Starting phenix.real_space_refine
on Mon Jan 13 19:37:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.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/9f6p_50237/01_2025/9f6p_50237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6p_50237/01_2025/9f6p_50237.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=   0.001 sd=   0.030
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: 5
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     S      22      5.16       5
     C    2460      2.51       5
     N     606      2.21       5
     O     631      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3720
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 482, 3719
          Classifications: {'peptide': 482}
          Link IDs: {'PTRANS': 19, 'TRANS': 462}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.90, per 1000 atoms: 0.78
  Number of scatterers: 3720
  At special positions: 0
  Unit cell: (83.328, 69.006, 79.422, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      1     24.99
     S      22     16.00
     O     631      8.00
     N     606      7.00
     C    2460      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 354 " distance=2.03

  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 433.1 milliseconds
  

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  886

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      84.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 73
      removed outlier: 3.913A  pdb=" N   SER A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 88
      removed outlier: 3.918A  pdb=" N   ASP A  81 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 118
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 130 through 164
      removed outlier: 3.566A  pdb=" N   SER A 164 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 188
      removed outlier: 3.849A  pdb=" N   GLY A 173 " --> pdb=" O   PRO A 169 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 218
      removed outlier: 3.627A  pdb=" N   ARG A 218 " --> pdb=" O   TYR A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 230
    Processing helix  chain 'A' and resid 237 through 252
      removed outlier: 4.224A  pdb=" N   ILE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 266
      removed outlier: 4.035A  pdb=" N   ILE A 257 " --> pdb=" O   MET A 253 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   TYR A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 311
      removed outlier: 4.347A  pdb=" N   ILE A 277 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 325
    Processing helix  chain 'A' and resid 328 through 333
    Processing helix  chain 'A' and resid 344 through 357
    Processing helix  chain 'A' and resid 357 through 391
      removed outlier: 4.293A  pdb=" N   LEU A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   TYR A 362 " --> pdb=" O   PRO A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 419
      Proline residue:  A 411  - end of helix
    Processing helix  chain 'A' and resid 420 through 439
    Processing helix  chain 'A' and resid 439 through 451
      Proline residue:  A 445  - end of helix
    Processing helix  chain 'A' and resid 462 through 488
    Processing helix  chain 'A' and resid 497 through 523
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.721A  pdb=" N   TYR A 537 " --> pdb=" O   HIS A 533 " (cutoff:3.500A)

    302 hydrogen bonds defined for protein.
    906 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: 1.00

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1151
        1.34 -     1.46: 954
        1.46 -     1.58: 1675
        1.58 -     1.70: 0
        1.70 -     1.82: 34
  Bond restraints: 3814
  Sorted by residual:
  bond pdb=" N   MET A 253 "
       pdb=" CA  MET A 253 "
    ideal  model  delta    sigma   weight residual
    1.454  1.477 -0.023 1.30e-02 5.92e+03 3.21e+00
  bond pdb=" N   LEU A 437 "
       pdb=" CA  LEU A 437 "
    ideal  model  delta    sigma   weight residual
    1.459  1.479 -0.020 1.28e-02 6.10e+03 2.45e+00
  bond pdb=" CA  ARG A 218 "
       pdb=" CB  ARG A 218 "
    ideal  model  delta    sigma   weight residual
    1.522  1.532 -0.010 7.00e-03 2.04e+04 1.86e+00
  bond pdb=" CB  GLU A 268 "
       pdb=" CG  GLU A 268 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.47e+00
  bond pdb=" CB  ARG A 193 "
       pdb=" CG  ARG A 193 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.23e+00
  ... (remaining 3809 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 5013
        2.10 -     4.19: 143
        4.19 -     6.29: 31
        6.29 -     8.39: 9
        8.39 -    10.48: 6
  Bond angle restraints: 5202
  Sorted by residual:
  angle pdb=" N   LEU A 437 "
        pdb=" CA  LEU A 437 "
        pdb=" CB  LEU A 437 "
      ideal   model   delta    sigma   weight residual
     110.28  104.86    5.42 1.55e+00 4.16e-01 1.22e+01
  angle pdb=" CB  MET A  68 "
        pdb=" CG  MET A  68 "
        pdb=" SD  MET A  68 "
      ideal   model   delta    sigma   weight residual
     112.70  123.09  -10.39 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" CA  GLN A 312 "
        pdb=" CB  GLN A 312 "
        pdb=" CG  GLN A 312 "
      ideal   model   delta    sigma   weight residual
     114.10  120.97   -6.87 2.00e+00 2.50e-01 1.18e+01
  angle pdb=" CA  LYS A  91 "
        pdb=" CB  LYS A  91 "
        pdb=" CG  LYS A  91 "
      ideal   model   delta    sigma   weight residual
     114.10  120.30   -6.20 2.00e+00 2.50e-01 9.60e+00
  angle pdb=" CA  LEU A 391 "
        pdb=" CB  LEU A 391 "
        pdb=" CG  LEU A 391 "
      ideal   model   delta    sigma   weight residual
     116.30  126.78  -10.48 3.50e+00 8.16e-02 8.97e+00
  ... (remaining 5197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.84: 1790
       15.84 -    31.68: 291
       31.68 -    47.52: 90
       47.52 -    63.36: 29
       63.36 -    79.20: 4
  Dihedral angle restraints: 2204
    sinusoidal: 819
      harmonic: 1385
  Sorted by residual:
  dihedral pdb=" CB  CYS A 322 "
           pdb=" SG  CYS A 322 "
           pdb=" SG  CYS A 354 "
           pdb=" CB  CYS A 354 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -156.87   70.87     1      1.00e+01 1.00e-02 6.45e+01
  dihedral pdb=" CA  ALA A 342 "
           pdb=" C   ALA A 342 "
           pdb=" N   VAL A 343 "
           pdb=" CA  VAL A 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.89  -19.11     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  TYR A 311 "
           pdb=" C   TYR A 311 "
           pdb=" N   GLN A 312 "
           pdb=" CA  GLN A 312 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.61  -18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 2201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 509
       0.062 -    0.124: 96
       0.124 -    0.186: 8
       0.186 -    0.247: 2
       0.247 -    0.309: 1
  Chirality restraints: 616
  Sorted by residual:
  chirality pdb=" CG  LEU A 102 "
            pdb=" CB  LEU A 102 "
            pdb=" CD1 LEU A 102 "
            pdb=" CD2 LEU A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" CB  VAL A 174 "
            pdb=" CA  VAL A 174 "
            pdb=" CG1 VAL A 174 "
            pdb=" CG2 VAL A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  THR A 177 "
            pdb=" CA  THR A 177 "
            pdb=" OG1 THR A 177 "
            pdb=" CG2 THR A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.09e-01
  ... (remaining 613 not shown)

  Planarity restraints: 643
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 311 "   -0.016 2.00e-02 2.50e+03   1.31e-02 3.43e+00
        pdb=" CG  TYR A 311 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 311 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 311 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 311 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 311 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 311 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 311 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 270 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" CG  ASP A 270 "    0.029 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 270 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 270 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 230 "   -0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO A 231 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 231 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 231 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 640 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 46
        2.65 -     3.21: 3781
        3.21 -     3.78: 6236
        3.78 -     4.34: 7513
        4.34 -     4.90: 12437
  Nonbonded interactions: 30013
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  77 "
            pdb="MN    MN A 701 "
     model   vdw
     2.090 2.320
  nonbonded pdb=" O   SER A 374 "
            pdb=" OG1 THR A 378 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   LYS A 131 "
            pdb=" OG1 THR A 135 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   CYS A 518 "
            pdb=" ND1 HIS A 522 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OG  SER A 451 "
            pdb=" OD1 ASN A 461 "
     model   vdw
     2.351 3.040
  ... (remaining 30008 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:             0.380
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.250
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
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      :  0.004   0.038   3814  Z= 0.253
  Angle     :  0.929  10.484   5202  Z= 0.454
  Chirality :  0.048   0.309    616
  Planarity :  0.005   0.040    643
  Dihedral  : 18.008  79.197   1312
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 44.10 %
    Favored  : 53.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.39 (0.38), residues: 480
  helix:  1.66 (0.26), residues: 377
  sheet:  None (None), residues: 0
  loop : -1.89 (0.59), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 138 
 HIS   0.003   0.001   HIS A 522 
 PHE   0.024   0.002   PHE A 184 
 TYR   0.029   0.002   TYR A 311 
 ARG   0.008   0.001   ARG A 400 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 LEU cc_start: 0.2433 (OUTLIER) cc_final: 0.2194 (tp)
REVERT: A   68 MET cc_start: 0.6634 (tpp) cc_final: 0.5464 (tpt)
REVERT: A  135 THR cc_start: 0.9084 (m) cc_final: 0.8877 (t)
REVERT: A  178 ILE cc_start: 0.8263 (tp) cc_final: 0.7995 (pt)
REVERT: A  214 TYR cc_start: 0.7164 (t80) cc_final: 0.6904 (t80)
REVERT: A  228 LEU cc_start: 0.8310 (tp) cc_final: 0.7999 (tt)
REVERT: A  278 ARG cc_start: 0.7002 (tmt170) cc_final: 0.6615 (mtm-85)
REVERT: A  287 GLU cc_start: 0.8032 (tt0) cc_final: 0.7327 (tm-30)
REVERT: A  393 LEU cc_start: 0.8120 (tt) cc_final: 0.7906 (mt)
REVERT: A  475 LEU cc_start: 0.8984 (tp) cc_final: 0.8659 (pp)
REVERT: A  537 TYR cc_start: 0.8050 (m-10) cc_final: 0.7696 (m-10)
  outliers start: 8
  outliers final: 4
  residues processed: 153
  average time/residue: 0.1456
  time to fit residues: 27.7291
Evaluate side-chains
  116 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 111
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0030
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 281 ASN
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
A 461 ASN
A 529 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.154610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.134675 restraints weight = 7421.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.138455 restraints weight = 3956.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.141049 restraints weight = 2474.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3814  Z= 0.212
  Angle     :  0.695   7.063   5202  Z= 0.345
  Chirality :  0.040   0.139    616
  Planarity :  0.005   0.040    643
  Dihedral  :  6.291  48.847    527
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 35.13 %
    Favored  : 58.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.42 (0.38), residues: 480
  helix:  1.73 (0.26), residues: 375
  sheet:  None (None), residues: 0
  loop : -2.05 (0.57), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  94 
 HIS   0.008   0.001   HIS A 126 
 PHE   0.036   0.002   PHE A  72 
 TYR   0.013   0.001   TYR A 311 
 ARG   0.005   0.001   ARG A 400 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.7766 (m-80) cc_final: 0.7505 (m-10)
REVERT: A   67 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7085 (pp)
REVERT: A   72 PHE cc_start: 0.7880 (m-80) cc_final: 0.7442 (m-80)
REVERT: A  107 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8690 (mm-40)
REVERT: A  178 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7862 (pt)
REVERT: A  214 TYR cc_start: 0.7285 (t80) cc_final: 0.7058 (t80)
REVERT: A  228 LEU cc_start: 0.8391 (tp) cc_final: 0.8052 (tt)
REVERT: A  278 ARG cc_start: 0.7229 (tmt170) cc_final: 0.6879 (mtm-85)
REVERT: A  287 GLU cc_start: 0.7978 (tt0) cc_final: 0.7698 (tm-30)
REVERT: A  364 TRP cc_start: 0.8561 (OUTLIER) cc_final: 0.8125 (t60)
REVERT: A  378 THR cc_start: 0.9203 (m) cc_final: 0.8948 (p)
REVERT: A  484 VAL cc_start: 0.7618 (t) cc_final: 0.7273 (p)
REVERT: A  535 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7424 (m-80)
  outliers start: 26
  outliers final: 9
  residues processed: 137
  average time/residue: 0.1279
  time to fit residues: 22.3750
Evaluate side-chains
  127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  364 TRP
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  535 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.152454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.131415 restraints weight = 7684.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.135122 restraints weight = 4216.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137659 restraints weight = 2720.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3814  Z= 0.228
  Angle     :  0.669   8.773   5202  Z= 0.332
  Chirality :  0.040   0.207    616
  Planarity :  0.005   0.040    643
  Dihedral  :  5.473  50.727    522
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 32.05 %
    Favored  : 59.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.31 (0.38), residues: 480
  helix:  1.60 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -2.04 (0.57), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  94 
 HIS   0.008   0.001   HIS A 126 
 PHE   0.027   0.002   PHE A 483 
 TYR   0.009   0.001   TYR A 283 
 ARG   0.003   0.000   ARG A 400 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7128 (pp)
REVERT: A   81 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7452 (t70)
REVERT: A   91 LYS cc_start: 0.8757 (mmtt) cc_final: 0.7645 (mtmt)
REVERT: A  178 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8192 (pt)
REVERT: A  195 LEU cc_start: 0.7377 (tp) cc_final: 0.6930 (tt)
REVERT: A  214 TYR cc_start: 0.7242 (t80) cc_final: 0.6629 (t80)
REVERT: A  228 LEU cc_start: 0.8530 (tp) cc_final: 0.8144 (tt)
REVERT: A  278 ARG cc_start: 0.7219 (tmt170) cc_final: 0.6884 (mtm-85)
REVERT: A  364 TRP cc_start: 0.8624 (OUTLIER) cc_final: 0.7072 (t-100)
REVERT: A  423 ASP cc_start: 0.8118 (m-30) cc_final: 0.7891 (m-30)
REVERT: A  466 LYS cc_start: 0.7774 (mttm) cc_final: 0.7367 (mttm)
REVERT: A  484 VAL cc_start: 0.7576 (t) cc_final: 0.7252 (p)
  outliers start: 33
  outliers final: 17
  residues processed: 132
  average time/residue: 0.1349
  time to fit residues: 22.7121
Evaluate side-chains
  131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  364 TRP
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  487 TYR
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 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 = 0.3923 r_free = 0.3923 target = 0.150468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.130383 restraints weight = 7534.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133946 restraints weight = 3993.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.136379 restraints weight = 2520.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   3814  Z= 0.247
  Angle     :  0.650   7.688   5202  Z= 0.325
  Chirality :  0.039   0.138    616
  Planarity :  0.005   0.038    643
  Dihedral  :  5.197  53.317    522
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  9.23 %
    Allowed  : 32.31 %
    Favored  : 58.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.33 (0.38), residues: 480
  helix:  1.64 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -2.15 (0.56), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  94 
 HIS   0.006   0.001   HIS A 126 
 PHE   0.016   0.002   PHE A 301 
 TYR   0.009   0.001   TYR A 190 
 ARG   0.002   0.000   ARG A 394 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 110
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7020 (pp)
REVERT: A   68 MET cc_start: 0.6152 (tpt) cc_final: 0.5482 (tpt)
REVERT: A   73 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8127 (tm)
REVERT: A   81 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7382 (t70)
REVERT: A   91 LYS cc_start: 0.8792 (mmtt) cc_final: 0.7635 (mtmt)
REVERT: A  135 THR cc_start: 0.9048 (m) cc_final: 0.8804 (t)
REVERT: A  154 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9254 (mp)
REVERT: A  206 MET cc_start: 0.9011 (ppp) cc_final: 0.8795 (ppp)
REVERT: A  228 LEU cc_start: 0.8541 (tp) cc_final: 0.8190 (tt)
REVERT: A  276 ASP cc_start: 0.7361 (m-30) cc_final: 0.7076 (m-30)
REVERT: A  278 ARG cc_start: 0.7212 (tmt170) cc_final: 0.6862 (mtm-85)
REVERT: A  364 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.7117 (t-100)
  outliers start: 36
  outliers final: 18
  residues processed: 131
  average time/residue: 0.1269
  time to fit residues: 21.3602
Evaluate side-chains
  121 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  364 TRP
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  487 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 46 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 532 HIS
A 533 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.148683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.128575 restraints weight = 7898.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.132183 restraints weight = 4236.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.134516 restraints weight = 2681.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3814  Z= 0.225
  Angle     :  0.680   8.732   5202  Z= 0.332
  Chirality :  0.040   0.145    616
  Planarity :  0.005   0.038    643
  Dihedral  :  4.474  35.775    520
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 31.79 %
    Favored  : 59.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.35 (0.38), residues: 480
  helix:  1.65 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -2.16 (0.55), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  94 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.035   0.002   PHE A  72 
 TYR   0.015   0.001   TYR A 214 
 ARG   0.003   0.000   ARG A 273 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 108
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7106 (pp)
REVERT: A   68 MET cc_start: 0.6067 (tpt) cc_final: 0.5651 (tpt)
REVERT: A   73 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8215 (tm)
REVERT: A   91 LYS cc_start: 0.8790 (mmtt) cc_final: 0.7632 (mtmt)
REVERT: A  135 THR cc_start: 0.8994 (m) cc_final: 0.8755 (t)
REVERT: A  152 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: A  206 MET cc_start: 0.9000 (ppp) cc_final: 0.8794 (ppp)
REVERT: A  228 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8173 (tt)
REVERT: A  276 ASP cc_start: 0.7302 (m-30) cc_final: 0.6990 (m-30)
REVERT: A  278 ARG cc_start: 0.7271 (tmt170) cc_final: 0.6937 (mtm-85)
REVERT: A  529 HIS cc_start: 0.3176 (m90) cc_final: 0.2920 (t-90)
  outliers start: 33
  outliers final: 22
  residues processed: 129
  average time/residue: 0.1243
  time to fit residues: 20.7239
Evaluate side-chains
  125 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  487 TYR
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0370
   chunk 3 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 GLN
A 532 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.152191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.132544 restraints weight = 7441.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.136265 restraints weight = 3913.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.138953 restraints weight = 2412.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3814  Z= 0.221
  Angle     :  0.689  12.019   5202  Z= 0.333
  Chirality :  0.040   0.141    616
  Planarity :  0.005   0.037    643
  Dihedral  :  4.464  35.231    520
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  7.44 %
    Allowed  : 34.10 %
    Favored  : 58.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.26 (0.38), residues: 480
  helix:  1.59 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -2.19 (0.56), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  94 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.050   0.002   PHE A  72 
 TYR   0.015   0.001   TYR A 214 
 ARG   0.004   0.000   ARG A 273 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7093 (pp)
REVERT: A   73 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8136 (tm)
REVERT: A   91 LYS cc_start: 0.8775 (mmtt) cc_final: 0.7614 (mtmt)
REVERT: A  135 THR cc_start: 0.9012 (m) cc_final: 0.8774 (t)
REVERT: A  152 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7622 (tm-30)
REVERT: A  183 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6970 (p90)
REVERT: A  228 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8175 (tt)
REVERT: A  276 ASP cc_start: 0.7328 (m-30) cc_final: 0.7074 (m-30)
REVERT: A  278 ARG cc_start: 0.7263 (tmt170) cc_final: 0.6938 (mtm-85)
REVERT: A  466 LYS cc_start: 0.7797 (mttm) cc_final: 0.7422 (mttm)
REVERT: A  529 HIS cc_start: 0.3009 (m90) cc_final: 0.2748 (t-90)
  outliers start: 29
  outliers final: 19
  residues processed: 124
  average time/residue: 0.1319
  time to fit residues: 21.1554
Evaluate side-chains
  121 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  487 TYR
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   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 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 435 GLN
A 532 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.151423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.131572 restraints weight = 7534.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.135245 restraints weight = 4006.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.137706 restraints weight = 2519.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3814  Z= 0.224
  Angle     :  0.716  12.525   5202  Z= 0.340
  Chirality :  0.039   0.135    616
  Planarity :  0.005   0.038    643
  Dihedral  :  4.460  34.824    520
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  7.44 %
    Allowed  : 34.36 %
    Favored  : 58.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.20 (0.38), residues: 480
  helix:  1.57 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.29 (0.53), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  94 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.044   0.002   PHE A  72 
 TYR   0.009   0.001   TYR A 214 
 ARG   0.004   0.000   ARG A 273 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 PHE cc_start: 0.6930 (m-80) cc_final: 0.6729 (m-80)
REVERT: A   73 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8071 (tm)
REVERT: A   91 LYS cc_start: 0.8773 (mmtt) cc_final: 0.7622 (mtmt)
REVERT: A   97 LEU cc_start: 0.8383 (tt) cc_final: 0.8031 (tp)
REVERT: A  135 THR cc_start: 0.9013 (m) cc_final: 0.8790 (t)
REVERT: A  152 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7691 (tm-30)
REVERT: A  187 LEU cc_start: 0.8246 (tt) cc_final: 0.7870 (pp)
REVERT: A  228 LEU cc_start: 0.8546 (tp) cc_final: 0.8175 (tt)
REVERT: A  278 ARG cc_start: 0.7341 (tmt170) cc_final: 0.6941 (mtm-85)
REVERT: A  364 TRP cc_start: 0.8773 (OUTLIER) cc_final: 0.7157 (t-100)
REVERT: A  466 LYS cc_start: 0.7801 (mttm) cc_final: 0.7419 (mttm)
  outliers start: 29
  outliers final: 22
  residues processed: 122
  average time/residue: 0.1236
  time to fit residues: 19.3467
Evaluate side-chains
  122 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  364 TRP
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  487 TYR
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 GLN
A 532 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.149661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.129398 restraints weight = 7535.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.133054 restraints weight = 3983.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135697 restraints weight = 2508.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   3814  Z= 0.246
  Angle     :  0.734  13.405   5202  Z= 0.348
  Chirality :  0.040   0.141    616
  Planarity :  0.005   0.038    643
  Dihedral  :  4.502  35.297    520
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 35.64 %
    Favored  : 56.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.10 (0.38), residues: 480
  helix:  1.50 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -2.36 (0.53), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 171 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.042   0.002   PHE A  72 
 TYR   0.017   0.001   TYR A 214 
 ARG   0.005   0.000   ARG A 273 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 MET cc_start: 0.5413 (tpt) cc_final: 0.5056 (tpt)
REVERT: A   73 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8068 (tm)
REVERT: A   91 LYS cc_start: 0.8823 (mmtt) cc_final: 0.7698 (mtmt)
REVERT: A  135 THR cc_start: 0.9048 (m) cc_final: 0.8843 (t)
REVERT: A  152 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: A  228 LEU cc_start: 0.8535 (tp) cc_final: 0.8148 (tt)
REVERT: A  269 ILE cc_start: 0.8445 (mt) cc_final: 0.7956 (mm)
REVERT: A  278 ARG cc_start: 0.7268 (tmt170) cc_final: 0.6853 (mtm-85)
REVERT: A  341 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6790 (p)
REVERT: A  364 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.7089 (t-100)
REVERT: A  466 LYS cc_start: 0.7867 (mttm) cc_final: 0.7467 (mttm)
REVERT: A  484 VAL cc_start: 0.7457 (t) cc_final: 0.7201 (p)
  outliers start: 30
  outliers final: 23
  residues processed: 119
  average time/residue: 0.1227
  time to fit residues: 18.8676
Evaluate side-chains
  125 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  364 TRP
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  487 TYR
Chi-restraints excluded: chain A residue  493 HIS
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 39 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   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 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 GLN
A 532 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.150863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130540 restraints weight = 7398.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.134268 restraints weight = 3956.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.136721 restraints weight = 2501.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   3814  Z= 0.232
  Angle     :  0.735  13.603   5202  Z= 0.350
  Chirality :  0.040   0.138    616
  Planarity :  0.005   0.039    643
  Dihedral  :  4.478  34.731    520
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  7.18 %
    Allowed  : 37.44 %
    Favored  : 55.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.16 (0.38), residues: 480
  helix:  1.57 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.41 (0.52), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 171 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.042   0.002   PHE A  72 
 TYR   0.015   0.001   TYR A 214 
 ARG   0.006   0.000   ARG A 273 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7980 (tm)
REVERT: A   91 LYS cc_start: 0.8798 (mmtt) cc_final: 0.7682 (mtmt)
REVERT: A  152 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: A  228 LEU cc_start: 0.8520 (tp) cc_final: 0.8173 (tt)
REVERT: A  269 ILE cc_start: 0.8689 (mt) cc_final: 0.8317 (mm)
REVERT: A  278 ARG cc_start: 0.7262 (tmt170) cc_final: 0.6840 (mtm-85)
REVERT: A  341 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6949 (p)
REVERT: A  364 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.7051 (t-100)
REVERT: A  466 LYS cc_start: 0.7943 (mttm) cc_final: 0.7548 (mttm)
  outliers start: 28
  outliers final: 23
  residues processed: 122
  average time/residue: 0.1247
  time to fit residues: 19.5369
Evaluate side-chains
  127 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  364 TRP
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  487 TYR
Chi-restraints excluded: chain A residue  493 HIS
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:    0.1980
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 GLN
A 532 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.152220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.132312 restraints weight = 7658.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.136087 restraints weight = 4039.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138771 restraints weight = 2522.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   3814  Z= 0.248
  Angle     :  0.764  13.489   5202  Z= 0.370
  Chirality :  0.042   0.254    616
  Planarity :  0.005   0.047    643
  Dihedral  :  4.562  35.237    520
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 38.21 %
    Favored  : 54.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.11 (0.38), residues: 480
  helix:  1.53 (0.26), residues: 379
  sheet:  None (None), residues: 0
  loop : -2.37 (0.52), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 171 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.041   0.002   PHE A  72 
 TYR   0.026   0.001   TYR A 214 
 ARG   0.006   0.000   ARG A 273 

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7862 (tm)
REVERT: A   91 LYS cc_start: 0.8818 (mmtt) cc_final: 0.7738 (mtmt)
REVERT: A   97 LEU cc_start: 0.8472 (tt) cc_final: 0.8162 (tp)
REVERT: A  152 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: A  228 LEU cc_start: 0.8492 (tp) cc_final: 0.8174 (tt)
REVERT: A  269 ILE cc_start: 0.8718 (mt) cc_final: 0.8339 (mm)
REVERT: A  278 ARG cc_start: 0.7238 (tmt170) cc_final: 0.6869 (mtm-85)
REVERT: A  466 LYS cc_start: 0.7910 (mttm) cc_final: 0.7516 (mttm)
  outliers start: 27
  outliers final: 24
  residues processed: 118
  average time/residue: 0.1292
  time to fit residues: 19.6778
Evaluate side-chains
  122 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  229 PHE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  428 ASN
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  487 TYR
Chi-restraints excluded: chain A residue  493 HIS
Chi-restraints excluded: chain A residue  525 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 44 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0670
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 532 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.151636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.131489 restraints weight = 7608.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.135254 restraints weight = 4023.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.137918 restraints weight = 2535.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.4549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   3814  Z= 0.239
  Angle     :  0.773  13.451   5202  Z= 0.373
  Chirality :  0.041   0.203    616
  Planarity :  0.005   0.047    643
  Dihedral  :  4.591  36.663    520
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 39.49 %
    Favored  : 54.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.13 (0.38), residues: 480
  helix:  1.55 (0.26), residues: 380
  sheet:  None (None), residues: 0
  loop : -2.45 (0.53), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 171 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.040   0.002   PHE A  72 
 TYR   0.018   0.001   TYR A 214 
 ARG   0.006   0.000   ARG A 273 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1409.52 seconds
wall clock time: 26 minutes 1.28 seconds (1561.28 seconds total)