Starting phenix.real_space_refine
on Thu Jul 18 19:00:50 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/07_2024/8xv2_38691.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/07_2024/8xv2_38691.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/07_2024/8xv2_38691.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/07_2024/8xv2_38691.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/07_2024/8xv2_38691.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/07_2024/8xv2_38691.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    2112      2.51       5
     N     470      2.21       5
     O     529      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   78": "NH1" <-> "NH2"
    Residue "A PHE  446": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  456": "NH1" <-> "NH2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 3128
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3110
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 14, 'TRANS': 373}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'VIB': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.66, per 1000 atoms: 0.85
  Number of scatterers: 3128
  At special positions: 0
  Unit cell: (69.55, 58.85, 79.18, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      17     16.00
     O     529      8.00
     N     470      7.00
     C    2112      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 1.40
  Conformation dependent library (CDL) restraints added in 513.9 milliseconds
  

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  736

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      84.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 28
    Processing helix  chain 'A' and resid 34 through 40
    Processing helix  chain 'A' and resid 47 through 55
      removed outlier: 3.880A  pdb=" N   ILE A  55 " --> pdb=" O   ILE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 66
      removed outlier: 4.013A  pdb=" N   THR A  60 " --> pdb=" O   PHE A  56 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 76
      removed outlier: 3.532A  pdb=" N   PHE A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL A  72 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR A  76 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 100
    Processing helix  chain 'A' and resid 104 through 126
      removed outlier: 3.540A  pdb=" N   VAL A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   VAL A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ALA A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
    Processing helix  chain 'A' and resid 132 through 134
      No H-bonds generated for 'chain 'A' and resid 132 through 134'
    Processing helix  chain 'A' and resid 135 through 166
      removed outlier: 4.002A  pdb=" N   SER A 140 " --> pdb=" O   TYR A 136 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 188
      removed outlier: 3.644A  pdb=" N   LEU A 172 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 188 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
      removed outlier: 3.587A  pdb=" N   CYS A 272 " --> pdb=" O   ASP A 268 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TYR A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 268 through 273'
    Processing helix  chain 'A' and resid 275 through 307
      removed outlier: 4.500A  pdb=" N   TYR A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   TRP A 281 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER A 282 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLN A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   ILE A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 335
      removed outlier: 3.993A  pdb=" N   GLY A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 366
      removed outlier: 4.167A  pdb=" N   GLU A 346 " --> pdb=" O   ASP A 342 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LEU A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   VAL A 350 " --> pdb=" O   GLU A 346 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 396
      removed outlier: 3.914A  pdb=" N   VAL A 396 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 426
      removed outlier: 3.571A  pdb=" N   ALA A 404 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 458
      removed outlier: 3.621A  pdb=" N   GLN A 438 " --> pdb=" O   PRO A 434 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE A 439 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)

    225 hydrogen bonds defined for protein.
    675 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.84

  Time building geometry restraints manager: 1.27 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: 885
        1.34 -     1.46: 853
        1.46 -     1.58: 1459
        1.58 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 3225
  Sorted by residual:
  bond pdb=" C5  VIB A 501 "
       pdb=" S1  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.721  1.507  0.214 2.00e-02 2.50e+03 1.14e+02
  bond pdb=" C2  VIB A 501 "
       pdb=" S1  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.670  1.541  0.129 2.00e-02 2.50e+03 4.16e+01
  bond pdb=" C2  VIB A 501 "
       pdb=" N3  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.315  1.420 -0.105 2.00e-02 2.50e+03 2.78e+01
  bond pdb=" C4A VIB A 501 "
       pdb=" N4A VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.347  1.449 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C4  VIB A 501 "
       pdb=" C5  VIB A 501 "
    ideal  model  delta    sigma   weight residual
    1.358  1.446 -0.088 2.00e-02 2.50e+03 1.92e+01
  ... (remaining 3220 not shown)

  Histogram of bond angle deviations from ideal:
       99.82 -   106.67: 87
      106.67 -   113.53: 1732
      113.53 -   120.38: 1376
      120.38 -   127.23: 1174
      127.23 -   134.09: 37
  Bond angle restraints: 4406
  Sorted by residual:
  angle pdb=" C2  VIB A 501 "
        pdb=" S1  VIB A 501 "
        pdb=" C5  VIB A 501 "
      ideal   model   delta    sigma   weight residual
      91.25  103.69  -12.44 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" C   VAL A  77 "
        pdb=" N   ARG A  78 "
        pdb=" CA  ARG A  78 "
      ideal   model   delta    sigma   weight residual
     122.46  127.56   -5.10 1.41e+00 5.03e-01 1.31e+01
  angle pdb=" C6A VIB A 501 "
        pdb=" C5A VIB A 501 "
        pdb=" C7A VIB A 501 "
      ideal   model   delta    sigma   weight residual
     121.49  111.43   10.06 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" CA  TRP A 284 "
        pdb=" CB  TRP A 284 "
        pdb=" CG  TRP A 284 "
      ideal   model   delta    sigma   weight residual
     113.60  107.61    5.99 1.90e+00 2.77e-01 9.96e+00
  angle pdb=" N   PHE A  56 "
        pdb=" CA  PHE A  56 "
        pdb=" C   PHE A  56 "
      ideal   model   delta    sigma   weight residual
     113.16  117.60   -4.44 1.42e+00 4.96e-01 9.77e+00
  ... (remaining 4401 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.74: 1716
       14.74 -    29.47: 87
       29.47 -    44.20: 16
       44.20 -    58.94: 0
       58.94 -    73.67: 2
  Dihedral angle restraints: 1821
    sinusoidal: 669
      harmonic: 1152
  Sorted by residual:
  dihedral pdb=" CA  ARG A  78 "
           pdb=" C   ARG A  78 "
           pdb=" N   TYR A  79 "
           pdb=" CA  TYR A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.93   23.07     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  TRP A  12 "
           pdb=" C   TRP A  12 "
           pdb=" N   ILE A  13 "
           pdb=" CA  ILE A  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.74  -20.26     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  VAL A 426 "
           pdb=" C   VAL A 426 "
           pdb=" N   ASP A 427 "
           pdb=" CA  ASP A 427 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.73  -19.27     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 1818 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 285
       0.040 -    0.081: 156
       0.081 -    0.121: 42
       0.121 -    0.161: 12
       0.161 -    0.202: 7
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" CA  PHE A  56 "
            pdb=" N   PHE A  56 "
            pdb=" C   PHE A  56 "
            pdb=" CB  PHE A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  VAL A 435 "
            pdb=" CA  VAL A 435 "
            pdb=" CG1 VAL A 435 "
            pdb=" CG2 VAL A 435 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.56e-01
  chirality pdb=" CA  TRP A  94 "
            pdb=" N   TRP A  94 "
            pdb=" C   TRP A  94 "
            pdb=" CB  TRP A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.39e-01
  ... (remaining 499 not shown)

  Planarity restraints: 528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  63 "    0.020 2.00e-02 2.50e+03   2.31e-02 1.07e+01
        pdb=" CG  TYR A  63 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  63 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  63 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  63 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  63 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A  63 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 373 "    0.025 2.00e-02 2.50e+03   2.04e-02 8.35e+00
        pdb=" CG  TYR A 373 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 373 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 373 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 373 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 373 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 373 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 373 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  61 "    0.013 2.00e-02 2.50e+03   2.54e-02 6.43e+00
        pdb=" C   TYR A  61 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   TYR A  61 "    0.016 2.00e-02 2.50e+03
        pdb=" N   SER A  62 "    0.015 2.00e-02 2.50e+03
  ... (remaining 525 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1027
        2.83 -     3.35: 3005
        3.35 -     3.87: 5221
        3.87 -     4.38: 5967
        4.38 -     4.90: 10133
  Nonbonded interactions: 25353
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 151 "
            pdb=" OE2 GLU A 320 "
     model   vdw
     2.318 2.440
  nonbonded pdb=" O   GLN A 418 "
            pdb=" OG1 THR A 422 "
     model   vdw
     2.371 2.440
  nonbonded pdb=" OE2 GLU A  54 "
            pdb=" NE2 GLN A 428 "
     model   vdw
     2.382 2.520
  nonbonded pdb=" NE2 GLN A 294 "
            pdb=" OG1 THR A 422 "
     model   vdw
     2.386 2.520
  nonbonded pdb=" ND2 ASN A  53 "
            pdb=" O   LEU A 433 "
     model   vdw
     2.414 2.520
  ... (remaining 25348 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:             0.740
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     12.900
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
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      :  0.009   0.214   3225  Z= 0.539
  Angle     :  0.986  12.443   4406  Z= 0.506
  Chirality :  0.056   0.202    502
  Planarity :  0.008   0.053    528
  Dihedral  :  9.841  73.672   1085
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  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: -3.54 (0.33), residues: 384
  helix: -1.92 (0.23), residues: 282
  sheet:  None (None), residues: 0
  loop : -3.09 (0.54), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A 284 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.028   0.003   PHE A 439 
 TYR   0.057   0.004   TYR A  63 
 ARG   0.001   0.000   ARG A  29 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.7993 (m-80) cc_final: 0.7793 (m-10)
REVERT: A   61 TYR cc_start: 0.7845 (m-10) cc_final: 0.7555 (m-80)
REVERT: A   73 LEU cc_start: 0.7463 (tp) cc_final: 0.7263 (tp)
REVERT: A   91 ILE cc_start: 0.8298 (mt) cc_final: 0.8070 (mm)
REVERT: A   98 LEU cc_start: 0.8166 (mt) cc_final: 0.7797 (mm)
REVERT: A  105 THR cc_start: 0.7228 (p) cc_final: 0.6995 (p)
REVERT: A  113 TYR cc_start: 0.7811 (t80) cc_final: 0.7598 (t80)
REVERT: A  159 GLN cc_start: 0.6641 (tm-30) cc_final: 0.6208 (tm-30)
REVERT: A  160 LEU cc_start: 0.7459 (mt) cc_final: 0.7219 (tp)
REVERT: A  161 LEU cc_start: 0.7954 (mt) cc_final: 0.7639 (tp)
REVERT: A  167 MET cc_start: 0.6672 (ttm) cc_final: 0.6041 (ttm)
REVERT: A  175 ILE cc_start: 0.8539 (mt) cc_final: 0.8178 (mp)
REVERT: A  176 SER cc_start: 0.8290 (m) cc_final: 0.7665 (p)
REVERT: A  198 PHE cc_start: 0.8204 (m-80) cc_final: 0.7754 (m-80)
REVERT: A  283 LEU cc_start: 0.7909 (tp) cc_final: 0.7682 (tp)
REVERT: A  300 GLN cc_start: 0.8328 (mt0) cc_final: 0.8091 (mt0)
REVERT: A  325 PHE cc_start: 0.8449 (t80) cc_final: 0.8103 (t80)
REVERT: A  361 PHE cc_start: 0.7886 (m-10) cc_final: 0.7586 (m-80)
REVERT: A  363 MET cc_start: 0.6951 (mtm) cc_final: 0.6643 (mtm)
REVERT: A  384 MET cc_start: 0.7864 (tpp) cc_final: 0.7482 (tpt)
REVERT: A  387 ILE cc_start: 0.8227 (tp) cc_final: 0.7806 (tp)
REVERT: A  403 TYR cc_start: 0.7903 (t80) cc_final: 0.7683 (t80)
REVERT: A  406 VAL cc_start: 0.7813 (t) cc_final: 0.6833 (p)
REVERT: A  410 ASN cc_start: 0.7593 (m-40) cc_final: 0.7231 (m-40)
REVERT: A  418 GLN cc_start: 0.8140 (tt0) cc_final: 0.7904 (tt0)
REVERT: A  425 VAL cc_start: 0.8383 (t) cc_final: 0.8162 (p)
REVERT: A  432 ASN cc_start: 0.7278 (t0) cc_final: 0.7034 (t0)
REVERT: A  438 GLN cc_start: 0.7665 (mt0) cc_final: 0.7374 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0976
  time to fit residues: 15.4183
Evaluate side-chains
  104 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0970
   chunk 22 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 159 GLN
A 200 HIS
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3225  Z= 0.229
  Angle     :  0.619   6.669   4406  Z= 0.328
  Chirality :  0.044   0.147    502
  Planarity :  0.005   0.044    528
  Dihedral  :  6.941  69.159    428
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.21 %
    Favored  : 84.68 %
  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: -0.71 (0.39), residues: 384
  helix:  0.21 (0.28), residues: 288
  sheet:  None (None), residues: 0
  loop : -2.39 (0.59), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 284 
 HIS   0.005   0.002   HIS A 364 
 PHE   0.017   0.002   PHE A 439 
 TYR   0.021   0.002   TYR A 373 
 ARG   0.001   0.000   ARG A 429 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.7958 (m-80) cc_final: 0.7682 (m-10)
REVERT: A   52 THR cc_start: 0.7919 (m) cc_final: 0.7513 (p)
REVERT: A   73 LEU cc_start: 0.7795 (tp) cc_final: 0.7315 (tp)
REVERT: A   86 GLN cc_start: 0.8223 (tt0) cc_final: 0.7878 (tt0)
REVERT: A   89 SER cc_start: 0.8146 (m) cc_final: 0.7876 (p)
REVERT: A  156 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7970 (m)
REVERT: A  161 LEU cc_start: 0.8155 (mt) cc_final: 0.7802 (tp)
REVERT: A  167 MET cc_start: 0.6783 (ttm) cc_final: 0.6110 (ttm)
REVERT: A  283 LEU cc_start: 0.7939 (tp) cc_final: 0.7720 (tp)
REVERT: A  300 GLN cc_start: 0.8322 (mt0) cc_final: 0.8122 (mt0)
REVERT: A  325 PHE cc_start: 0.8462 (t80) cc_final: 0.8252 (t80)
REVERT: A  352 PHE cc_start: 0.7278 (m-80) cc_final: 0.6973 (m-80)
REVERT: A  361 PHE cc_start: 0.7870 (m-10) cc_final: 0.7597 (m-80)
REVERT: A  384 MET cc_start: 0.7861 (tpp) cc_final: 0.7599 (mmm)
REVERT: A  387 ILE cc_start: 0.8103 (tp) cc_final: 0.7823 (tp)
REVERT: A  406 VAL cc_start: 0.7807 (t) cc_final: 0.6840 (p)
REVERT: A  410 ASN cc_start: 0.7664 (m-40) cc_final: 0.7302 (m-40)
REVERT: A  432 ASN cc_start: 0.7493 (t0) cc_final: 0.7271 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 117
  average time/residue: 0.0892
  time to fit residues: 13.6222
Evaluate side-chains
  118 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  449 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 11 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3225  Z= 0.220
  Angle     :  0.591   7.118   4406  Z= 0.311
  Chirality :  0.043   0.133    502
  Planarity :  0.004   0.044    528
  Dihedral  :  6.721  70.244    428
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.22 %
    Favored  : 81.08 %
  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:  0.19 (0.41), residues: 384
  helix:  0.91 (0.29), residues: 298
  sheet:  None (None), residues: 0
  loop : -2.58 (0.62), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 284 
 HIS   0.005   0.001   HIS A 364 
 PHE   0.016   0.002   PHE A  99 
 TYR   0.020   0.002   TYR A  63 
 ARG   0.002   0.000   ARG A  78 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.8073 (m-80) cc_final: 0.7746 (m-10)
REVERT: A   36 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8424 (mm)
REVERT: A   52 THR cc_start: 0.7945 (m) cc_final: 0.7531 (p)
REVERT: A   63 TYR cc_start: 0.8618 (t80) cc_final: 0.8226 (t80)
REVERT: A   73 LEU cc_start: 0.7849 (tp) cc_final: 0.7630 (tp)
REVERT: A   89 SER cc_start: 0.8156 (m) cc_final: 0.7847 (p)
REVERT: A  101 GLN cc_start: 0.6659 (mm-40) cc_final: 0.6428 (mm110)
REVERT: A  152 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8073 (t)
REVERT: A  156 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7941 (m)
REVERT: A  161 LEU cc_start: 0.8206 (mt) cc_final: 0.7748 (tp)
REVERT: A  167 MET cc_start: 0.6854 (ttm) cc_final: 0.6107 (ttm)
REVERT: A  197 MET cc_start: 0.7977 (tpp) cc_final: 0.7750 (tpp)
REVERT: A  283 LEU cc_start: 0.7943 (tp) cc_final: 0.7684 (tp)
REVERT: A  325 PHE cc_start: 0.8438 (t80) cc_final: 0.8125 (t80)
REVERT: A  361 PHE cc_start: 0.7883 (m-10) cc_final: 0.7633 (m-80)
REVERT: A  363 MET cc_start: 0.7208 (mtm) cc_final: 0.6900 (mtm)
REVERT: A  376 TYR cc_start: 0.8636 (t80) cc_final: 0.8165 (t80)
REVERT: A  380 LYS cc_start: 0.8361 (tttt) cc_final: 0.8147 (ttmm)
REVERT: A  384 MET cc_start: 0.7844 (tpp) cc_final: 0.7565 (mmm)
REVERT: A  387 ILE cc_start: 0.8079 (tp) cc_final: 0.7781 (tp)
REVERT: A  406 VAL cc_start: 0.7835 (t) cc_final: 0.6817 (p)
REVERT: A  407 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7280 (m-10)
REVERT: A  410 ASN cc_start: 0.7656 (m-40) cc_final: 0.7226 (m-40)
REVERT: A  432 ASN cc_start: 0.7646 (t0) cc_final: 0.7400 (t0)
  outliers start: 9
  outliers final: 2
  residues processed: 118
  average time/residue: 0.1000
  time to fit residues: 15.2148
Evaluate side-chains
  119 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  407 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0270
   chunk 30 optimal weight:    0.3980
   chunk 20 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
A 300 GLN
A 356 ASN
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3225  Z= 0.230
  Angle     :  0.593   6.331   4406  Z= 0.311
  Chirality :  0.043   0.143    502
  Planarity :  0.004   0.043    528
  Dihedral  :  6.539  71.442    428
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.12 %
    Favored  : 76.58 %
  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:  0.63 (0.42), residues: 384
  helix:  1.15 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.33 (0.63), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.018   0.002   PHE A  99 
 TYR   0.018   0.002   TYR A  63 
 ARG   0.001   0.000   ARG A  78 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   33 PRO cc_start: 0.8408 (Cg_exo) cc_final: 0.8206 (Cg_endo)
REVERT: A   34 PHE cc_start: 0.8090 (m-80) cc_final: 0.7877 (m-10)
REVERT: A   48 SER cc_start: 0.8144 (m) cc_final: 0.7831 (t)
REVERT: A   52 THR cc_start: 0.7882 (m) cc_final: 0.7483 (p)
REVERT: A   59 TRP cc_start: 0.8450 (t60) cc_final: 0.7696 (t60)
REVERT: A   73 LEU cc_start: 0.8024 (tp) cc_final: 0.7789 (tp)
REVERT: A   81 PRO cc_start: 0.8319 (Cg_exo) cc_final: 0.8066 (Cg_endo)
REVERT: A   89 SER cc_start: 0.8097 (m) cc_final: 0.7856 (p)
REVERT: A  152 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8020 (t)
REVERT: A  156 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7940 (m)
REVERT: A  161 LEU cc_start: 0.8225 (mt) cc_final: 0.7755 (tp)
REVERT: A  167 MET cc_start: 0.6846 (ttm) cc_final: 0.6001 (ttm)
REVERT: A  283 LEU cc_start: 0.7917 (tp) cc_final: 0.7696 (tp)
REVERT: A  325 PHE cc_start: 0.8460 (t80) cc_final: 0.8205 (t80)
REVERT: A  361 PHE cc_start: 0.7864 (m-10) cc_final: 0.7648 (m-80)
REVERT: A  363 MET cc_start: 0.7230 (mtm) cc_final: 0.6968 (mtm)
REVERT: A  376 TYR cc_start: 0.8659 (t80) cc_final: 0.8193 (t80)
REVERT: A  384 MET cc_start: 0.7838 (tpp) cc_final: 0.7551 (mmm)
REVERT: A  387 ILE cc_start: 0.8077 (tp) cc_final: 0.7782 (tp)
REVERT: A  406 VAL cc_start: 0.7864 (t) cc_final: 0.6799 (p)
REVERT: A  407 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7558 (m-80)
REVERT: A  410 ASN cc_start: 0.7640 (m-40) cc_final: 0.7239 (m-40)
REVERT: A  419 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7784 (p)
REVERT: A  432 ASN cc_start: 0.7675 (t0) cc_final: 0.7415 (t0)
REVERT: A  438 GLN cc_start: 0.7253 (mt0) cc_final: 0.6769 (mt0)
  outliers start: 11
  outliers final: 5
  residues processed: 118
  average time/residue: 0.1031
  time to fit residues: 15.7947
Evaluate side-chains
  121 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  152 THR
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0770
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3225  Z= 0.218
  Angle     :  0.591   6.646   4406  Z= 0.311
  Chirality :  0.043   0.159    502
  Planarity :  0.004   0.043    528
  Dihedral  :  6.403  69.634    428
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.82 %
    Favored  : 75.98 %
  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:  0.90 (0.42), residues: 384
  helix:  1.38 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -2.37 (0.60), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.020   0.001   PHE A  99 
 TYR   0.015   0.002   TYR A 383 
 ARG   0.001   0.000   ARG A  78 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   42 PRO cc_start: 0.7707 (Cg_endo) cc_final: 0.7406 (Cg_exo)
REVERT: A   52 THR cc_start: 0.7862 (m) cc_final: 0.7442 (p)
REVERT: A   59 TRP cc_start: 0.8427 (t60) cc_final: 0.7729 (t60)
REVERT: A   89 SER cc_start: 0.8156 (m) cc_final: 0.7922 (p)
REVERT: A  101 GLN cc_start: 0.6941 (mm110) cc_final: 0.6700 (mm110)
REVERT: A  283 LEU cc_start: 0.7883 (tp) cc_final: 0.7667 (tp)
REVERT: A  325 PHE cc_start: 0.8468 (t80) cc_final: 0.8222 (t80)
REVERT: A  361 PHE cc_start: 0.7870 (m-10) cc_final: 0.7648 (m-80)
REVERT: A  363 MET cc_start: 0.7279 (mtm) cc_final: 0.6989 (mtm)
REVERT: A  376 TYR cc_start: 0.8618 (t80) cc_final: 0.7951 (t80)
REVERT: A  380 LYS cc_start: 0.8399 (tttm) cc_final: 0.8191 (ttmm)
REVERT: A  384 MET cc_start: 0.7804 (tpp) cc_final: 0.7583 (mmm)
REVERT: A  387 ILE cc_start: 0.8082 (tp) cc_final: 0.7795 (tp)
REVERT: A  406 VAL cc_start: 0.7862 (t) cc_final: 0.6805 (p)
REVERT: A  407 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7595 (m-80)
REVERT: A  410 ASN cc_start: 0.7641 (m-40) cc_final: 0.7229 (m-40)
REVERT: A  419 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7789 (p)
REVERT: A  432 ASN cc_start: 0.7680 (t0) cc_final: 0.7333 (t0)
REVERT: A  433 LEU cc_start: 0.8186 (mt) cc_final: 0.7729 (mt)
REVERT: A  438 GLN cc_start: 0.7117 (mt0) cc_final: 0.6700 (mt0)
  outliers start: 14
  outliers final: 8
  residues processed: 114
  average time/residue: 0.0846
  time to fit residues: 12.5971
Evaluate side-chains
  116 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  320 GLU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 19 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0970
   overall best weight:    0.2978

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3225  Z= 0.175
  Angle     :  0.592   6.215   4406  Z= 0.303
  Chirality :  0.042   0.140    502
  Planarity :  0.003   0.040    528
  Dihedral  :  6.264  67.974    428
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 22.52 %
    Favored  : 74.17 %
  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 (0.42), residues: 384
  helix:  1.62 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -2.31 (0.61), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 284 
 HIS   0.005   0.002   HIS A 364 
 PHE   0.022   0.001   PHE A  99 
 TYR   0.015   0.002   TYR A 383 
 ARG   0.001   0.000   ARG A  29 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7851 (m) cc_final: 0.7475 (p)
REVERT: A   59 TRP cc_start: 0.8387 (t60) cc_final: 0.7622 (t60)
REVERT: A   89 SER cc_start: 0.8152 (m) cc_final: 0.7902 (p)
REVERT: A  161 LEU cc_start: 0.8108 (mt) cc_final: 0.7689 (tp)
REVERT: A  283 LEU cc_start: 0.7872 (tp) cc_final: 0.7669 (tp)
REVERT: A  298 TYR cc_start: 0.8179 (m-80) cc_final: 0.7930 (m-80)
REVERT: A  325 PHE cc_start: 0.8416 (t80) cc_final: 0.8187 (t80)
REVERT: A  361 PHE cc_start: 0.7862 (m-10) cc_final: 0.7631 (m-80)
REVERT: A  363 MET cc_start: 0.7257 (mtm) cc_final: 0.7008 (mtm)
REVERT: A  376 TYR cc_start: 0.8640 (t80) cc_final: 0.8060 (t80)
REVERT: A  387 ILE cc_start: 0.8073 (tp) cc_final: 0.7723 (tp)
REVERT: A  406 VAL cc_start: 0.7843 (t) cc_final: 0.6765 (p)
REVERT: A  407 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7553 (m-80)
REVERT: A  410 ASN cc_start: 0.7544 (m-40) cc_final: 0.7136 (m-40)
REVERT: A  419 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7812 (p)
REVERT: A  432 ASN cc_start: 0.7630 (t0) cc_final: 0.7303 (t0)
REVERT: A  433 LEU cc_start: 0.8173 (mt) cc_final: 0.7759 (mt)
  outliers start: 11
  outliers final: 8
  residues processed: 108
  average time/residue: 0.1068
  time to fit residues: 14.8588
Evaluate side-chains
  115 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    0.0770
   chunk 30 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 173 ASN
A 310 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3225  Z= 0.217
  Angle     :  0.629   6.890   4406  Z= 0.320
  Chirality :  0.043   0.141    502
  Planarity :  0.004   0.041    528
  Dihedral  :  6.274  68.830    428
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.02 %
    Favored  : 72.67 %
  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:  1.22 (0.42), residues: 384
  helix:  1.60 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.25 (0.61), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.027   0.002   PHE A  99 
 TYR   0.013   0.002   TYR A 383 
 ARG   0.001   0.000   ARG A  29 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7875 (m) cc_final: 0.7636 (t)
REVERT: A   59 TRP cc_start: 0.8375 (t60) cc_final: 0.7603 (t60)
REVERT: A   67 LEU cc_start: 0.8465 (tp) cc_final: 0.8195 (tt)
REVERT: A   89 SER cc_start: 0.8165 (m) cc_final: 0.7914 (p)
REVERT: A  161 LEU cc_start: 0.8098 (mt) cc_final: 0.7707 (tp)
REVERT: A  298 TYR cc_start: 0.8183 (m-80) cc_final: 0.7937 (m-80)
REVERT: A  325 PHE cc_start: 0.8402 (t80) cc_final: 0.8185 (t80)
REVERT: A  361 PHE cc_start: 0.7868 (m-10) cc_final: 0.7638 (m-80)
REVERT: A  363 MET cc_start: 0.7293 (mtm) cc_final: 0.7029 (mtm)
REVERT: A  376 TYR cc_start: 0.8405 (t80) cc_final: 0.7750 (t80)
REVERT: A  387 ILE cc_start: 0.8068 (tp) cc_final: 0.7795 (tp)
REVERT: A  406 VAL cc_start: 0.7833 (t) cc_final: 0.6731 (p)
REVERT: A  407 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7465 (m-80)
REVERT: A  410 ASN cc_start: 0.7549 (m-40) cc_final: 0.7148 (m-40)
REVERT: A  419 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7796 (p)
REVERT: A  432 ASN cc_start: 0.7667 (t0) cc_final: 0.7357 (t0)
REVERT: A  433 LEU cc_start: 0.8204 (mt) cc_final: 0.7783 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 110
  average time/residue: 0.1106
  time to fit residues: 15.6093
Evaluate side-chains
  111 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.3721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3225  Z= 0.263
  Angle     :  0.652   6.816   4406  Z= 0.338
  Chirality :  0.045   0.145    502
  Planarity :  0.004   0.043    528
  Dihedral  :  6.290  69.479    428
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 23.42 %
    Favored  : 72.97 %
  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 (0.42), residues: 384
  helix:  1.57 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -2.24 (0.61), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 284 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.024   0.002   PHE A  99 
 TYR   0.015   0.002   TYR A 383 
 ARG   0.001   0.000   ARG A  78 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7883 (m) cc_final: 0.7668 (t)
REVERT: A   67 LEU cc_start: 0.8480 (tp) cc_final: 0.8192 (tt)
REVERT: A   86 GLN cc_start: 0.8298 (tt0) cc_final: 0.7822 (tt0)
REVERT: A   89 SER cc_start: 0.8164 (m) cc_final: 0.7921 (p)
REVERT: A  161 LEU cc_start: 0.8116 (mt) cc_final: 0.7711 (tp)
REVERT: A  298 TYR cc_start: 0.8180 (m-80) cc_final: 0.7978 (m-80)
REVERT: A  314 ILE cc_start: 0.8129 (pt) cc_final: 0.7867 (pt)
REVERT: A  325 PHE cc_start: 0.8389 (t80) cc_final: 0.8185 (t80)
REVERT: A  361 PHE cc_start: 0.7951 (m-10) cc_final: 0.7724 (m-80)
REVERT: A  363 MET cc_start: 0.7314 (mtm) cc_final: 0.7037 (mtm)
REVERT: A  376 TYR cc_start: 0.8431 (t80) cc_final: 0.7906 (t80)
REVERT: A  387 ILE cc_start: 0.8077 (tp) cc_final: 0.7760 (tp)
REVERT: A  406 VAL cc_start: 0.7863 (t) cc_final: 0.6973 (p)
REVERT: A  407 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7344 (m-10)
REVERT: A  410 ASN cc_start: 0.7660 (m-40) cc_final: 0.7319 (m-40)
REVERT: A  419 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7797 (p)
REVERT: A  432 ASN cc_start: 0.7702 (t0) cc_final: 0.7339 (t0)
REVERT: A  433 LEU cc_start: 0.8217 (mt) cc_final: 0.7774 (mt)
  outliers start: 12
  outliers final: 8
  residues processed: 114
  average time/residue: 0.1037
  time to fit residues: 15.3972
Evaluate side-chains
  119 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   3225  Z= 0.246
  Angle     :  0.639   6.988   4406  Z= 0.329
  Chirality :  0.043   0.157    502
  Planarity :  0.004   0.041    528
  Dihedral  :  6.257  68.969    428
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 24.62 %
    Favored  : 71.77 %
  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:  1.37 (0.42), residues: 384
  helix:  1.66 (0.29), residues: 303
  sheet:  None (None), residues: 0
  loop : -2.02 (0.65), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.025   0.001   PHE A  99 
 TYR   0.015   0.002   TYR A 383 
 ARG   0.002   0.000   ARG A  78 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 SER cc_start: 0.8086 (p) cc_final: 0.7758 (t)
REVERT: A   52 THR cc_start: 0.7876 (m) cc_final: 0.7671 (t)
REVERT: A   67 LEU cc_start: 0.8418 (tp) cc_final: 0.8146 (tt)
REVERT: A   86 GLN cc_start: 0.8281 (tt0) cc_final: 0.7899 (tt0)
REVERT: A   89 SER cc_start: 0.8159 (m) cc_final: 0.7936 (p)
REVERT: A  298 TYR cc_start: 0.8185 (m-80) cc_final: 0.7980 (m-80)
REVERT: A  314 ILE cc_start: 0.8121 (pt) cc_final: 0.7853 (pt)
REVERT: A  325 PHE cc_start: 0.8395 (t80) cc_final: 0.8182 (t80)
REVERT: A  361 PHE cc_start: 0.7938 (m-10) cc_final: 0.7706 (m-80)
REVERT: A  363 MET cc_start: 0.7322 (mtm) cc_final: 0.7064 (mtm)
REVERT: A  387 ILE cc_start: 0.8086 (tp) cc_final: 0.7763 (tp)
REVERT: A  406 VAL cc_start: 0.7855 (t) cc_final: 0.6805 (p)
REVERT: A  407 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7260 (m-10)
REVERT: A  410 ASN cc_start: 0.7524 (m-40) cc_final: 0.7161 (m-40)
REVERT: A  419 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7802 (p)
REVERT: A  432 ASN cc_start: 0.7691 (t0) cc_final: 0.7333 (t0)
REVERT: A  433 LEU cc_start: 0.8224 (mt) cc_final: 0.7806 (mt)
  outliers start: 12
  outliers final: 8
  residues processed: 114
  average time/residue: 0.1039
  time to fit residues: 15.4231
Evaluate side-chains
  119 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0870
   chunk 4 optimal weight:    0.0980
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.3758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   3225  Z= 0.218
  Angle     :  0.645   9.927   4406  Z= 0.328
  Chirality :  0.042   0.148    502
  Planarity :  0.004   0.040    528
  Dihedral  :  6.156  67.573    428
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 26.13 %
    Favored  : 71.17 %
  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:  1.54 (0.43), residues: 384
  helix:  1.78 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.96 (0.66), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.033   0.001   PHE A  99 
 TYR   0.015   0.001   TYR A 383 
 ARG   0.001   0.000   ARG A  78 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 PRO cc_start: 0.7736 (Cg_endo) cc_final: 0.7508 (Cg_exo)
REVERT: A   52 THR cc_start: 0.7856 (m) cc_final: 0.7644 (t)
REVERT: A   67 LEU cc_start: 0.8443 (tp) cc_final: 0.8174 (tt)
REVERT: A   89 SER cc_start: 0.8167 (m) cc_final: 0.7915 (p)
REVERT: A  161 LEU cc_start: 0.8040 (mt) cc_final: 0.7709 (tt)
REVERT: A  298 TYR cc_start: 0.8189 (m-80) cc_final: 0.7986 (m-80)
REVERT: A  325 PHE cc_start: 0.8379 (t80) cc_final: 0.8150 (t80)
REVERT: A  361 PHE cc_start: 0.7925 (m-10) cc_final: 0.7712 (m-80)
REVERT: A  363 MET cc_start: 0.7284 (mtm) cc_final: 0.7051 (mtm)
REVERT: A  387 ILE cc_start: 0.8073 (tp) cc_final: 0.7750 (tp)
REVERT: A  406 VAL cc_start: 0.7854 (t) cc_final: 0.6823 (p)
REVERT: A  407 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7302 (m-10)
REVERT: A  410 ASN cc_start: 0.7489 (m-40) cc_final: 0.7120 (m-40)
REVERT: A  419 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7820 (p)
REVERT: A  431 LEU cc_start: 0.7536 (mt) cc_final: 0.7040 (mm)
REVERT: A  432 ASN cc_start: 0.7675 (t0) cc_final: 0.7363 (t0)
REVERT: A  433 LEU cc_start: 0.8210 (mt) cc_final: 0.7824 (mt)
  outliers start: 9
  outliers final: 6
  residues processed: 111
  average time/residue: 0.1004
  time to fit residues: 14.5929
Evaluate side-chains
  116 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    0.0870
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 14 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.100310 restraints weight = 5618.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.103566 restraints weight = 2836.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.105736 restraints weight = 1720.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   3225  Z= 0.256
  Angle     :  0.660   9.644   4406  Z= 0.337
  Chirality :  0.044   0.152    502
  Planarity :  0.004   0.041    528
  Dihedral  :  6.159  68.055    428
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 25.83 %
    Favored  : 71.17 %
  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:  1.45 (0.43), residues: 384
  helix:  1.70 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.87 (0.67), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.029   0.002   PHE A  99 
 TYR   0.014   0.002   TYR A 383 
 ARG   0.001   0.000   ARG A 138 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1104.43 seconds
wall clock time: 22 minutes 58.66 seconds (1378.66 seconds total)