Starting phenix.real_space_refine
on Wed Mar  5 21:51:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6p_50237/03_2025/9f6p_50237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6p_50237/03_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_50237/03_2025/9f6p_50237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6p_50237/03_2025/9f6p_50237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6p_50237/03_2025/9f6p_50237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6p_50237/03_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-5624/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: 2.81, per 1000 atoms: 0.76
  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: 1.07
  Conformation dependent library (CDL) restraints added in 476.0 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: 0.39
  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: 1.11

  Time building geometry restraints manager: 1.20 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:             0.350
  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:                    0.030
  Process input model:                     14.120
  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:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.670
-------------------------------------------------------------------------------
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  : 0.394 
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: 0.1342
  time to fit residues: 25.7237
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  : 0.386 
-------------------------------------------------------------------------------
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 = 34)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.138453 restraints weight = 3956.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.141045 restraints weight = 2474.827|
|-----------------------------------------------------------------------------|
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  : 0.546 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 PHE cc_start: 0.7765 (m-80) cc_final: 0.7506 (m-10)
REVERT: A   67 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7084 (pp)
REVERT: A   72 PHE cc_start: 0.7880 (m-80) cc_final: 0.7443 (m-80)
REVERT: A  107 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8691 (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: 0.7697 (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: 0.7274 (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: 0.1364
  time to fit residues: 24.1881
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  : 0.413 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 10 optimal weight:    0.1980
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.152577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.131652 restraints weight = 7649.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.135349 restraints weight = 4188.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.137957 restraints weight = 2698.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   3814  Z= 0.223
  Angle     :  0.664   8.543   5202  Z= 0.329
  Chirality :  0.040   0.190    616
  Planarity :  0.005   0.041    643
  Dihedral  :  5.473  50.525    522
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 14.61
  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:  1.32 (0.38), residues: 480
  helix:  1.61 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -2.05 (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  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7132 (pp)
REVERT: A   91 LYS cc_start: 0.8749 (mmtt) cc_final: 0.7634 (mtmt)
REVERT: A  178 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8183 (pt)
REVERT: A  195 LEU cc_start: 0.7351 (tp) cc_final: 0.6922 (tt)
REVERT: A  228 LEU cc_start: 0.8482 (tp) cc_final: 0.8140 (tt)
REVERT: A  278 ARG cc_start: 0.7211 (tmt170) cc_final: 0.6880 (mtm-85)
REVERT: A  364 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.7071 (t-100)
REVERT: A  423 ASP cc_start: 0.8115 (m-30) cc_final: 0.7886 (m-30)
REVERT: A  466 LYS cc_start: 0.7763 (mttm) cc_final: 0.7358 (mttm)
REVERT: A  484 VAL cc_start: 0.7567 (t) cc_final: 0.7235 (p)
  outliers start: 33
  outliers final: 18
  residues processed: 132
  average time/residue: 0.1406
  time to fit residues: 23.8833
Evaluate side-chains
  129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0970
   chunk 44 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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 533 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.151619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.131250 restraints weight = 7617.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.134925 restraints weight = 4091.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137335 restraints weight = 2588.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3814  Z= 0.220
  Angle     :  0.648   7.779   5202  Z= 0.320
  Chirality :  0.039   0.141    616
  Planarity :  0.005   0.039    643
  Dihedral  :  5.203  52.403    522
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  8.21 %
    Allowed  : 32.56 %
    Favored  : 59.23 %
  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:  1.40 (0.38), residues: 480
  helix:  1.69 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -2.17 (0.56), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  94 
 HIS   0.006   0.001   HIS A 126 
 PHE   0.017   0.001   PHE A  72 
 TYR   0.009   0.001   TYR A 214 
 ARG   0.003   0.000   ARG A 108 

*********************** 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
  142 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6995 (pp)
REVERT: A   68 MET cc_start: 0.6135 (tpt) cc_final: 0.5565 (tpt)
REVERT: A   72 PHE cc_start: 0.8099 (m-80) cc_final: 0.7898 (m-80)
REVERT: A   73 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8096 (tm)
REVERT: A   91 LYS cc_start: 0.8764 (mmtt) cc_final: 0.7614 (mtmt)
REVERT: A  178 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8230 (pt)
REVERT: A  195 LEU cc_start: 0.7461 (tp) cc_final: 0.7184 (tt)
REVERT: A  206 MET cc_start: 0.8958 (ppp) cc_final: 0.8372 (tmm)
REVERT: A  228 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8174 (tt)
REVERT: A  276 ASP cc_start: 0.7329 (m-30) cc_final: 0.7018 (m-30)
REVERT: A  278 ARG cc_start: 0.7206 (tmt170) cc_final: 0.6854 (mtm-85)
REVERT: A  364 TRP cc_start: 0.8639 (OUTLIER) cc_final: 0.7082 (t-100)
REVERT: A  466 LYS cc_start: 0.7780 (mttm) cc_final: 0.7366 (mttm)
  outliers start: 32
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1264
  time to fit residues: 21.0518
Evaluate side-chains
  124 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  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  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  216 VAL
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  252 ILE
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  456 MET
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:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 151 GLN ** 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 = 0.3924 r_free = 0.3924 target = 0.151001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.130692 restraints weight = 7906.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.134316 restraints weight = 4223.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.136872 restraints weight = 2686.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   3814  Z= 0.232
  Angle     :  0.685  11.406   5202  Z= 0.331
  Chirality :  0.039   0.134    616
  Planarity :  0.005   0.038    643
  Dihedral  :  4.500  37.504    520
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  8.21 %
    Allowed  : 32.31 %
    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:  1.33 (0.38), residues: 480
  helix:  1.64 (0.26), residues: 381
  sheet:  None (None), residues: 0
  loop : -2.15 (0.55), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  94 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.017   0.001   PHE A  72 
 TYR   0.011   0.001   TYR A 346 
 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
  145 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6996 (pp)
REVERT: A   68 MET cc_start: 0.6079 (tpt) cc_final: 0.5256 (tpt)
REVERT: A   73 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8194 (tm)
REVERT: A   91 LYS cc_start: 0.8770 (mmtt) cc_final: 0.7630 (mtmt)
REVERT: A  135 THR cc_start: 0.9043 (m) cc_final: 0.8794 (t)
REVERT: A  152 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7427 (tm-30)
REVERT: A  178 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8307 (pt)
REVERT: A  206 MET cc_start: 0.9012 (ppp) cc_final: 0.8403 (tmm)
REVERT: A  228 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8185 (tt)
REVERT: A  276 ASP cc_start: 0.7346 (m-30) cc_final: 0.7053 (m-30)
REVERT: A  278 ARG cc_start: 0.7205 (tmt170) cc_final: 0.6874 (mtm-85)
REVERT: A  529 HIS cc_start: 0.3360 (m90) cc_final: 0.3034 (t-90)
  outliers start: 32
  outliers final: 23
  residues processed: 132
  average time/residue: 0.1246
  time to fit residues: 21.5788
Evaluate side-chains
  131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
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  158 ILE
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  178 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  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  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  525 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0570
   chunk 3 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.152227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.132807 restraints weight = 7616.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.136472 restraints weight = 4027.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.139066 restraints weight = 2520.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.3617

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= 0.210
  Angle     :  0.688  11.889   5202  Z= 0.328
  Chirality :  0.039   0.137    616
  Planarity :  0.005   0.038    643
  Dihedral  :  4.428  35.608    520
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  8.97 %
    Allowed  : 33.33 %
    Favored  : 57.69 %
  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:  1.63 (0.26), residues: 382
  sheet:  None (None), residues: 0
  loop : -2.17 (0.56), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  94 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.034   0.002   PHE A  72 
 TYR   0.011   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
  144 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7069 (pp)
REVERT: A   68 MET cc_start: 0.5857 (tpt) cc_final: 0.5416 (tpt)
REVERT: A   73 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8171 (tm)
REVERT: A   91 LYS cc_start: 0.8759 (mmtt) cc_final: 0.7611 (mtmt)
REVERT: A  135 THR cc_start: 0.9004 (m) cc_final: 0.8762 (t)
REVERT: A  152 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7535 (tm-30)
REVERT: A  206 MET cc_start: 0.8959 (ppp) cc_final: 0.8371 (tmm)
REVERT: A  228 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8256 (tt)
REVERT: A  276 ASP cc_start: 0.7288 (m-30) cc_final: 0.6982 (m-30)
REVERT: A  278 ARG cc_start: 0.7258 (tmt170) cc_final: 0.6934 (mtm-85)
REVERT: A  466 LYS cc_start: 0.7770 (mttm) cc_final: 0.7402 (mttm)
  outliers start: 35
  outliers final: 25
  residues processed: 129
  average time/residue: 0.1175
  time to fit residues: 19.5780
Evaluate side-chains
  136 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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  162 LEU
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  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  428 ASN
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  444 LEU
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:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   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 373 GLN
A 435 GLN
A 532 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.152199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.131847 restraints weight = 7432.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.135528 restraints weight = 3963.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.138159 restraints weight = 2506.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3814  Z= 0.231
  Angle     :  0.715  12.798   5202  Z= 0.340
  Chirality :  0.040   0.138    616
  Planarity :  0.005   0.038    643
  Dihedral  :  4.454  34.578    520
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 33.85 %
    Favored  : 57.69 %
  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:  1.27 (0.38), residues: 480
  helix:  1.62 (0.26), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.18 (0.54), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  94 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.049   0.002   PHE A  72 
 TYR   0.007   0.001   TYR A 190 
 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
  146 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7187 (pp)
REVERT: A   73 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8100 (tm)
REVERT: A   91 LYS cc_start: 0.8772 (mmtt) cc_final: 0.7624 (mtmt)
REVERT: A   97 LEU cc_start: 0.8384 (tt) cc_final: 0.8057 (tp)
REVERT: A  135 THR cc_start: 0.9020 (m) cc_final: 0.8792 (t)
REVERT: A  152 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7653 (tm-30)
REVERT: A  228 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8175 (tt)
REVERT: A  276 ASP cc_start: 0.7441 (m-30) cc_final: 0.7186 (m-30)
REVERT: A  278 ARG cc_start: 0.7285 (tmt170) cc_final: 0.6923 (mtm-85)
REVERT: A  364 TRP cc_start: 0.8672 (OUTLIER) cc_final: 0.7074 (t-100)
REVERT: A  466 LYS cc_start: 0.7743 (mttm) cc_final: 0.7355 (mttm)
  outliers start: 33
  outliers final: 23
  residues processed: 131
  average time/residue: 0.1241
  time to fit residues: 20.9405
Evaluate side-chains
  130 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
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  162 LEU
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  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  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  525 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 47 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.152434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.132297 restraints weight = 7453.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.136017 restraints weight = 3931.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.138424 restraints weight = 2469.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3814  Z= 0.215
  Angle     :  0.728  12.459   5202  Z= 0.344
  Chirality :  0.039   0.138    616
  Planarity :  0.005   0.038    643
  Dihedral  :  4.415  33.882    520
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  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:  1.25 (0.38), residues: 480
  helix:  1.64 (0.26), residues: 378
  sheet:  None (None), residues: 0
  loop : -2.35 (0.52), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 171 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.043   0.002   PHE A  72 
 TYR   0.007   0.001   TYR A 190 
 ARG   0.004   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
  137 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8017 (tm)
REVERT: A   91 LYS cc_start: 0.8787 (mmtt) cc_final: 0.7687 (mtmt)
REVERT: A   97 LEU cc_start: 0.8321 (tt) cc_final: 0.7958 (tp)
REVERT: A  135 THR cc_start: 0.9032 (m) cc_final: 0.8824 (t)
REVERT: A  152 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7749 (tm-30)
REVERT: A  187 LEU cc_start: 0.8220 (tt) cc_final: 0.7845 (pp)
REVERT: A  228 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8200 (tt)
REVERT: A  269 ILE cc_start: 0.8325 (mt) cc_final: 0.7847 (mm)
REVERT: A  276 ASP cc_start: 0.7361 (m-30) cc_final: 0.7127 (m-30)
REVERT: A  278 ARG cc_start: 0.7265 (tmt170) cc_final: 0.6903 (mtm-85)
REVERT: A  364 TRP cc_start: 0.8705 (OUTLIER) cc_final: 0.7026 (t-100)
REVERT: A  466 LYS cc_start: 0.7892 (mttm) cc_final: 0.7499 (mttm)
  outliers start: 29
  outliers final: 22
  residues processed: 126
  average time/residue: 0.1215
  time to fit residues: 19.8388
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  : 0.395 
-------------------------------------------------------------------------------
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  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  162 LEU
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  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  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  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:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.151686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.132095 restraints weight = 7393.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135725 restraints weight = 3953.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.138332 restraints weight = 2496.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3814  Z= 0.240
  Angle     :  0.740  12.385   5202  Z= 0.354
  Chirality :  0.040   0.136    616
  Planarity :  0.005   0.039    643
  Dihedral  :  4.509  37.186    520
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 35.64 %
    Favored  : 57.44 %
  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:  1.21 (0.38), residues: 480
  helix:  1.65 (0.26), residues: 376
  sheet:  None (None), residues: 0
  loop : -2.44 (0.51), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 171 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.028   0.002   PHE A  72 
 TYR   0.012   0.001   TYR A 258 
 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
  135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7832 (tm)
REVERT: A   91 LYS cc_start: 0.8812 (mmtt) cc_final: 0.7713 (mtmt)
REVERT: A   97 LEU cc_start: 0.8329 (tt) cc_final: 0.7966 (tp)
REVERT: A  135 THR cc_start: 0.9033 (m) cc_final: 0.8825 (t)
REVERT: A  152 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7752 (tm-30)
REVERT: A  187 LEU cc_start: 0.8253 (tt) cc_final: 0.7959 (pp)
REVERT: A  228 LEU cc_start: 0.8485 (tp) cc_final: 0.8093 (tt)
REVERT: A  269 ILE cc_start: 0.8531 (mt) cc_final: 0.8065 (mm)
REVERT: A  278 ARG cc_start: 0.7264 (tmt170) cc_final: 0.6864 (mtm-85)
REVERT: A  364 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.6977 (t-100)
REVERT: A  466 LYS cc_start: 0.7940 (mttm) cc_final: 0.7540 (mttm)
REVERT: A  484 VAL cc_start: 0.7392 (t) cc_final: 0.7115 (p)
REVERT: A  535 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6633 (m-80)
  outliers start: 27
  outliers final: 22
  residues processed: 125
  average time/residue: 0.1250
  time to fit residues: 20.1402
Evaluate side-chains
  131 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
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  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  162 LEU
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  428 ASN
Chi-restraints excluded: chain A residue  434 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
Chi-restraints excluded: chain A residue  535 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 32 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 256 ASN
A 373 GLN
A 532 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.151491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.131212 restraints weight = 7611.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.134988 restraints weight = 4059.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.137536 restraints weight = 2566.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   3814  Z= 0.251
  Angle     :  0.763  13.238   5202  Z= 0.369
  Chirality :  0.042   0.279    616
  Planarity :  0.005   0.039    643
  Dihedral  :  4.572  38.875    520
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 36.41 %
    Favored  : 57.18 %
  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:  1.14 (0.38), residues: 480
  helix:  1.59 (0.26), residues: 376
  sheet:  None (None), residues: 0
  loop : -2.41 (0.51), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 171 
 HIS   0.005   0.001   HIS A 126 
 PHE   0.027   0.002   PHE A  72 
 TYR   0.008   0.001   TYR A 258 
 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
  135 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7737 (tm)
REVERT: A   91 LYS cc_start: 0.8801 (mmtt) cc_final: 0.7703 (mtmt)
REVERT: A   97 LEU cc_start: 0.8488 (tt) cc_final: 0.8184 (tp)
REVERT: A  152 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7775 (tm-30)
REVERT: A  187 LEU cc_start: 0.8268 (tt) cc_final: 0.7969 (pp)
REVERT: A  228 LEU cc_start: 0.8492 (tp) cc_final: 0.8100 (tt)
REVERT: A  269 ILE cc_start: 0.8648 (mt) cc_final: 0.8276 (mm)
REVERT: A  278 ARG cc_start: 0.7255 (tmt170) cc_final: 0.6869 (mtm-85)
REVERT: A  341 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6956 (p)
REVERT: A  364 TRP cc_start: 0.8691 (OUTLIER) cc_final: 0.7032 (t-100)
REVERT: A  466 LYS cc_start: 0.7939 (mttm) cc_final: 0.7552 (mttm)
REVERT: A  535 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6597 (m-80)
  outliers start: 25
  outliers final: 21
  residues processed: 125
  average time/residue: 0.1180
  time to fit residues: 19.0922
Evaluate side-chains
  129 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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  149 ASP
Chi-restraints excluded: chain A residue  153 VAL
Chi-restraints excluded: chain A residue  162 LEU
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  428 ASN
Chi-restraints excluded: chain A residue  434 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
Chi-restraints excluded: chain A residue  535 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   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

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 = 0.151718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.131409 restraints weight = 7516.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.135164 restraints weight = 4004.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.137781 restraints weight = 2545.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.4531

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= 0.253
  Angle     :  0.793  13.481   5202  Z= 0.389
  Chirality :  0.042   0.263    616
  Planarity :  0.005   0.048    643
  Dihedral  :  4.673  38.747    520
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 36.41 %
    Favored  : 55.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.17 (0.37), residues: 480
  helix:  1.60 (0.26), residues: 376
  sheet:  None (None), residues: 0
  loop : -2.37 (0.50), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 171 
 HIS   0.004   0.001   HIS A 126 
 PHE   0.035   0.002   PHE A  72 
 TYR   0.007   0.001   TYR A 190 
 ARG   0.006   0.001   ARG A 273 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1485.06 seconds
wall clock time: 26 minutes 26.52 seconds (1586.52 seconds total)