Starting phenix.real_space_refine
on Wed May 14 06:57:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uq6_42462/05_2025/8uq6_42462.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uq6_42462/05_2025/8uq6_42462.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uq6_42462/05_2025/8uq6_42462.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uq6_42462/05_2025/8uq6_42462.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uq6_42462/05_2025/8uq6_42462.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uq6_42462/05_2025/8uq6_42462.cif"
  }
  resolution = 3.6
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    3734      2.51       5
     N    1073      2.21       5
     O    1147      1.98       5
     H    5689      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11700
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 765, 11700
          Classifications: {'peptide': 765}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 6, 'PTRANS': 58, 'TRANS': 700}
          Chain breaks: 1
  Time building chain proxies: 7.48, per 1000 atoms: 0.64
  Number of scatterers: 11700
  At special positions: 0
  Unit cell: (80.311, 97.02, 111.034, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     O    1147      8.00
     N    1073      7.00
     C    3734      6.00
     H    5689      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.32
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      6.7% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 67 through 70
      removed outlier: 3.787A  pdb=" N   GLU A  70 " --> pdb=" O   HIS A  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 67 through 70'
    Processing helix  chain 'A' and resid 96 through 101
    Processing helix  chain 'A' and resid 224 through 228
      removed outlier: 3.778A  pdb=" N   LYS A 227 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.648A  pdb=" N   THR A 303 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 412 through 416
    Processing helix  chain 'A' and resid 517 through 521
    Processing helix  chain 'A' and resid 796 through 798
      No H-bonds generated for 'chain 'A' and resid 796 through 798'
    Processing helix  chain 'A' and resid 799 through 804
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42
    Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 245
    Processing sheet with id=AA4, first strand: chain 'A' and resid 438 through 441
      removed outlier: 5.538A  pdb=" N   THR A 439 " --> pdb=" O   TRP A 446 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   TRP A 446 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP A 441 " --> pdb=" O   VAL A 444 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 495 through 496
    Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 543
    Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619
    Processing sheet with id=AA8, first strand: chain 'A' and resid 698 through 703
    Processing sheet with id=AA9, first strand: chain 'A' and resid 763 through 766
      removed outlier: 5.655A  pdb=" N   LEU A 764 " --> pdb=" O   GLN A 775 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLN A 775 " --> pdb=" O   LEU A 764 " (cutoff:3.500A)

    51 hydrogen bonds defined for protein.
    90 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: 6.20

  Time building geometry restraints manager: 3.96 seconds

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

  Histogram of bond lengths:
        0.95 -     1.13: 5682
        1.13 -     1.30: 1093
        1.30 -     1.48: 2438
        1.48 -     1.66: 2593
        1.66 -     1.84: 67
  Bond restraints: 11873
  Sorted by residual:
  bond pdb=" CE3 TRP A 299 "
       pdb=" HE3 TRP A 299 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   SER A 292 "
       pdb=" H   SER A 292 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CH2 TRP A 244 "
       pdb=" HH2 TRP A 244 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CE2 PHE A 658 "
       pdb=" HE2 PHE A 658 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   TYR A 633 "
       pdb=" H   TYR A 633 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 11868 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.37: 21159
        7.37 -    14.74: 257
       14.74 -    22.10: 1
       22.10 -    29.47: 4
       29.47 -    36.84: 5
  Bond angle restraints: 21426
  Sorted by residual:
  angle pdb=" C   ARG A 386 "
        pdb=" CA  ARG A 386 "
        pdb=" HA  ARG A 386 "
      ideal   model   delta    sigma   weight residual
     109.00   72.16   36.84 3.00e+00 1.11e-01 1.51e+02
  angle pdb=" N   TYR A 385 "
        pdb=" CA  TYR A 385 "
        pdb=" HA  TYR A 385 "
      ideal   model   delta    sigma   weight residual
     110.00   73.80   36.20 3.00e+00 1.11e-01 1.46e+02
  angle pdb=" N   ASN A 450 "
        pdb=" CA  ASN A 450 "
        pdb=" HA  ASN A 450 "
      ideal   model   delta    sigma   weight residual
     110.00   74.61   35.39 3.00e+00 1.11e-01 1.39e+02
  angle pdb=" C   TYR A 385 "
        pdb=" CA  TYR A 385 "
        pdb=" HA  TYR A 385 "
      ideal   model   delta    sigma   weight residual
     109.00   75.27   33.73 3.00e+00 1.11e-01 1.26e+02
  angle pdb=" C   ASN A 450 "
        pdb=" CA  ASN A 450 "
        pdb=" HA  ASN A 450 "
      ideal   model   delta    sigma   weight residual
     109.00   77.16   31.84 3.00e+00 1.11e-01 1.13e+02
  ... (remaining 21421 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 4828
       16.45 -    32.89: 580
       32.89 -    49.34: 167
       49.34 -    65.79: 104
       65.79 -    82.23: 15
  Dihedral angle restraints: 5694
    sinusoidal: 3086
      harmonic: 2608
  Sorted by residual:
  dihedral pdb=" C   ARG A 386 "
           pdb=" N   ARG A 386 "
           pdb=" CA  ARG A 386 "
           pdb=" CB  ARG A 386 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.39   16.79     0      2.50e+00 1.60e-01 4.51e+01
  dihedral pdb=" C   TYR A 385 "
           pdb=" N   TYR A 385 "
           pdb=" CA  TYR A 385 "
           pdb=" CB  TYR A 385 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.69   15.09     0      2.50e+00 1.60e-01 3.64e+01
  dihedral pdb=" CA  GLN A 297 "
           pdb=" C   GLN A 297 "
           pdb=" N   HIS A 298 "
           pdb=" CA  HIS A 298 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.45   29.55     0      5.00e+00 4.00e-02 3.49e+01
  ... (remaining 5691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.137: 641
       0.137 -    0.274: 194
       0.274 -    0.410: 26
       0.410 -    0.547: 3
       0.547 -    0.684: 4
  Chirality restraints: 868
  Sorted by residual:
  chirality pdb=" CA  ARG A 386 "
            pdb=" N   ARG A 386 "
            pdb=" C   ARG A 386 "
            pdb=" CB  ARG A 386 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.83    0.68 2.00e-01 2.50e+01 1.17e+01
  chirality pdb=" CA  TYR A 385 "
            pdb=" N   TYR A 385 "
            pdb=" C   TYR A 385 "
            pdb=" CB  TYR A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.85    0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" CA  ASN A 450 "
            pdb=" N   ASN A 450 "
            pdb=" C   ASN A 450 "
            pdb=" CB  ASN A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.87    0.64 2.00e-01 2.50e+01 1.02e+01
  ... (remaining 865 not shown)

  Planarity restraints: 1816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  62 "    0.051 9.50e-02 1.11e+02   1.82e-01 7.40e+02
        pdb=" NE  ARG A  62 "   -0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  62 "    0.042 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  62 "    0.190 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  62 "   -0.027 2.00e-02 2.50e+03
        pdb="HH11 ARG A  62 "    0.103 2.00e-02 2.50e+03
        pdb="HH12 ARG A  62 "   -0.390 2.00e-02 2.50e+03
        pdb="HH21 ARG A  62 "   -0.145 2.00e-02 2.50e+03
        pdb="HH22 ARG A  62 "    0.267 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 446 "   -0.329 2.00e-02 2.50e+03   1.14e-01 5.18e+02
        pdb=" CG  TRP A 446 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 446 "    0.088 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 446 "    0.030 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 446 "    0.107 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 446 "    0.018 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 446 "    0.061 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 446 "   -0.072 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 446 "    0.042 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 446 "   -0.049 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 446 "    0.044 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 446 "    0.101 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 446 "    0.123 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 446 "   -0.148 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 446 "    0.086 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 446 "   -0.091 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 704 "    0.283 2.00e-02 2.50e+03   1.12e-01 5.04e+02
        pdb=" CG  TRP A 704 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 704 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 704 "   -0.073 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 704 "   -0.096 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 704 "   -0.059 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 704 "   -0.123 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 704 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 704 "   -0.021 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 704 "    0.054 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 704 "    0.079 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 704 "   -0.124 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 704 "   -0.172 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 704 "    0.093 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 704 "    0.028 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 704 "    0.156 2.00e-02 2.50e+03
  ... (remaining 1813 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 861
        2.16 -     2.77: 18837
        2.77 -     3.38: 31982
        3.38 -     3.99: 38674
        3.99 -     4.60: 55478
  Nonbonded interactions: 145832
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 665 "
            pdb=" HG  SER A 779 "
     model   vdw
     1.552 2.450
  nonbonded pdb=" OE1 GLU A 660 "
            pdb=" HG1 THR A 662 "
     model   vdw
     1.584 2.450
  nonbonded pdb=" HG1 THR A 495 "
            pdb=" HA  CYS A 555 "
     model   vdw
     1.601 2.270
  nonbonded pdb=" OD1 ASP A 441 "
            pdb=" HG  SER A 443 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OE1 GLU A  78 "
            pdb=" HG  SER A  82 "
     model   vdw
     1.608 2.450
  ... (remaining 145827 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:             2.430
  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:             0.240
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.830
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0070
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      :  0.016   0.072   6184  Z= 0.992
  Angle     :  2.365  17.659   8410  Z= 1.515
  Chirality :  0.133   0.684    868
  Planarity :  0.020   0.147   1117
  Dihedral  : 16.350  82.235   2311
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  4.86 %
    Allowed  : 23.52 %
    Favored  : 71.62 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  :  8.35 %
    Favored  : 85.69 %
  Cbeta Deviations :  1.42 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -4.36 (0.27), residues: 761
  helix: -4.84 (0.38), residues: 14
  sheet: -2.20 (1.15), residues: 24
  loop : -3.27 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.208   0.041   TRP A 446 
 HIS   0.012   0.004   HIS A 336 
 PHE   0.073   0.014   PHE A 700 
 TYR   0.176   0.024   TYR A 552 
 ARG   0.011   0.001   ARG A 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14037 (   51)
  hydrogen bonds       : angle      15.84497 (   90)
  covalent geometry    : bond        0.01558 ( 6184)
  covalent geometry    : angle       2.36494 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 77
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: -0.0107 (tmm) cc_final: -0.0529 (tpp)
REVERT: A  342 VAL cc_start: -0.2607 (OUTLIER) cc_final: -0.3227 (m)
REVERT: A  632 SER cc_start: 0.0514 (OUTLIER) cc_final: 0.0251 (p)
REVERT: A  728 VAL cc_start: 0.4233 (t) cc_final: 0.3563 (t)
  outliers start: 40
  outliers final: 15
  residues processed: 113
  average time/residue: 0.5455
  time to fit residues: 75.6757
Evaluate side-chains
  62 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 PHE
Chi-restraints excluded: chain A residue   62 ARG
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  265 PRO
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  547 ASN
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  810 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:   20.0000
   chunk 57 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 30 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   overall best weight:    8.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 212 GLN
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 648 HIS
A 775 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5448 r_free = 0.5448 target = 0.268549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5349 r_free = 0.5349 target = 0.258886 restraints weight = 123726.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5375 r_free = 0.5375 target = 0.261065 restraints weight = 81024.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5393 r_free = 0.5393 target = 0.262712 restraints weight = 55861.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.5319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0774
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   6184  Z= 0.234
  Angle     :  1.007  11.094   8410  Z= 0.532
  Chirality :  0.055   0.440    868
  Planarity :  0.009   0.108   1117
  Dihedral  : 11.531  57.407    869
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  1.31 %
    Allowed  : 18.27 %
    Favored  : 80.42 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 12.82 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.57 %

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: -4.41 (0.26), residues: 761
  helix: -4.48 (0.47), residues: 13
  sheet: -2.36 (0.90), residues: 33
  loop : -3.32 (0.20), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 127 
 HIS   0.007   0.002   HIS A  67 
 PHE   0.020   0.002   PHE A  94 
 TYR   0.016   0.002   TYR A 793 
 ARG   0.007   0.001   ARG A 309 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04605 (   51)
  hydrogen bonds       : angle      13.24358 (   90)
  covalent geometry    : bond        0.00529 ( 6184)
  covalent geometry    : angle       1.00731 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.0970 (tmm) cc_final: -0.0200 (mmt)
REVERT: A  445 ARG cc_start: 0.3770 (mtm-85) cc_final: 0.3065 (mtt180)
REVERT: A  482 MET cc_start: -0.2020 (mmt) cc_final: -0.2333 (mmt)
  outliers start: 24
  outliers final: 15
  residues processed: 71
  average time/residue: 0.3663
  time to fit residues: 35.2687
Evaluate side-chains
  55 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  734 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 57 optimal weight:   30.0000
   chunk 49 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 12 optimal weight:   50.0000
   chunk 46 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 68 optimal weight:   30.0000
   chunk 62 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 424 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5435 r_free = 0.5435 target = 0.266175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5346 r_free = 0.5346 target = 0.256129 restraints weight = 124530.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5373 r_free = 0.5373 target = 0.258457 restraints weight = 80836.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5389 r_free = 0.5389 target = 0.260112 restraints weight = 56036.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.5318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0815
moved from start:          0.6127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6184  Z= 0.179
  Angle     :  0.830   8.347   8410  Z= 0.434
  Chirality :  0.053   0.426    868
  Planarity :  0.008   0.102   1117
  Dihedral  :  9.279  57.374    845
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 20.63 %
    Favored  : 78.58 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 14.16 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -4.01 (0.28), residues: 761
  helix: -3.91 (0.73), residues: 13
  sheet: -2.04 (0.90), residues: 33
  loop : -3.03 (0.22), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 446 
 HIS   0.004   0.001   HIS A 622 
 PHE   0.017   0.002   PHE A  64 
 TYR   0.020   0.002   TYR A 691 
 ARG   0.003   0.000   ARG A 253 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (   51)
  hydrogen bonds       : angle      12.16935 (   90)
  covalent geometry    : bond        0.00393 ( 6184)
  covalent geometry    : angle       0.83015 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 42
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.1096 (tmm) cc_final: -0.0080 (mmm)
  outliers start: 22
  outliers final: 15
  residues processed: 61
  average time/residue: 0.3686
  time to fit residues: 30.4900
Evaluate side-chains
  53 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  734 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:   30.0000
   chunk 71 optimal weight:   50.0000
   chunk 29 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 46 optimal weight:   20.0000
   chunk 26 optimal weight:    9.9990
   chunk 47 optimal weight:    7.9990
   chunk 4 optimal weight:   40.0000
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 GLN
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5424 r_free = 0.5424 target = 0.263623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5341 r_free = 0.5341 target = 0.254143 restraints weight = 121840.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5363 r_free = 0.5363 target = 0.256094 restraints weight = 76079.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5379 r_free = 0.5379 target = 0.257611 restraints weight = 53405.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.5308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0983
moved from start:          0.7541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6184  Z= 0.170
  Angle     :  0.764   7.427   8410  Z= 0.397
  Chirality :  0.051   0.419    868
  Planarity :  0.008   0.098   1117
  Dihedral  :  8.456  57.250    844
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 18.92 %
    Favored  : 80.68 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.31 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.90 (0.28), residues: 761
  helix: -4.39 (0.61), residues: 12
  sheet: -1.87 (0.88), residues: 33
  loop : -2.94 (0.22), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 446 
 HIS   0.006   0.001   HIS A 622 
 PHE   0.017   0.002   PHE A  64 
 TYR   0.016   0.001   TYR A 233 
 ARG   0.005   0.001   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03379 (   51)
  hydrogen bonds       : angle      11.15343 (   90)
  covalent geometry    : bond        0.00366 ( 6184)
  covalent geometry    : angle       0.76431 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.0020 (mmp) cc_final: -0.0598 (mmt)
REVERT: A  201 MET cc_start: 0.1509 (tmm) cc_final: 0.0059 (mmm)
REVERT: A  658 PHE cc_start: 0.3227 (OUTLIER) cc_final: 0.2621 (t80)
REVERT: A  679 ASP cc_start: 0.6013 (p0) cc_final: 0.5204 (t70)
  outliers start: 21
  outliers final: 17
  residues processed: 58
  average time/residue: 0.3922
  time to fit residues: 30.0657
Evaluate side-chains
  53 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 35
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  760 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 43 optimal weight:   30.0000
   chunk 50 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 313 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5406 r_free = 0.5406 target = 0.260486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5317 r_free = 0.5317 target = 0.250893 restraints weight = 119278.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5344 r_free = 0.5344 target = 0.253171 restraints weight = 74683.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.5361 r_free = 0.5361 target = 0.254634 restraints weight = 50600.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.5285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1032
moved from start:          0.8522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6184  Z= 0.157
  Angle     :  0.745   6.831   8410  Z= 0.384
  Chirality :  0.051   0.417    868
  Planarity :  0.007   0.091   1117
  Dihedral  :  7.994  57.577    844
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 19.97 %
    Favored  : 79.63 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 14.31 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -3.82 (0.28), residues: 761
  helix: -4.14 (0.77), residues: 12
  sheet: -1.91 (0.71), residues: 43
  loop : -2.88 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 446 
 HIS   0.006   0.001   HIS A 605 
 PHE   0.015   0.001   PHE A  94 
 TYR   0.016   0.002   TYR A 793 
 ARG   0.002   0.000   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03270 (   51)
  hydrogen bonds       : angle      10.85943 (   90)
  covalent geometry    : bond        0.00355 ( 6184)
  covalent geometry    : angle       0.74496 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 34
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.0035 (mmp) cc_final: -0.0546 (mmt)
REVERT: A  201 MET cc_start: 0.1935 (tmm) cc_final: 0.0150 (mmm)
REVERT: A  438 PHE cc_start: 0.1806 (OUTLIER) cc_final: 0.1090 (t80)
REVERT: A  658 PHE cc_start: 0.3564 (OUTLIER) cc_final: 0.2981 (t80)
REVERT: A  679 ASP cc_start: 0.6231 (p0) cc_final: 0.5919 (t70)
  outliers start: 23
  outliers final: 18
  residues processed: 56
  average time/residue: 0.4025
  time to fit residues: 30.4502
Evaluate side-chains
  52 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 32
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  760 SER
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 0 optimal weight:   40.0000
   chunk 69 optimal weight:   10.0000
   chunk 38 optimal weight:   40.0000
   chunk 5 optimal weight:   30.0000
   chunk 75 optimal weight:    8.9990
   chunk 1 optimal weight:   50.0000
   overall best weight:    5.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
A 313 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5390 r_free = 0.5390 target = 0.258255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5311 r_free = 0.5311 target = 0.248687 restraints weight = 120398.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5337 r_free = 0.5337 target = 0.250901 restraints weight = 74448.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.5353 r_free = 0.5353 target = 0.252444 restraints weight = 50998.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.5273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1095
moved from start:          0.9057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6184  Z= 0.146
  Angle     :  0.697   7.420   8410  Z= 0.360
  Chirality :  0.050   0.421    868
  Planarity :  0.007   0.088   1117
  Dihedral  :  7.906  57.932    844
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 18.66 %
    Favored  : 80.81 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 15.05 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    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: -3.80 (0.28), residues: 761
  helix: -4.14 (0.79), residues: 12
  sheet: -1.83 (0.93), residues: 31
  loop : -2.87 (0.22), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 446 
 HIS   0.005   0.001   HIS A 605 
 PHE   0.013   0.001   PHE A  94 
 TYR   0.010   0.001   TYR A 793 
 ARG   0.003   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03147 (   51)
  hydrogen bonds       : angle      10.32478 (   90)
  covalent geometry    : bond        0.00324 ( 6184)
  covalent geometry    : angle       0.69714 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 33
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: -0.0094 (mmp) cc_final: -0.0786 (mmt)
REVERT: A  201 MET cc_start: 0.2039 (tmm) cc_final: 0.0117 (mmm)
REVERT: A  438 PHE cc_start: 0.1796 (OUTLIER) cc_final: 0.1120 (t80)
REVERT: A  658 PHE cc_start: 0.3744 (OUTLIER) cc_final: 0.3392 (t80)
  outliers start: 22
  outliers final: 18
  residues processed: 52
  average time/residue: 0.4478
  time to fit residues: 30.0799
Evaluate side-chains
  50 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 30
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  760 SER
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:   30.0000
   chunk 63 optimal weight:    0.0980
   chunk 70 optimal weight:   50.0000
   chunk 3 optimal weight:   50.0000
   chunk 49 optimal weight:    9.9990
   chunk 48 optimal weight:    5.9990
   chunk 66 optimal weight:   30.0000
   chunk 67 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    6.0188

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN
A 294 HIS
A 313 ASN
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5351 r_free = 0.5351 target = 0.254470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5262 r_free = 0.5262 target = 0.244002 restraints weight = 127452.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5291 r_free = 0.5291 target = 0.246355 restraints weight = 81396.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.248050 restraints weight = 56933.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.5239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1195
moved from start:          1.0241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6184  Z= 0.155
  Angle     :  0.709   7.382   8410  Z= 0.365
  Chirality :  0.051   0.415    868
  Planarity :  0.007   0.082   1117
  Dihedral  :  7.637  58.907    844
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 20.50 %
    Favored  : 79.11 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.20 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.77 (0.27), residues: 761
  helix: -4.24 (0.70), residues: 12
  sheet: -1.67 (0.93), residues: 31
  loop : -2.85 (0.22), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 334 
 HIS   0.007   0.001   HIS A 605 
 PHE   0.011   0.001   PHE A  64 
 TYR   0.010   0.001   TYR A 283 
 ARG   0.007   0.001   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03200 (   51)
  hydrogen bonds       : angle       9.94450 (   90)
  covalent geometry    : bond        0.00353 ( 6184)
  covalent geometry    : angle       0.70947 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 33
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: -0.0123 (mmp) cc_final: -0.0851 (mmt)
REVERT: A  201 MET cc_start: 0.2165 (tmm) cc_final: 0.0330 (tpp)
REVERT: A  438 PHE cc_start: 0.1415 (OUTLIER) cc_final: 0.0796 (t80)
  outliers start: 23
  outliers final: 17
  residues processed: 54
  average time/residue: 0.4555
  time to fit residues: 31.7058
Evaluate side-chains
  46 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 28
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 55 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0770
   chunk 8 optimal weight:   20.0000
   chunk 62 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   overall best weight:    5.4146

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5348 r_free = 0.5348 target = 0.253123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5261 r_free = 0.5261 target = 0.242964 restraints weight = 126604.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5291 r_free = 0.5291 target = 0.245332 restraints weight = 80106.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5307 r_free = 0.5307 target = 0.246832 restraints weight = 55162.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.5206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1313
moved from start:          1.0911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6184  Z= 0.141
  Angle     :  0.683   8.472   8410  Z= 0.346
  Chirality :  0.050   0.414    868
  Planarity :  0.007   0.079   1117
  Dihedral  :  7.154  54.817    842
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 17.48 %
    Favored  : 82.26 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.65 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.78 (0.27), residues: 761
  helix: -4.46 (0.68), residues: 17
  sheet: -1.34 (1.00), residues: 26
  loop : -2.84 (0.21), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 334 
 HIS   0.007   0.001   HIS A 605 
 PHE   0.008   0.001   PHE A  94 
 TYR   0.015   0.001   TYR A 283 
 ARG   0.008   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02942 (   51)
  hydrogen bonds       : angle       9.64537 (   90)
  covalent geometry    : bond        0.00310 ( 6184)
  covalent geometry    : angle       0.68273 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 30
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: -0.0129 (mmp) cc_final: -0.0828 (mmt)
REVERT: A  201 MET cc_start: 0.2356 (tmm) cc_final: 0.0544 (tpp)
REVERT: A  438 PHE cc_start: 0.1767 (OUTLIER) cc_final: 0.1132 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 46
  average time/residue: 0.4479
  time to fit residues: 27.2952
Evaluate side-chains
  37 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 23
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 15 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 51 optimal weight:    0.1980
   chunk 47 optimal weight:   50.0000
   chunk 72 optimal weight:   20.0000
   chunk 5 optimal weight:   40.0000
   chunk 14 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    5.6390

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
A 322 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 622 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5341 r_free = 0.5341 target = 0.251239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5244 r_free = 0.5244 target = 0.240803 restraints weight = 127178.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5277 r_free = 0.5277 target = 0.243166 restraints weight = 81850.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.5292 r_free = 0.5292 target = 0.244793 restraints weight = 56880.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.5197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1379
moved from start:          1.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6184  Z= 0.142
  Angle     :  0.685   7.834   8410  Z= 0.350
  Chirality :  0.050   0.410    868
  Planarity :  0.007   0.076   1117
  Dihedral  :  7.003  53.700    842
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 20.76 %
    Favored  : 78.98 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.24 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.73 (0.27), residues: 761
  helix: -4.13 (0.77), residues: 17
  sheet: -1.30 (1.04), residues: 26
  loop : -2.82 (0.21), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 334 
 HIS   0.007   0.001   HIS A 605 
 PHE   0.009   0.001   PHE A 711 
 TYR   0.017   0.001   TYR A 151 
 ARG   0.007   0.001   ARG A  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02915 (   51)
  hydrogen bonds       : angle       9.61513 (   90)
  covalent geometry    : bond        0.00317 ( 6184)
  covalent geometry    : angle       0.68491 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 26
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: -0.0165 (mmp) cc_final: -0.0649 (mmt)
REVERT: A  201 MET cc_start: 0.2487 (tmm) cc_final: 0.0599 (tpp)
REVERT: A  438 PHE cc_start: 0.1564 (OUTLIER) cc_final: 0.0915 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 42
  average time/residue: 0.5025
  time to fit residues: 27.0282
Evaluate side-chains
  40 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 26
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 52 optimal weight:    0.2980
   chunk 72 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 63 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:   30.0000
   chunk 31 optimal weight:    9.9990
   chunk 43 optimal weight:   50.0000
   chunk 58 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    4.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 775 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5337 r_free = 0.5337 target = 0.250836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5241 r_free = 0.5241 target = 0.240414 restraints weight = 126213.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.5274 r_free = 0.5274 target = 0.242747 restraints weight = 82045.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.244371 restraints weight = 57210.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.5204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1379
moved from start:          1.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6184  Z= 0.128
  Angle     :  0.662   8.355   8410  Z= 0.335
  Chirality :  0.049   0.413    868
  Planarity :  0.007   0.075   1117
  Dihedral  :  6.971  53.405    842
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 18.40 %
    Favored  : 81.34 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.84 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.74 (0.27), residues: 761
  helix: -4.06 (0.81), residues: 17
  sheet: -1.46 (1.02), residues: 26
  loop : -2.82 (0.21), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 334 
 HIS   0.010   0.001   HIS A 622 
 PHE   0.007   0.001   PHE A  94 
 TYR   0.015   0.001   TYR A 283 
 ARG   0.004   0.000   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02783 (   51)
  hydrogen bonds       : angle       9.40463 (   90)
  covalent geometry    : bond        0.00287 ( 6184)
  covalent geometry    : angle       0.66197 ( 8410)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 28
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: -0.0094 (mmp) cc_final: -0.0608 (mmt)
REVERT: A  201 MET cc_start: 0.2475 (tmm) cc_final: 0.0552 (tpp)
REVERT: A  276 LEU cc_start: 0.7167 (mm) cc_final: 0.6847 (mp)
REVERT: A  438 PHE cc_start: 0.1416 (OUTLIER) cc_final: 0.0821 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 42
  average time/residue: 0.4925
  time to fit residues: 26.3653
Evaluate side-chains
  40 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 27
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 47 optimal weight:    0.0050
   chunk 74 optimal weight:    0.9990
   chunk 62 optimal weight:   20.0000
   chunk 68 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    4.4002

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 HIS
A 775 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5336 r_free = 0.5336 target = 0.249651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5239 r_free = 0.5239 target = 0.239115 restraints weight = 126629.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5266 r_free = 0.5266 target = 0.241384 restraints weight = 82584.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.5281 r_free = 0.5281 target = 0.243012 restraints weight = 58374.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.5198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1453
moved from start:          1.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6184  Z= 0.130
  Angle     :  0.654   8.488   8410  Z= 0.331
  Chirality :  0.049   0.412    868
  Planarity :  0.007   0.075   1117
  Dihedral  :  6.558  52.199    842
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 19.05 %
    Favored  : 80.55 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.14 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.75 (0.28), residues: 761
  helix: -3.83 (0.86), residues: 23
  sheet: -1.50 (1.02), residues: 26
  loop : -2.81 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 334 
 HIS   0.014   0.001   HIS A 622 
 PHE   0.008   0.001   PHE A 711 
 TYR   0.016   0.001   TYR A 283 
 ARG   0.004   0.001   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02762 (   51)
  hydrogen bonds       : angle       8.97924 (   90)
  covalent geometry    : bond        0.00294 ( 6184)
  covalent geometry    : angle       0.65422 ( 8410)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4195.05 seconds
wall clock time: 73 minutes 6.08 seconds (4386.08 seconds total)