Starting phenix.real_space_refine
on Fri May  9 15:09:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gix_51380/05_2025/9gix_51380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gix_51380/05_2025/9gix_51380.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gix_51380/05_2025/9gix_51380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gix_51380/05_2025/9gix_51380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gix_51380/05_2025/9gix_51380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gix_51380/05_2025/9gix_51380.cif"
  }
  resolution = 3.65
  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=   0.009
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      18      5.16       5
     C    1769      2.51       5
     N     469      2.21       5
     O     477      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2733
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 837
          Classifications: {'peptide': 102}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97}
    Chain: "B"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 917
          Classifications: {'peptide': 114}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 106}
    Chain: "C"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 979
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
  Time building chain proxies: 3.38, per 1000 atoms: 1.24
  Number of scatterers: 2733
  At special positions: 0
  Unit cell: (69.255, 64.881, 103.518, 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      18     16.00
     O     477      8.00
     N     469      7.00
     C    1769      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  25 " - pdb=" SG  CYS C 104 " distance=2.14

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 306.2 milliseconds
  

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  634

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 3 sheets defined
      63.4% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 17
    Processing helix  chain 'A' and resid 17 through 26
    Processing helix  chain 'A' and resid 26 through 36
      removed outlier: 4.146A  pdb=" N   TRP A  30 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
      Proline residue:  A  32  - end of helix
    Processing helix  chain 'A' and resid 36 through 47
      removed outlier: 3.835A  pdb=" N   LYS A  47 " --> pdb=" O   PHE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 53
      removed outlier: 6.177A  pdb=" N   GLU A  51 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 75
    Processing helix  chain 'A' and resid 79 through 107
    Processing helix  chain 'B' and resid 9 through 22
    Processing helix  chain 'B' and resid 28 through 34
    Processing helix  chain 'B' and resid 40 through 61
      removed outlier: 3.722A  pdb=" N   TRP B  44 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      Proline residue:  B  46  - end of helix
      removed outlier: 3.882A  pdb=" N   ALA B  58 " --> pdb=" O   CYS B  54 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ASP B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 89
    Processing helix  chain 'B' and resid 93 through 121
      removed outlier: 3.726A  pdb=" N   TRP B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR B 117 " --> pdb=" O   ARG B 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 36
    Processing helix  chain 'C' and resid 37 through 40
    Processing helix  chain 'C' and resid 95 through 99
    Processing helix  chain 'C' and resid 114 through 118
      removed outlier: 3.668A  pdb=" N   MET C 118 " --> pdb=" O   VAL C 115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'C' and resid 13 through 14
      removed outlier: 6.393A  pdb=" N   GLY C  13 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   ARG C  46 " --> pdb=" O   PHE C  55 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   PHE C  55 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 13 through 14
      removed outlier: 6.393A  pdb=" N   GLY C  13 " --> pdb=" O   THR C 128 " (cutoff:3.500A)

    185 hydrogen bonds defined for protein.
    510 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: 0.73

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 820
        1.34 -     1.46: 770
        1.46 -     1.58: 1189
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 2810
  Sorted by residual:
  bond pdb=" CA  SER A  65 "
       pdb=" CB  SER A  65 "
    ideal  model  delta    sigma   weight residual
    1.528  1.496  0.032 1.59e-02 3.96e+03 4.12e+00
  bond pdb=" C   ILE B  89 "
       pdb=" N   ILE B  90 "
    ideal  model  delta    sigma   weight residual
    1.324  1.341 -0.017 8.60e-03 1.35e+04 3.75e+00
  bond pdb=" CA  SER B  83 "
       pdb=" CB  SER B  83 "
    ideal  model  delta    sigma   weight residual
    1.529  1.500  0.029 1.55e-02 4.16e+03 3.55e+00
  bond pdb=" CA  SER B  72 "
       pdb=" CB  SER B  72 "
    ideal  model  delta    sigma   weight residual
    1.528  1.499  0.029 1.59e-02 3.96e+03 3.40e+00
  bond pdb=" C   VAL C 129 "
       pdb=" N   PRO C 130 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.021 1.15e-02 7.56e+03 3.26e+00
  ... (remaining 2805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 3405
        1.38 -     2.77: 349
        2.77 -     4.15: 47
        4.15 -     5.53: 6
        5.53 -     6.91: 2
  Bond angle restraints: 3809
  Sorted by residual:
  angle pdb=" CA  TRP A  36 "
        pdb=" CB  TRP A  36 "
        pdb=" CG  TRP A  36 "
      ideal   model   delta    sigma   weight residual
     113.60  119.37   -5.77 1.90e+00 2.77e-01 9.23e+00
  angle pdb=" CB  ARG B  84 "
        pdb=" CG  ARG B  84 "
        pdb=" CD  ARG B  84 "
      ideal   model   delta    sigma   weight residual
     111.30  118.21   -6.91 2.30e+00 1.89e-01 9.03e+00
  angle pdb=" N   ARG B  84 "
        pdb=" CA  ARG B  84 "
        pdb=" CB  ARG B  84 "
      ideal   model   delta    sigma   weight residual
     110.12  114.42   -4.30 1.47e+00 4.63e-01 8.57e+00
  angle pdb=" N   PRO B  46 "
        pdb=" CA  PRO B  46 "
        pdb=" C   PRO B  46 "
      ideal   model   delta    sigma   weight residual
     113.75  117.70   -3.95 1.49e+00 4.50e-01 7.02e+00
  angle pdb=" C   THR B  40 "
        pdb=" N   VAL B  41 "
        pdb=" CA  VAL B  41 "
      ideal   model   delta    sigma   weight residual
     120.47  124.63   -4.16 1.58e+00 4.01e-01 6.94e+00
  ... (remaining 3804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.41: 1515
       15.41 -    30.81: 92
       30.81 -    46.21: 20
       46.21 -    61.62: 8
       61.62 -    77.02: 4
  Dihedral angle restraints: 1639
    sinusoidal: 643
      harmonic: 996
  Sorted by residual:
  dihedral pdb=" CA  PRO B  63 "
           pdb=" C   PRO B  63 "
           pdb=" N   ALA B  64 "
           pdb=" CA  ALA B  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.37  -20.63     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CG  ARG A  70 "
           pdb=" CD  ARG A  70 "
           pdb=" NE  ARG A  70 "
           pdb=" CZ  ARG A  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.57  -44.57     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG A  99 "
           pdb=" CD  ARG A  99 "
           pdb=" NE  ARG A  99 "
           pdb=" CZ  ARG A  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.94   42.94     2      1.50e+01 4.44e-03 9.90e+00
  ... (remaining 1636 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 219
       0.049 -    0.098: 117
       0.098 -    0.147: 50
       0.147 -    0.197: 9
       0.197 -    0.246: 5
  Chirality restraints: 400
  Sorted by residual:
  chirality pdb=" CA  PRO B  46 "
            pdb=" N   PRO B  46 "
            pdb=" C   PRO B  46 "
            pdb=" CB  PRO B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  HIS A  86 "
            pdb=" N   HIS A  86 "
            pdb=" C   HIS A  86 "
            pdb=" CB  HIS A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  PRO A  39 "
            pdb=" N   PRO A  39 "
            pdb=" C   PRO A  39 "
            pdb=" CB  PRO A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.21 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 397 not shown)

  Planarity restraints: 481
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 112 "    0.186 9.50e-02 1.11e+02   8.34e-02 4.59e+00
        pdb=" NE  ARG C 112 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 112 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 112 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 112 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  36 "    0.015 2.00e-02 2.50e+03   9.33e-03 2.18e+00
        pdb=" CG  TRP A  36 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  36 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  36 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  36 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  36 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  36 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 113 "    0.126 9.50e-02 1.11e+02   5.65e-02 2.16e+00
        pdb=" NE  ARG B 113 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 113 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 113 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 113 "    0.002 2.00e-02 2.50e+03
  ... (remaining 478 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 1249
        2.97 -     3.45: 2684
        3.45 -     3.94: 4413
        3.94 -     4.42: 4875
        4.42 -     4.90: 8048
  Nonbonded interactions: 21269
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  72 "
            pdb=" NE2 GLN B 110 "
     model   vdw
     2.488 3.120
  nonbonded pdb=" OG  SER A  65 "
            pdb=" ND2 ASN A  89 "
     model   vdw
     2.524 3.120
  nonbonded pdb=" NH1 ARG C  61 "
            pdb=" O   SER C 108 "
     model   vdw
     2.563 3.120
  nonbonded pdb=" OE1 GLU A  51 "
            pdb=" OH  TYR A 103 "
     model   vdw
     2.564 3.040
  nonbonded pdb=" NE  ARG C  46 "
            pdb=" OE2 GLU C  54 "
     model   vdw
     2.577 3.120
  ... (remaining 21264 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             4.110
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.400
  Find NCS groups from input model:        0.030
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
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      :  0.007   0.108   2811  Z= 0.461
  Angle     :  0.890   6.913   3811  Z= 0.569
  Chirality :  0.069   0.246    400
  Planarity :  0.009   0.083    481
  Dihedral  : 12.015  77.018   1002
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 0.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  0.66 (0.43), residues: 338
  helix:  0.03 (0.32), residues: 182
  sheet:  0.74 (0.73), residues: 52
  loop :  1.51 (0.68), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.005   TRP A  36 
 HIS   0.008   0.002   HIS A  86 
 PHE   0.013   0.002   PHE B  43 
 TYR   0.023   0.004   TYR A  64 
 ARG   0.010   0.002   ARG C 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15070 (  181)
  hydrogen bonds       : angle       6.61691 (  510)
  SS BOND              : bond        0.10778 (    1)
  SS BOND              : angle       3.41295 (    2)
  covalent geometry    : bond        0.00715 ( 2810)
  covalent geometry    : angle       0.88642 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.6015 (ttp-170) cc_final: 0.5764 (tpt170)
REVERT: A   57 MET cc_start: 0.6818 (tpp) cc_final: 0.6521 (tpt)
REVERT: A   69 MET cc_start: 0.7209 (ttt) cc_final: 0.6827 (ttp)
REVERT: A   70 ARG cc_start: 0.6566 (mtt180) cc_final: 0.5898 (mmm160)
REVERT: A   74 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.6782 (mtt180)
REVERT: B   19 LYS cc_start: 0.7844 (tttt) cc_final: 0.7204 (mtpt)
REVERT: B   21 GLU cc_start: 0.7640 (tt0) cc_final: 0.7385 (tm-30)
REVERT: B   48 MET cc_start: 0.7761 (mmt) cc_final: 0.7438 (mmm)
REVERT: B   60 MET cc_start: 0.6768 (mtm) cc_final: 0.6352 (mtt)
REVERT: C   35 TYR cc_start: 0.7125 (m-80) cc_final: 0.6814 (m-80)
REVERT: C   42 MET cc_start: 0.8517 (mmm) cc_final: 0.8131 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.2800
  time to fit residues: 29.0890
Evaluate side-chains
  61 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 25 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.137264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113247 restraints weight = 4463.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.112893 restraints weight = 3369.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113039 restraints weight = 3296.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2811  Z= 0.162
  Angle     :  0.596   7.088   3811  Z= 0.319
  Chirality :  0.041   0.141    400
  Planarity :  0.005   0.039    481
  Dihedral  :  4.557  16.537    385
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 12.50 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.93 (0.44), residues: 338
  helix:  1.33 (0.36), residues: 183
  sheet:  0.93 (0.73), residues: 45
  loop :  1.69 (0.64), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B  34 
 PHE   0.012   0.002   PHE A  71 
 TYR   0.014   0.002   TYR A  64 
 ARG   0.006   0.001   ARG A  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05036 (  181)
  hydrogen bonds       : angle       4.52694 (  510)
  SS BOND              : bond        0.00998 (    1)
  SS BOND              : angle       0.32106 (    2)
  covalent geometry    : bond        0.00356 ( 2810)
  covalent geometry    : angle       0.59610 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.6897 (mtt180) cc_final: 0.6638 (mmm160)
REVERT: A   74 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7018 (mtt180)
REVERT: A  104 TYR cc_start: 0.6031 (m-80) cc_final: 0.5786 (m-80)
REVERT: B   16 LEU cc_start: 0.7817 (mt) cc_final: 0.7037 (tt)
REVERT: B   19 LYS cc_start: 0.7558 (tttt) cc_final: 0.7267 (mtpt)
REVERT: C   35 TYR cc_start: 0.7687 (m-80) cc_final: 0.7354 (m-80)
REVERT: C  112 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7456 (mtp85)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.2362
  time to fit residues: 17.7893
Evaluate side-chains
  65 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.135811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.113615 restraints weight = 4167.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.113125 restraints weight = 3132.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113194 restraints weight = 3570.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2811  Z= 0.137
  Angle     :  0.505   4.936   3811  Z= 0.273
  Chirality :  0.040   0.143    400
  Planarity :  0.004   0.033    481
  Dihedral  :  4.132  14.578    385
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.93 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.31 (0.45), residues: 338
  helix:  1.75 (0.36), residues: 183
  sheet:  1.29 (0.65), residues: 52
  loop :  1.52 (0.67), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.012   0.001   PHE A  71 
 TYR   0.011   0.001   TYR A 104 
 ARG   0.003   0.000   ARG A   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04314 (  181)
  hydrogen bonds       : angle       4.27743 (  510)
  SS BOND              : bond        0.00464 (    1)
  SS BOND              : angle       0.11646 (    2)
  covalent geometry    : bond        0.00305 ( 2810)
  covalent geometry    : angle       0.50472 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.7088 (tmm) cc_final: 0.6863 (tmm)
REVERT: A   57 MET cc_start: 0.7097 (tpp) cc_final: 0.6520 (tpt)
REVERT: A   70 ARG cc_start: 0.6950 (mtt180) cc_final: 0.6557 (mmm160)
REVERT: A   74 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7093 (mtt180)
REVERT: A  104 TYR cc_start: 0.5915 (m-80) cc_final: 0.5443 (m-80)
REVERT: B   16 LEU cc_start: 0.7812 (mt) cc_final: 0.7067 (tt)
REVERT: B   19 LYS cc_start: 0.7540 (tttt) cc_final: 0.7293 (mtpt)
REVERT: B   84 ARG cc_start: 0.7597 (tmt170) cc_final: 0.7166 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7706 (m-80) cc_final: 0.7317 (m-80)
REVERT: C   42 MET cc_start: 0.8484 (mmm) cc_final: 0.7955 (mmt)
  outliers start: 5
  outliers final: 4
  residues processed: 71
  average time/residue: 0.2192
  time to fit residues: 17.6649
Evaluate side-chains
  69 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue   21 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0170
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4016

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.137434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115421 restraints weight = 4193.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.114863 restraints weight = 3113.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.115070 restraints weight = 3347.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2811  Z= 0.110
  Angle     :  0.479   4.871   3811  Z= 0.253
  Chirality :  0.038   0.141    400
  Planarity :  0.004   0.028    481
  Dihedral  :  4.008  14.651    385
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.36 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.50 (0.44), residues: 338
  helix:  1.97 (0.36), residues: 184
  sheet:  1.40 (0.61), residues: 52
  loop :  1.44 (0.67), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  36 
 HIS   0.001   0.001   HIS B  34 
 PHE   0.009   0.001   PHE A  71 
 TYR   0.010   0.001   TYR A 104 
 ARG   0.006   0.000   ARG A   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  181)
  hydrogen bonds       : angle       4.16019 (  510)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       0.32208 (    2)
  covalent geometry    : bond        0.00235 ( 2810)
  covalent geometry    : angle       0.47867 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7074 (tpp) cc_final: 0.6589 (tpt)
REVERT: A   70 ARG cc_start: 0.6887 (mtt180) cc_final: 0.6537 (mmm160)
REVERT: A   74 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7034 (mtt180)
REVERT: B   16 LEU cc_start: 0.7738 (mt) cc_final: 0.7125 (tt)
REVERT: B   19 LYS cc_start: 0.7586 (tttt) cc_final: 0.7368 (mtpt)
REVERT: B   84 ARG cc_start: 0.7587 (tmt170) cc_final: 0.7145 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7714 (m-80) cc_final: 0.7291 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 71
  average time/residue: 0.2166
  time to fit residues: 17.4085
Evaluate side-chains
  68 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   87 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    0.4980
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0370
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.136708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.113421 restraints weight = 4338.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.113769 restraints weight = 3306.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.114002 restraints weight = 3230.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2811  Z= 0.125
  Angle     :  0.509   7.109   3811  Z= 0.262
  Chirality :  0.039   0.145    400
  Planarity :  0.004   0.027    481
  Dihedral  :  3.953  13.380    385
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.36 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.62 (0.45), residues: 338
  helix:  2.12 (0.36), residues: 184
  sheet:  1.46 (0.62), residues: 52
  loop :  1.37 (0.68), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  44 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.011   0.001   PHE A  71 
 TYR   0.010   0.001   TYR A  64 
 ARG   0.003   0.000   ARG C 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03865 (  181)
  hydrogen bonds       : angle       4.20358 (  510)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.42893 (    2)
  covalent geometry    : bond        0.00282 ( 2810)
  covalent geometry    : angle       0.50914 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7145 (tpp) cc_final: 0.6709 (tpt)
REVERT: A   70 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6620 (mmm160)
REVERT: A   74 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7575 (tpp80)
REVERT: B   84 ARG cc_start: 0.7607 (tmt170) cc_final: 0.7175 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7766 (m-80) cc_final: 0.7374 (m-80)
REVERT: C   42 MET cc_start: 0.8422 (mmm) cc_final: 0.8093 (mmt)
  outliers start: 8
  outliers final: 8
  residues processed: 70
  average time/residue: 0.2159
  time to fit residues: 17.0969
Evaluate side-chains
  71 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue   21 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0770
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.5138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.136729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.113359 restraints weight = 4371.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.113518 restraints weight = 3337.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.113625 restraints weight = 3192.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2811  Z= 0.118
  Angle     :  0.514   7.416   3811  Z= 0.261
  Chirality :  0.039   0.142    400
  Planarity :  0.004   0.027    481
  Dihedral  :  3.842  13.252    385
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 15.71 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.70 (0.45), residues: 338
  helix:  2.20 (0.36), residues: 185
  sheet:  1.60 (0.61), residues: 52
  loop :  1.29 (0.69), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B  14 
 PHE   0.010   0.001   PHE A  71 
 TYR   0.009   0.001   TYR A  64 
 ARG   0.004   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03720 (  181)
  hydrogen bonds       : angle       4.14939 (  510)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       0.21677 (    2)
  covalent geometry    : bond        0.00263 ( 2810)
  covalent geometry    : angle       0.51405 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   57 MET cc_start: 0.7096 (tpp) cc_final: 0.6664 (tpt)
REVERT: A   70 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6591 (mmm160)
REVERT: A   74 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7475 (ttt180)
REVERT: B   67 LEU cc_start: 0.7693 (mt) cc_final: 0.7316 (tt)
REVERT: C   35 TYR cc_start: 0.7751 (m-80) cc_final: 0.7351 (m-80)
REVERT: C   42 MET cc_start: 0.8472 (mmm) cc_final: 0.8169 (mmt)
  outliers start: 10
  outliers final: 8
  residues processed: 69
  average time/residue: 0.2041
  time to fit residues: 16.1072
Evaluate side-chains
  70 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  28 HIS
B  34 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.135480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.112023 restraints weight = 4434.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.112100 restraints weight = 3356.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.112315 restraints weight = 3169.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2811  Z= 0.147
  Angle     :  0.579  15.311   3811  Z= 0.284
  Chirality :  0.040   0.143    400
  Planarity :  0.004   0.028    481
  Dihedral  :  3.942  14.039    385
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.07 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.67 (0.45), residues: 338
  helix:  2.19 (0.36), residues: 180
  sheet:  1.64 (0.62), residues: 52
  loop :  1.28 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  30 
 HIS   0.003   0.001   HIS B  14 
 PHE   0.014   0.001   PHE A  71 
 TYR   0.012   0.001   TYR A  64 
 ARG   0.005   0.000   ARG A   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03997 (  181)
  hydrogen bonds       : angle       4.22145 (  510)
  SS BOND              : bond        0.00196 (    1)
  SS BOND              : angle       0.24990 (    2)
  covalent geometry    : bond        0.00337 ( 2810)
  covalent geometry    : angle       0.57900 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A   57 MET cc_start: 0.7152 (tpp) cc_final: 0.6755 (tpt)
REVERT: A   70 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6609 (mmm160)
REVERT: A   74 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.7341 (ttt180)
REVERT: C   35 TYR cc_start: 0.7777 (m-80) cc_final: 0.7411 (m-80)
REVERT: C   42 MET cc_start: 0.8453 (mmm) cc_final: 0.8125 (mmt)
  outliers start: 11
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1843
  time to fit residues: 14.4199
Evaluate side-chains
  72 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 TRP
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 7 optimal weight:    0.3980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.137142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.111606 restraints weight = 4272.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.113801 restraints weight = 3042.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.115144 restraints weight = 2448.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.4914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2811  Z= 0.115
  Angle     :  0.573  16.120   3811  Z= 0.274
  Chirality :  0.039   0.142    400
  Planarity :  0.004   0.032    481
  Dihedral  :  3.830  13.383    385
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.71 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.79 (0.45), residues: 338
  helix:  2.29 (0.37), residues: 180
  sheet:  1.66 (0.60), residues: 52
  loop :  1.33 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  36 
 HIS   0.001   0.001   HIS B  34 
 PHE   0.010   0.001   PHE A  71 
 TYR   0.009   0.001   TYR A  64 
 ARG   0.006   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03648 (  181)
  hydrogen bonds       : angle       4.15745 (  510)
  SS BOND              : bond        0.00192 (    1)
  SS BOND              : angle       0.42365 (    2)
  covalent geometry    : bond        0.00259 ( 2810)
  covalent geometry    : angle       0.57269 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7085 (tpp) cc_final: 0.6702 (tpt)
REVERT: A   70 ARG cc_start: 0.7099 (mtt180) cc_final: 0.6714 (mmm160)
REVERT: B   67 LEU cc_start: 0.7656 (mt) cc_final: 0.7392 (tt)
REVERT: C   35 TYR cc_start: 0.7765 (m-80) cc_final: 0.7456 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 69
  average time/residue: 0.1854
  time to fit residues: 14.7173
Evaluate side-chains
  69 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 TRP
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.135910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.112364 restraints weight = 4369.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.112474 restraints weight = 3304.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.112632 restraints weight = 3171.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2811  Z= 0.142
  Angle     :  0.596  15.372   3811  Z= 0.289
  Chirality :  0.040   0.172    400
  Planarity :  0.004   0.032    481
  Dihedral  :  3.913  13.993    385
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.79 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.63 (0.44), residues: 338
  helix:  2.16 (0.37), residues: 181
  sheet:  1.65 (0.61), residues: 52
  loop :  1.23 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  30 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.013   0.001   PHE A  71 
 TYR   0.012   0.001   TYR A  64 
 ARG   0.006   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  181)
  hydrogen bonds       : angle       4.22629 (  510)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       0.38772 (    2)
  covalent geometry    : bond        0.00328 ( 2810)
  covalent geometry    : angle       0.59651 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   57 MET cc_start: 0.7147 (tpp) cc_final: 0.6768 (tpt)
REVERT: A   70 ARG cc_start: 0.7056 (mtt180) cc_final: 0.6582 (mmm160)
REVERT: A   74 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7323 (ttt180)
REVERT: C   35 TYR cc_start: 0.7802 (m-80) cc_final: 0.7463 (m-80)
  outliers start: 9
  outliers final: 8
  residues processed: 66
  average time/residue: 0.1999
  time to fit residues: 15.1433
Evaluate side-chains
  71 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.135094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.109288 restraints weight = 4346.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.111473 restraints weight = 3095.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.112818 restraints weight = 2511.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.5068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2811  Z= 0.154
  Angle     :  0.625  14.988   3811  Z= 0.300
  Chirality :  0.041   0.165    400
  Planarity :  0.004   0.030    481
  Dihedral  :  4.158  19.674    385
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.79 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.46 (0.45), residues: 338
  helix:  2.10 (0.37), residues: 181
  sheet:  1.37 (0.63), residues: 57
  loop :  1.09 (0.66), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  30 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.015   0.001   PHE A  71 
 TYR   0.012   0.001   TYR A  64 
 ARG   0.007   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03984 (  181)
  hydrogen bonds       : angle       4.27366 (  510)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       0.55772 (    2)
  covalent geometry    : bond        0.00359 ( 2810)
  covalent geometry    : angle       0.62491 ( 3809)

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

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

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  676 Ramachandran restraints generated.
    338 Oldfield, 0 Emsley, 338 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   57 MET cc_start: 0.7145 (tpp) cc_final: 0.6771 (tpt)
REVERT: A   70 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6723 (mmm160)
REVERT: A   74 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7319 (ttt180)
REVERT: C   35 TYR cc_start: 0.7859 (m-80) cc_final: 0.7545 (m-80)
  outliers start: 11
  outliers final: 10
  residues processed: 70
  average time/residue: 0.2092
  time to fit residues: 16.6462
Evaluate side-chains
  77 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.112373 restraints weight = 4258.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.112255 restraints weight = 3188.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.112586 restraints weight = 3067.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.5134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2811  Z= 0.130
  Angle     :  0.597  14.819   3811  Z= 0.286
  Chirality :  0.040   0.161    400
  Planarity :  0.004   0.030    481
  Dihedral  :  3.926  13.363    385
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.14 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  2.55 (0.44), residues: 338
  helix:  2.13 (0.37), residues: 181
  sheet:  1.84 (0.62), residues: 51
  loop :  0.98 (0.64), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.012   0.001   PHE A  71 
 TYR   0.010   0.001   TYR A  64 
 ARG   0.006   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  181)
  hydrogen bonds       : angle       4.19350 (  510)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       0.33455 (    2)
  covalent geometry    : bond        0.00301 ( 2810)
  covalent geometry    : angle       0.59721 ( 3809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1535.78 seconds
wall clock time: 27 minutes 34.52 seconds (1654.52 seconds total)