590 (m)
REVERT: A  376 GLU cc_start: 0.8171 (tp30) cc_final: 0.7732 (tp30)
REVERT: A  409 TYR cc_start: 0.8787 (t80) cc_final: 0.8563 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 105
  average time/residue: 0.1571
  time to fit residues: 20.2953
Evaluate side-chains
  107 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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  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 38 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 14 optimal weight:    0.1980
   chunk 13 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 123 HIS
** A 279 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 = 0.4307 r_free = 0.4307 target = 0.186520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.157661 restraints weight = 6214.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.163195 restraints weight = 3812.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.167428 restraints weight = 2656.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.2841

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= 0.139
  Angle     :  0.685   9.533   4964  Z= 0.326
  Chirality :  0.041   0.344    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.412  12.442    490
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  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 (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:  2.25 (0.41), residues: 439
  helix:  1.84 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop :  0.71 (0.65), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A  72 
 PHE   0.044   0.002   PHE A 232 
 TYR   0.023   0.001   TYR A 159 
 ARG   0.004   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  248)
  hydrogen bonds       : angle       4.48578 (  723)
  covalent geometry    : bond        0.00281 ( 3634)
  covalent geometry    : angle       0.68462 ( 4964)

*********************** 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  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7932 (tttt) cc_final: 0.7632 (tttt)
REVERT: A   52 HIS cc_start: 0.6699 (m90) cc_final: 0.6320 (m90)
REVERT: A  120 GLN cc_start: 0.7202 (tp40) cc_final: 0.6765 (tp-100)
REVERT: A  130 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6333 (pmm)
REVERT: A  376 GLU cc_start: 0.8199 (tp30) cc_final: 0.7761 (tp30)
REVERT: A  409 TYR cc_start: 0.8794 (t80) cc_final: 0.8555 (t80)
  outliers start: 11
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1442
  time to fit residues: 18.0348
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  : 0.354 
-------------------------------------------------------------------------------
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  206 LEU
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:    5.9990
   chunk 26 optimal weight:    0.0070
   chunk 17 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0070
   chunk 28 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.2974

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 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 = 0.4322 r_free = 0.4322 target = 0.188093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.160322 restraints weight = 6061.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.166258 restraints weight = 3690.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.170129 restraints weight = 2556.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6566
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3634  Z= 0.132
  Angle     :  0.693  10.550   4964  Z= 0.328
  Chirality :  0.042   0.365    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.482  12.377    490
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.99 %
    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 (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:  1.69 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop :  0.42 (0.65), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.043   0.002   PHE A 232 
 TYR   0.020   0.001   TYR A 159 
 ARG   0.008   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  248)
  hydrogen bonds       : angle       4.44992 (  723)
  covalent geometry    : bond        0.00262 ( 3634)
  covalent geometry    : angle       0.69302 ( 4964)

*********************** 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
  107 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7822 (tttt) cc_final: 0.7532 (tttt)
REVERT: A   52 HIS cc_start: 0.6580 (m90) cc_final: 0.6221 (m90)
REVERT: A  120 GLN cc_start: 0.7121 (tp40) cc_final: 0.6730 (tp-100)
REVERT: A  130 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6339 (pmm)
REVERT: A  376 GLU cc_start: 0.8210 (tp30) cc_final: 0.7792 (tp30)
REVERT: A  409 TYR cc_start: 0.8746 (t80) cc_final: 0.8511 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 100
  average time/residue: 0.1411
  time to fit residues: 17.4013
Evaluate side-chains
  105 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
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  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  206 LEU
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:    0.7980
   chunk 8 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0470
   chunk 6 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0670
   chunk 31 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3394

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.188793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.160938 restraints weight = 6265.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.166817 restraints weight = 3762.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.171089 restraints weight = 2578.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3634  Z= 0.129
  Angle     :  0.723  13.670   4964  Z= 0.335
  Chirality :  0.042   0.375    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.402  12.414    490
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 21.55 %
    Favored  : 75.69 %
  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:  2.00 (0.42), residues: 439
  helix:  1.73 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop :  0.31 (0.65), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.045   0.002   PHE A 232 
 TYR   0.019   0.001   TYR A 159 
 ARG   0.003   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  248)
  hydrogen bonds       : angle       4.43414 (  723)
  covalent geometry    : bond        0.00260 ( 3634)
  covalent geometry    : angle       0.72280 ( 4964)

********************** 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
  102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7753 (tttt) cc_final: 0.7424 (tttt)
REVERT: A  120 GLN cc_start: 0.7207 (tp40) cc_final: 0.6811 (tp-100)
REVERT: A  130 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6254 (pmm)
REVERT: A  234 MET cc_start: 0.5810 (ppp) cc_final: 0.5501 (ppp)
REVERT: A  249 TRP cc_start: 0.7580 (m-10) cc_final: 0.7194 (m-10)
REVERT: A  376 GLU cc_start: 0.8278 (tp30) cc_final: 0.7879 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1339
  time to fit residues: 16.1534
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  : 0.383 
-------------------------------------------------------------------------------
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  126 GLN
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  200 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.187510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.159177 restraints weight = 6209.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.164782 restraints weight = 3772.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.169024 restraints weight = 2605.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6586
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3634  Z= 0.138
  Angle     :  0.716  12.978   4964  Z= 0.335
  Chirality :  0.042   0.380    537
  Planarity :  0.005   0.043    612
  Dihedral  :  3.420  12.698    490
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.93 %
    Favored  : 75.14 %
  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:  1.93 (0.42), residues: 439
  helix:  1.69 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop :  0.28 (0.64), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 196 
 HIS   0.002   0.000   HIS A  72 
 PHE   0.044   0.002   PHE A 232 
 TYR   0.031   0.002   TYR A 409 
 ARG   0.005   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  248)
  hydrogen bonds       : angle       4.46581 (  723)
  covalent geometry    : bond        0.00281 ( 3634)
  covalent geometry    : angle       0.71641 ( 4964)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1654.92 seconds
wall clock time: 29 minutes 32.88 seconds (1772.88 seconds total)