Starting phenix.real_space_refine
on Mon Jun 24 14:46:46 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/06_2024/8xv2_38691_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/06_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_38691/06_2024/8xv2_38691.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/06_2024/8xv2_38691.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/06_2024/8xv2_38691_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv2_38691/06_2024/8xv2_38691_updated.pdb"
  }
  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-5370/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: 2.76, per 1000 atoms: 0.88
  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: 1.15
  Conformation dependent library (CDL) restraints added in 705.4 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...
  running ksdssp...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      77.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 27
    Processing helix  chain 'A' and resid 35 through 39
    Processing helix  chain 'A' and resid 48 through 54
    Processing helix  chain 'A' and resid 56 through 75
      removed outlier: 4.467A  pdb=" N   VAL A  65 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   LEU A  66 " --> pdb=" O   TYR A  63 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   LEU A  68 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
      removed outlier: 4.281A  pdb=" N   ASP A  75 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 99
    Processing helix  chain 'A' and resid 105 through 125
      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 127 through 130
      No H-bonds generated for 'chain 'A' and resid 127 through 130'
    Processing helix  chain 'A' and resid 133 through 165
      removed outlier: 3.698A  pdb=" N   TYR A 136 " --> pdb=" O   PRO A 133 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   GLN A 137 " --> pdb=" O   GLU A 134 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A 138 " --> pdb=" O   HIS A 135 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   VAL A 139 " --> pdb=" O   TYR A 136 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER A 140 " --> pdb=" O   GLN A 137 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY A 141 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG A 144 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   THR A 152 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 157 " --> pdb=" O   GLY A 154 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A 160 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER A 163 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 164 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA A 165 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 187
    Processing helix  chain 'A' and resid 267 through 272
      removed outlier: 3.951A  pdb=" N   LYS A 270 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 306
      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 316 through 336
      removed outlier: 3.993A  pdb=" N   GLY A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TYR A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 365
      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 369 through 395
    Processing helix  chain 'A' and resid 401 through 425
      removed outlier: 3.829A  pdb=" N   LEU A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 457
      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)

    201 hydrogen bonds defined for protein.
    519 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: 0.79

  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: 1031
        2.83 -     3.35: 3029
        3.35 -     3.87: 5223
        3.87 -     4.38: 6020
        4.38 -     4.90: 10146
  Nonbonded interactions: 25449
  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 25444 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:             0.700
  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:             0.000
  Extract box with map and model:          3.440
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.250
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.390
-------------------------------------------------------------------------------
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= 0.588
  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  : 0.340 
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: 0.1023
  time to fit residues: 16.1038
Evaluate side-chains
  104 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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:    0.0170
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 9 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.3418

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 135 HIS
A 159 GLN
A 173 ASN
A 200 HIS
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3225  Z= 0.183
  Angle     :  0.589   7.535   4406  Z= 0.308
  Chirality :  0.042   0.157    502
  Planarity :  0.005   0.036    528
  Dihedral  :  7.003  68.059    428
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.91 %
    Favored  : 85.89 %
  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: -1.03 (0.39), residues: 384
  helix:  0.02 (0.28), residues: 276
  sheet:  None (None), residues: 0
  loop : -2.39 (0.56), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 284 
 HIS   0.005   0.002   HIS A 364 
 PHE   0.016   0.002   PHE A 439 
 TYR   0.023   0.002   TYR A  63 
 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
  115 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.7972 (m-80) cc_final: 0.7763 (m-10)
REVERT: A   36 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8474 (mm)
REVERT: A   52 THR cc_start: 0.7745 (m) cc_final: 0.7401 (p)
REVERT: A   89 SER cc_start: 0.8107 (m) cc_final: 0.7823 (p)
REVERT: A  115 MET cc_start: 0.7301 (ttp) cc_final: 0.7099 (tpp)
REVERT: A  145 SER cc_start: 0.7934 (m) cc_final: 0.7647 (p)
REVERT: A  159 GLN cc_start: 0.6931 (tm130) cc_final: 0.6624 (tm130)
REVERT: A  175 ILE cc_start: 0.8464 (mt) cc_final: 0.8141 (mp)
REVERT: A  283 LEU cc_start: 0.7926 (tp) cc_final: 0.7705 (tp)
REVERT: A  325 PHE cc_start: 0.8479 (t80) cc_final: 0.8231 (t80)
REVERT: A  361 PHE cc_start: 0.7869 (m-10) cc_final: 0.7555 (m-80)
REVERT: A  363 MET cc_start: 0.7028 (mtm) cc_final: 0.6745 (mtm)
REVERT: A  384 MET cc_start: 0.7800 (tpp) cc_final: 0.7594 (mmm)
REVERT: A  387 ILE cc_start: 0.8104 (tp) cc_final: 0.7767 (tp)
REVERT: A  406 VAL cc_start: 0.7846 (t) cc_final: 0.6889 (p)
REVERT: A  410 ASN cc_start: 0.7572 (m-40) cc_final: 0.7200 (m-40)
REVERT: A  432 ASN cc_start: 0.7440 (t0) cc_final: 0.7208 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 113
  average time/residue: 0.1015
  time to fit residues: 14.9138
Evaluate side-chains
  106 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  449 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 GLN
A 418 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3225  Z= 0.287
  Angle     :  0.623   9.114   4406  Z= 0.327
  Chirality :  0.045   0.166    502
  Planarity :  0.004   0.032    528
  Dihedral  :  6.788  71.927    428
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.22 %
    Favored  : 80.18 %
  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: -0.33 (0.42), residues: 384
  helix:  0.38 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -1.93 (0.67), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 284 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.015   0.002   PHE A  99 
 TYR   0.023   0.002   TYR A  63 
 ARG   0.001   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
  123 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.7992 (m-80) cc_final: 0.7754 (m-10)
REVERT: A   52 THR cc_start: 0.8002 (m) cc_final: 0.7601 (p)
REVERT: A   73 LEU cc_start: 0.7744 (tp) cc_final: 0.7510 (tp)
REVERT: A   89 SER cc_start: 0.8142 (m) cc_final: 0.7788 (t)
REVERT: A  142 TYR cc_start: 0.7597 (m-10) cc_final: 0.7260 (m-10)
REVERT: A  145 SER cc_start: 0.8066 (m) cc_final: 0.7864 (p)
REVERT: A  159 GLN cc_start: 0.6888 (tm130) cc_final: 0.6548 (tm130)
REVERT: A  175 ILE cc_start: 0.8465 (mt) cc_final: 0.8091 (mp)
REVERT: A  197 MET cc_start: 0.8032 (tpp) cc_final: 0.7823 (tpp)
REVERT: A  283 LEU cc_start: 0.7880 (tp) cc_final: 0.7638 (tp)
REVERT: A  325 PHE cc_start: 0.8378 (t80) cc_final: 0.8083 (t80)
REVERT: A  361 PHE cc_start: 0.8064 (m-10) cc_final: 0.7738 (m-80)
REVERT: A  363 MET cc_start: 0.7118 (mtm) cc_final: 0.6791 (mtm)
REVERT: A  384 MET cc_start: 0.7834 (tpp) cc_final: 0.7531 (mmm)
REVERT: A  385 LEU cc_start: 0.7915 (tt) cc_final: 0.7710 (tp)
REVERT: A  387 ILE cc_start: 0.8065 (tp) cc_final: 0.7764 (tp)
REVERT: A  403 TYR cc_start: 0.7862 (t80) cc_final: 0.7656 (t80)
REVERT: A  406 VAL cc_start: 0.7855 (t) cc_final: 0.6847 (p)
REVERT: A  407 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7488 (m-80)
REVERT: A  410 ASN cc_start: 0.7645 (m-40) cc_final: 0.7242 (m-40)
REVERT: A  432 ASN cc_start: 0.7654 (t0) cc_final: 0.7443 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 115
  average time/residue: 0.1034
  time to fit residues: 15.3658
Evaluate side-chains
  121 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  458 MET
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:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 36 optimal weight:    0.4980
   chunk 18 optimal weight:    0.1980
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
A 356 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3225  Z= 0.220
  Angle     :  0.579   6.587   4406  Z= 0.300
  Chirality :  0.042   0.137    502
  Planarity :  0.004   0.029    528
  Dihedral  :  6.566  70.412    428
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.22 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.43), residues: 384
  helix:  0.70 (0.30), residues: 293
  sheet:  None (None), residues: 0
  loop : -1.54 (0.68), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 284 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.018   0.002   PHE A  99 
 TYR   0.016   0.002   TYR A  63 
 ARG   0.000   0.000   ARG A 138 

*********************** 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
  123 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.7969 (m-80) cc_final: 0.7716 (m-10)
REVERT: A   52 THR cc_start: 0.7890 (m) cc_final: 0.7493 (p)
REVERT: A   67 LEU cc_start: 0.8528 (tp) cc_final: 0.8270 (tt)
REVERT: A   89 SER cc_start: 0.8156 (m) cc_final: 0.7880 (p)
REVERT: A  142 TYR cc_start: 0.7664 (m-10) cc_final: 0.7346 (m-10)
REVERT: A  145 SER cc_start: 0.8031 (m) cc_final: 0.7787 (p)
REVERT: A  159 GLN cc_start: 0.6787 (tm-30) cc_final: 0.6316 (tm-30)
REVERT: A  197 MET cc_start: 0.7957 (tpp) cc_final: 0.7667 (tpp)
REVERT: A  198 PHE cc_start: 0.8288 (m-80) cc_final: 0.7743 (m-80)
REVERT: A  283 LEU cc_start: 0.7908 (tp) cc_final: 0.7689 (tp)
REVERT: A  320 GLU cc_start: 0.7139 (tp30) cc_final: 0.6726 (tp30)
REVERT: A  325 PHE cc_start: 0.8398 (t80) cc_final: 0.8119 (t80)
REVERT: A  361 PHE cc_start: 0.8099 (m-10) cc_final: 0.7776 (m-80)
REVERT: A  363 MET cc_start: 0.7119 (mtm) cc_final: 0.6812 (mtm)
REVERT: A  380 LYS cc_start: 0.8374 (tttt) cc_final: 0.8125 (ttmm)
REVERT: A  384 MET cc_start: 0.7808 (tpp) cc_final: 0.7509 (mmm)
REVERT: A  387 ILE cc_start: 0.8054 (tp) cc_final: 0.7690 (tp)
REVERT: A  406 VAL cc_start: 0.7930 (t) cc_final: 0.6846 (p)
REVERT: A  407 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7458 (m-80)
REVERT: A  410 ASN cc_start: 0.7618 (m-40) cc_final: 0.7195 (m-40)
REVERT: A  432 ASN cc_start: 0.7684 (t0) cc_final: 0.7417 (t0)
REVERT: A  438 GLN cc_start: 0.7330 (mt0) cc_final: 0.6797 (mt0)
REVERT: A  442 TYR cc_start: 0.7842 (m-80) cc_final: 0.7458 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 118
  average time/residue: 0.1086
  time to fit residues: 16.5738
Evaluate side-chains
  117 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  458 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 32 optimal weight:    0.0970
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0010
   chunk 33 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.2984

-------------------------------------------------------------------------------
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: 0.7251
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3225  Z= 0.174
  Angle     :  0.570  10.510   4406  Z= 0.290
  Chirality :  0.041   0.141    502
  Planarity :  0.003   0.021    528
  Dihedral  :  6.289  66.582    428
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 21.92 %
    Favored  : 76.28 %
  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 (0.43), residues: 384
  helix:  1.04 (0.30), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.46 (0.67), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 284 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.020   0.001   PHE A  99 
 TYR   0.016   0.001   TYR A 383 
 ARG   0.000   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
  114 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   52 THR cc_start: 0.7863 (m) cc_final: 0.7509 (p)
REVERT: A   67 LEU cc_start: 0.8504 (tp) cc_final: 0.8199 (tt)
REVERT: A   89 SER cc_start: 0.8105 (m) cc_final: 0.7855 (p)
REVERT: A  142 TYR cc_start: 0.7613 (m-10) cc_final: 0.7272 (m-10)
REVERT: A  145 SER cc_start: 0.8012 (m) cc_final: 0.7754 (p)
REVERT: A  198 PHE cc_start: 0.8254 (m-80) cc_final: 0.7708 (m-80)
REVERT: A  283 LEU cc_start: 0.7894 (tp) cc_final: 0.7691 (tp)
REVERT: A  320 GLU cc_start: 0.7125 (tp30) cc_final: 0.6742 (tp30)
REVERT: A  325 PHE cc_start: 0.8352 (t80) cc_final: 0.8105 (t80)
REVERT: A  363 MET cc_start: 0.7101 (mtm) cc_final: 0.6836 (mtm)
REVERT: A  380 LYS cc_start: 0.8379 (tttt) cc_final: 0.8157 (ttmm)
REVERT: A  387 ILE cc_start: 0.8020 (tp) cc_final: 0.7681 (tp)
REVERT: A  406 VAL cc_start: 0.7859 (t) cc_final: 0.6818 (p)
REVERT: A  407 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7456 (m-80)
REVERT: A  410 ASN cc_start: 0.7575 (m-40) cc_final: 0.7160 (m-40)
REVERT: A  431 LEU cc_start: 0.7475 (mt) cc_final: 0.7048 (mm)
REVERT: A  432 ASN cc_start: 0.7631 (t0) cc_final: 0.7325 (t0)
REVERT: A  433 LEU cc_start: 0.8195 (mt) cc_final: 0.7668 (mt)
REVERT: A  438 GLN cc_start: 0.7094 (mt0) cc_final: 0.6631 (mt0)
  outliers start: 6
  outliers final: 3
  residues processed: 109
  average time/residue: 0.1056
  time to fit residues: 14.7949
Evaluate side-chains
  112 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
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:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0040
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3225  Z= 0.258
  Angle     :  0.613   9.846   4406  Z= 0.316
  Chirality :  0.043   0.143    502
  Planarity :  0.004   0.022    528
  Dihedral  :  6.283  66.727    428
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.12 %
    Favored  : 75.08 %
  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:  0.60 (0.43), residues: 384
  helix:  1.05 (0.30), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.55 (0.67), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 284 
 HIS   0.001   0.001   HIS A 200 
 PHE   0.021   0.002   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
  122 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A   42 PRO cc_start: 0.7732 (Cg_endo) cc_final: 0.7501 (Cg_exo)
REVERT: A   52 THR cc_start: 0.7896 (m) cc_final: 0.7480 (p)
REVERT: A   67 LEU cc_start: 0.8451 (tp) cc_final: 0.8129 (tt)
REVERT: A   89 SER cc_start: 0.8163 (m) cc_final: 0.7905 (p)
REVERT: A  142 TYR cc_start: 0.7664 (m-10) cc_final: 0.7352 (m-10)
REVERT: A  145 SER cc_start: 0.8065 (m) cc_final: 0.7848 (p)
REVERT: A  198 PHE cc_start: 0.8282 (m-80) cc_final: 0.7801 (m-80)
REVERT: A  283 LEU cc_start: 0.7892 (tp) cc_final: 0.7678 (tp)
REVERT: A  320 GLU cc_start: 0.7173 (tp30) cc_final: 0.6785 (tp30)
REVERT: A  325 PHE cc_start: 0.8377 (t80) cc_final: 0.8155 (t80)
REVERT: A  361 PHE cc_start: 0.8146 (m-80) cc_final: 0.7786 (m-80)
REVERT: A  363 MET cc_start: 0.7174 (mtm) cc_final: 0.6898 (mtm)
REVERT: A  380 LYS cc_start: 0.8430 (tttt) cc_final: 0.8188 (ttmm)
REVERT: A  387 ILE cc_start: 0.8009 (tp) cc_final: 0.7692 (tp)
REVERT: A  406 VAL cc_start: 0.7923 (t) cc_final: 0.7049 (p)
REVERT: A  407 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7517 (m-80)
REVERT: A  410 ASN cc_start: 0.7723 (m-40) cc_final: 0.7353 (m-40)
REVERT: A  432 ASN cc_start: 0.7694 (t0) cc_final: 0.7446 (t0)
REVERT: A  438 GLN cc_start: 0.7335 (mt0) cc_final: 0.6887 (mt0)
  outliers start: 6
  outliers final: 2
  residues processed: 117
  average time/residue: 0.1074
  time to fit residues: 16.1682
Evaluate side-chains
  120 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 117
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
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:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0070
   chunk 22 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0980
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.2980
   overall best weight:    0.3198

-------------------------------------------------------------------------------
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: 0.7264
moved from start:          0.3571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3225  Z= 0.180
  Angle     :  0.592  10.058   4406  Z= 0.295
  Chirality :  0.041   0.142    502
  Planarity :  0.004   0.021    528
  Dihedral  :  6.080  63.785    428
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.72 %
    Favored  : 74.47 %
  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:  0.93 (0.44), residues: 384
  helix:  1.27 (0.30), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.35 (0.68), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 284 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.024   0.001   PHE A  99 
 TYR   0.015   0.001   TYR A 383 
 ARG   0.001   0.000   ARG A  78 

*********************** 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
  122 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   52 THR cc_start: 0.7874 (m) cc_final: 0.7486 (p)
REVERT: A   67 LEU cc_start: 0.8442 (tp) cc_final: 0.8129 (tt)
REVERT: A   89 SER cc_start: 0.8122 (m) cc_final: 0.7898 (p)
REVERT: A  142 TYR cc_start: 0.7662 (m-10) cc_final: 0.7286 (m-10)
REVERT: A  145 SER cc_start: 0.8024 (m) cc_final: 0.7777 (p)
REVERT: A  198 PHE cc_start: 0.8232 (m-80) cc_final: 0.7765 (m-80)
REVERT: A  320 GLU cc_start: 0.7193 (tp30) cc_final: 0.6917 (tp30)
REVERT: A  325 PHE cc_start: 0.8341 (t80) cc_final: 0.8123 (t80)
REVERT: A  361 PHE cc_start: 0.8124 (m-80) cc_final: 0.7873 (m-80)
REVERT: A  363 MET cc_start: 0.7125 (mtm) cc_final: 0.6863 (mtm)
REVERT: A  380 LYS cc_start: 0.8408 (tttt) cc_final: 0.8192 (ttmm)
REVERT: A  387 ILE cc_start: 0.8057 (tp) cc_final: 0.7697 (tp)
REVERT: A  406 VAL cc_start: 0.7910 (t) cc_final: 0.6879 (p)
REVERT: A  407 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7483 (m-80)
REVERT: A  410 ASN cc_start: 0.7577 (m-40) cc_final: 0.7161 (m-40)
REVERT: A  432 ASN cc_start: 0.7637 (t0) cc_final: 0.7354 (t0)
REVERT: A  433 LEU cc_start: 0.8196 (mt) cc_final: 0.7754 (mt)
REVERT: A  438 GLN cc_start: 0.7092 (mt0) cc_final: 0.6692 (mt0)
  outliers start: 6
  outliers final: 5
  residues processed: 118
  average time/residue: 0.1008
  time to fit residues: 15.4334
Evaluate side-chains
  121 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  407 PHE
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:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.1980
   chunk 26 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   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 173 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   3225  Z= 0.294
  Angle     :  0.620   9.029   4406  Z= 0.321
  Chirality :  0.044   0.153    502
  Planarity :  0.004   0.022    528
  Dihedral  :  6.185  65.333    428
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 25.23 %
    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:  0.65 (0.43), residues: 384
  helix:  1.04 (0.30), residues: 290
  sheet:  None (None), residues: 0
  loop : -1.36 (0.69), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 284 
 HIS   0.001   0.001   HIS A 200 
 PHE   0.025   0.002   PHE A  99 
 TYR   0.014   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
  126 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A   52 THR cc_start: 0.7855 (m) cc_final: 0.7443 (p)
REVERT: A   67 LEU cc_start: 0.8433 (tp) cc_final: 0.8121 (tt)
REVERT: A   89 SER cc_start: 0.8156 (m) cc_final: 0.7886 (p)
REVERT: A  142 TYR cc_start: 0.7686 (m-10) cc_final: 0.7369 (m-10)
REVERT: A  320 GLU cc_start: 0.7224 (tp30) cc_final: 0.6948 (tp30)
REVERT: A  325 PHE cc_start: 0.8378 (t80) cc_final: 0.8171 (t80)
REVERT: A  361 PHE cc_start: 0.8177 (m-80) cc_final: 0.7683 (m-80)
REVERT: A  363 MET cc_start: 0.7179 (mtm) cc_final: 0.6897 (mtm)
REVERT: A  380 LYS cc_start: 0.8446 (tttt) cc_final: 0.8195 (ttmm)
REVERT: A  387 ILE cc_start: 0.8003 (tp) cc_final: 0.7685 (tp)
REVERT: A  406 VAL cc_start: 0.7946 (t) cc_final: 0.7135 (p)
REVERT: A  407 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7500 (m-80)
REVERT: A  410 ASN cc_start: 0.7689 (m-40) cc_final: 0.7339 (m-40)
REVERT: A  432 ASN cc_start: 0.7716 (t0) cc_final: 0.7457 (t0)
REVERT: A  438 GLN cc_start: 0.7362 (mt0) cc_final: 0.6935 (mt0)
REVERT: A  439 PHE cc_start: 0.8381 (m-80) cc_final: 0.8033 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 121
  average time/residue: 0.1050
  time to fit residues: 16.3973
Evaluate side-chains
  119 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
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:    0.2980
   chunk 32 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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: 0.7281
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3225  Z= 0.237
  Angle     :  0.602   6.894   4406  Z= 0.312
  Chirality :  0.042   0.141    502
  Planarity :  0.004   0.028    528
  Dihedral  :  6.130  62.895    428
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 27.33 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.43), residues: 384
  helix:  1.12 (0.30), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.18 (0.71), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 284 
 HIS   0.001   0.000   HIS A 364 
 PHE   0.029   0.002   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
  123 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   52 THR cc_start: 0.7851 (m) cc_final: 0.7452 (p)
REVERT: A   67 LEU cc_start: 0.8444 (tp) cc_final: 0.8136 (tt)
REVERT: A   89 SER cc_start: 0.8112 (m) cc_final: 0.7889 (p)
REVERT: A  320 GLU cc_start: 0.7210 (tp30) cc_final: 0.6956 (tp30)
REVERT: A  325 PHE cc_start: 0.8361 (t80) cc_final: 0.8136 (t80)
REVERT: A  361 PHE cc_start: 0.8161 (m-80) cc_final: 0.7913 (m-80)
REVERT: A  363 MET cc_start: 0.7156 (mtm) cc_final: 0.6895 (mtm)
REVERT: A  380 LYS cc_start: 0.8423 (tttt) cc_final: 0.8179 (ttmm)
REVERT: A  387 ILE cc_start: 0.7991 (tp) cc_final: 0.7678 (tp)
REVERT: A  406 VAL cc_start: 0.7900 (t) cc_final: 0.7024 (p)
REVERT: A  407 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7505 (m-80)
REVERT: A  410 ASN cc_start: 0.7563 (m-40) cc_final: 0.7217 (m-40)
REVERT: A  438 GLN cc_start: 0.7139 (mt0) cc_final: 0.6743 (mt0)
REVERT: A  439 PHE cc_start: 0.8330 (m-80) cc_final: 0.7976 (m-80)
  outliers start: 6
  outliers final: 3
  residues processed: 118
  average time/residue: 0.0985
  time to fit residues: 15.1336
Evaluate side-chains
  120 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
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:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0970
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 3 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.3556

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3225  Z= 0.214
  Angle     :  0.599   7.702   4406  Z= 0.312
  Chirality :  0.041   0.140    502
  Planarity :  0.004   0.025    528
  Dihedral  :  6.041  60.958    428
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 27.33 %
    Favored  : 71.47 %
  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 (0.44), residues: 384
  helix:  1.18 (0.30), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.15 (0.71), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 284 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.031   0.002   PHE A  99 
 TYR   0.015   0.001   TYR A 383 
 ARG   0.002   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
  119 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   52 THR cc_start: 0.7913 (m) cc_final: 0.7536 (p)
REVERT: A   67 LEU cc_start: 0.8439 (tp) cc_final: 0.8134 (tt)
REVERT: A   89 SER cc_start: 0.8098 (m) cc_final: 0.7873 (p)
REVERT: A  198 PHE cc_start: 0.8221 (m-80) cc_final: 0.7826 (m-80)
REVERT: A  320 GLU cc_start: 0.7215 (tp30) cc_final: 0.6946 (tp30)
REVERT: A  361 PHE cc_start: 0.8138 (m-80) cc_final: 0.7901 (m-80)
REVERT: A  363 MET cc_start: 0.7138 (mtm) cc_final: 0.6895 (mtm)
REVERT: A  380 LYS cc_start: 0.8421 (tttt) cc_final: 0.8188 (ttmm)
REVERT: A  387 ILE cc_start: 0.7983 (tp) cc_final: 0.7654 (tp)
REVERT: A  406 VAL cc_start: 0.7886 (t) cc_final: 0.6873 (p)
REVERT: A  407 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7492 (m-80)
REVERT: A  410 ASN cc_start: 0.7506 (m-40) cc_final: 0.7120 (m-40)
REVERT: A  438 GLN cc_start: 0.7087 (mt0) cc_final: 0.6687 (mt0)
REVERT: A  439 PHE cc_start: 0.8327 (m-80) cc_final: 0.7987 (m-80)
  outliers start: 4
  outliers final: 3
  residues processed: 116
  average time/residue: 0.1059
  time to fit residues: 15.8585
Evaluate side-chains
  118 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  407 PHE
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:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0770
   chunk 23 optimal weight:    0.0000
   chunk 14 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.3742

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.114473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.100013 restraints weight = 5565.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.103238 restraints weight = 2778.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.105461 restraints weight = 1667.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3225  Z= 0.219
  Angle     :  0.599   6.372   4406  Z= 0.318
  Chirality :  0.042   0.138    502
  Planarity :  0.004   0.027    528
  Dihedral  :  5.931  60.375    428
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 27.03 %
    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:  1.01 (0.44), residues: 384
  helix:  1.25 (0.30), residues: 292
  sheet:  None (None), residues: 0
  loop : -1.12 (0.74), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 284 
 HIS   0.002   0.000   HIS A 364 
 PHE   0.030   0.002   PHE A  99 
 TYR   0.015   0.001   TYR A 383 
 ARG   0.002   0.000   ARG A  78 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1171.15 seconds
wall clock time: 21 minutes 36.93 seconds (1296.93 seconds total)