Starting phenix.real_space_refine
on Wed Jun  4 12:17:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gix_51380/06_2025/9gix_51380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gix_51380/06_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_51380/06_2025/9gix_51380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gix_51380/06_2025/9gix_51380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gix_51380/06_2025/9gix_51380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gix_51380/06_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-5710/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: 4.21, per 1000 atoms: 1.54
  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: 0.69
  Conformation dependent library (CDL) restraints added in 343.4 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: 0.33
  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: 0.75

  Time building geometry restraints manager: 0.83 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:             2.960
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.130
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.360
-------------------------------------------------------------------------------
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  : 0.316 
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: 0.2850
  time to fit residues: 29.7120
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  : 0.285 
-------------------------------------------------------------------------------
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 = 3369.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113039 restraints weight = 3296.816|
|-----------------------------------------------------------------------------|
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  : 0.280 
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: 0.2293
  time to fit residues: 17.2482
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  : 0.282 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.135145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.111905 restraints weight = 4183.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.111806 restraints weight = 3070.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.112023 restraints weight = 2966.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3883

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= 0.158
  Angle     :  0.527   4.964   3811  Z= 0.285
  Chirality :  0.041   0.139    400
  Planarity :  0.004   0.034    481
  Dihedral  :  4.217  14.152    385
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.00 %
    Favored  : 83.57 %
  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:  2.20 (0.45), residues: 338
  helix:  1.66 (0.36), residues: 184
  sheet:  1.27 (0.66), residues: 52
  loop :  1.47 (0.68), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B  34 
 PHE   0.014   0.001   PHE A  71 
 TYR   0.012   0.002   TYR A 104 
 ARG   0.004   0.001   ARG A   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04510 (  181)
  hydrogen bonds       : angle       4.31865 (  510)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       0.12857 (    2)
  covalent geometry    : bond        0.00359 ( 2810)
  covalent geometry    : angle       0.52696 ( 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
  73 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7097 (tpp) cc_final: 0.6515 (tpt)
REVERT: A   70 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6492 (mmm160)
REVERT: A   74 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7052 (mtt180)
REVERT: A  104 TYR cc_start: 0.5946 (m-80) cc_final: 0.5437 (m-80)
REVERT: B   19 LYS cc_start: 0.7587 (tttt) cc_final: 0.7271 (mtpt)
REVERT: B   84 ARG cc_start: 0.7638 (tmt170) cc_final: 0.7100 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7709 (m-80) cc_final: 0.7313 (m-80)
REVERT: C   42 MET cc_start: 0.8491 (mmm) cc_final: 0.8058 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 71
  average time/residue: 0.2273
  time to fit residues: 18.3151
Evaluate side-chains
  68 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.135513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.112578 restraints weight = 4390.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.112016 restraints weight = 4045.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.112226 restraints weight = 4200.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4239

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= 0.145
  Angle     :  0.526   6.887   3811  Z= 0.274
  Chirality :  0.039   0.141    400
  Planarity :  0.004   0.035    481
  Dihedral  :  4.188  14.999    385
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.36 %
    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:  2.26 (0.44), residues: 338
  helix:  1.76 (0.36), residues: 184
  sheet:  1.19 (0.65), residues: 52
  loop :  1.43 (0.67), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A   8 
 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   0.007   0.001   ARG A   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04201 (  181)
  hydrogen bonds       : angle       4.27235 (  510)
  SS BOND              : bond        0.00279 (    1)
  SS BOND              : angle       0.28171 (    2)
  covalent geometry    : bond        0.00330 ( 2810)
  covalent geometry    : angle       0.52608 ( 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
  78 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7151 (tpp) cc_final: 0.6682 (tpt)
REVERT: A   70 ARG cc_start: 0.7043 (mtt180) cc_final: 0.6622 (mmm160)
REVERT: A   74 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7081 (mtt180)
REVERT: B   84 ARG cc_start: 0.7623 (tmt170) cc_final: 0.7199 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7779 (m-80) cc_final: 0.7382 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 71
  average time/residue: 0.2109
  time to fit residues: 17.1385
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  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue   91 MET
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   88 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0770
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0970
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 = 0.137016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113519 restraints weight = 4320.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113595 restraints weight = 3332.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113757 restraints weight = 3271.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2811  Z= 0.113
  Angle     :  0.563  13.929   3811  Z= 0.274
  Chirality :  0.039   0.156    400
  Planarity :  0.003   0.027    481
  Dihedral  :  3.952  15.022    385
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.43 %
    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:  2.49 (0.44), residues: 338
  helix:  2.02 (0.36), residues: 185
  sheet:  1.40 (0.64), residues: 52
  loop :  1.30 (0.67), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  36 
 HIS   0.004   0.001   HIS B  14 
 PHE   0.009   0.001   PHE A  71 
 TYR   0.009   0.001   TYR A  64 
 ARG   0.003   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  181)
  hydrogen bonds       : angle       4.25440 (  510)
  SS BOND              : bond        0.00118 (    1)
  SS BOND              : angle       0.28751 (    2)
  covalent geometry    : bond        0.00247 ( 2810)
  covalent geometry    : angle       0.56309 ( 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
  74 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7108 (tpp) cc_final: 0.6668 (tpt)
REVERT: A   70 ARG cc_start: 0.6981 (mtt180) cc_final: 0.6574 (mmm160)
REVERT: A   74 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7578 (tpp80)
REVERT: B   67 LEU cc_start: 0.7709 (mt) cc_final: 0.7256 (tt)
REVERT: B   84 ARG cc_start: 0.7604 (tmt170) cc_final: 0.7178 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7782 (m-80) cc_final: 0.7389 (m-80)
REVERT: C   42 MET cc_start: 0.8385 (mmm) cc_final: 0.8050 (mmt)
  outliers start: 8
  outliers final: 8
  residues processed: 69
  average time/residue: 0.1988
  time to fit residues: 15.6490
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  : 0.284 
-------------------------------------------------------------------------------
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  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   76 MET
Chi-restraints excluded: chain B residue   87 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.135260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.111651 restraints weight = 4393.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.111886 restraints weight = 3351.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.111971 restraints weight = 3219.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.4681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2811  Z= 0.138
  Angle     :  0.553  11.191   3811  Z= 0.275
  Chirality :  0.040   0.143    400
  Planarity :  0.004   0.027    481
  Dihedral  :  3.958  14.216    385
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  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:  2.66 (0.45), residues: 338
  helix:  2.18 (0.36), residues: 180
  sheet:  1.49 (0.63), residues: 52
  loop :  1.36 (0.67), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B  34 
 PHE   0.013   0.001   PHE A  71 
 TYR   0.011   0.001   TYR A  64 
 ARG   0.003   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03988 (  181)
  hydrogen bonds       : angle       4.23708 (  510)
  SS BOND              : bond        0.00175 (    1)
  SS BOND              : angle       0.14009 (    2)
  covalent geometry    : bond        0.00316 ( 2810)
  covalent geometry    : angle       0.55297 ( 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
  75 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   57 MET cc_start: 0.7154 (tpp) cc_final: 0.6734 (tpt)
REVERT: A   70 ARG cc_start: 0.7050 (mtt180) cc_final: 0.6624 (mmm160)
REVERT: A   74 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7053 (mtt180)
REVERT: B   84 ARG cc_start: 0.7540 (tmt170) cc_final: 0.7096 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7781 (m-80) cc_final: 0.7416 (m-80)
REVERT: C   42 MET cc_start: 0.8443 (mmm) cc_final: 0.8104 (mmt)
  outliers start: 11
  outliers final: 10
  residues processed: 67
  average time/residue: 0.2149
  time to fit residues: 16.4556
Evaluate side-chains
  71 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue   91 MET
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    0.2980
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   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 = 0.3781 r_free = 0.3781 target = 0.136602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.113164 restraints weight = 4418.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113278 restraints weight = 3385.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.113455 restraints weight = 3298.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.4874

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= 0.127
  Angle     :  0.544   9.879   3811  Z= 0.271
  Chirality :  0.039   0.142    400
  Planarity :  0.004   0.029    481
  Dihedral  :  3.878  13.701    385
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.79 %
    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:  2.71 (0.45), residues: 338
  helix:  2.27 (0.36), residues: 180
  sheet:  1.58 (0.61), residues: 52
  loop :  1.25 (0.66), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  36 
 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   0.005   0.000   ARG A   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03787 (  181)
  hydrogen bonds       : angle       4.18713 (  510)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       0.29037 (    2)
  covalent geometry    : bond        0.00290 ( 2810)
  covalent geometry    : angle       0.54408 ( 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
  78 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7137 (tpp) cc_final: 0.6756 (tpt)
REVERT: A   70 ARG cc_start: 0.7057 (mtt180) cc_final: 0.6625 (mmm160)
REVERT: B   84 ARG cc_start: 0.7541 (tmt170) cc_final: 0.7107 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7787 (m-80) cc_final: 0.7494 (m-80)
  outliers start: 12
  outliers final: 11
  residues processed: 70
  average time/residue: 0.1959
  time to fit residues: 15.7225
Evaluate side-chains
  74 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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   91 MET
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   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:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.136722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.113543 restraints weight = 4284.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.113575 restraints weight = 3237.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113749 restraints weight = 3164.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
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   0.024   2811  Z= 0.119
  Angle     :  0.572  14.184   3811  Z= 0.278
  Chirality :  0.039   0.163    400
  Planarity :  0.004   0.031    481
  Dihedral  :  3.847  13.634    385
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.43 %
    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:  2.71 (0.44), residues: 338
  helix:  2.27 (0.37), residues: 180
  sheet:  1.61 (0.60), residues: 52
  loop :  1.24 (0.65), 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  14 
 PHE   0.010   0.001   PHE A  71 
 TYR   0.009   0.001   TYR A  64 
 ARG   0.005   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  181)
  hydrogen bonds       : angle       4.18826 (  510)
  SS BOND              : bond        0.00185 (    1)
  SS BOND              : angle       0.39027 (    2)
  covalent geometry    : bond        0.00268 ( 2810)
  covalent geometry    : angle       0.57243 ( 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
  78 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   57 MET cc_start: 0.7087 (tpp) cc_final: 0.6688 (tpt)
REVERT: A   70 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6556 (mmm160)
REVERT: A   74 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7365 (ttt180)
REVERT: B   67 LEU cc_start: 0.7676 (mt) cc_final: 0.7447 (tt)
REVERT: C   35 TYR cc_start: 0.7805 (m-80) cc_final: 0.7507 (m-80)
REVERT: C   61 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7537 (ttm170)
  outliers start: 12
  outliers final: 9
  residues processed: 69
  average time/residue: 0.2144
  time to fit residues: 16.7793
Evaluate side-chains
  73 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue   91 MET
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   61 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0570
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 13 optimal weight:    0.1980
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.4898

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.137077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.113732 restraints weight = 4313.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.113843 restraints weight = 3232.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114030 restraints weight = 3129.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.5108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2811  Z= 0.119
  Angle     :  0.598  14.201   3811  Z= 0.287
  Chirality :  0.039   0.188    400
  Planarity :  0.004   0.033    481
  Dihedral  :  3.818  13.601    385
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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:  2.77 (0.44), residues: 338
  helix:  2.30 (0.37), residues: 181
  sheet:  1.69 (0.61), residues: 52
  loop :  1.24 (0.66), residues: 105

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   0.006   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (  181)
  hydrogen bonds       : angle       4.14579 (  510)
  SS BOND              : bond        0.00175 (    1)
  SS BOND              : angle       0.40727 (    2)
  covalent geometry    : bond        0.00273 ( 2810)
  covalent geometry    : angle       0.59814 ( 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
  78 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A   57 MET cc_start: 0.7076 (tpp) cc_final: 0.6692 (tpt)
REVERT: A   70 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6558 (mmm160)
REVERT: A   74 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.7372 (ttt180)
REVERT: B   67 LEU cc_start: 0.7638 (mt) cc_final: 0.7431 (tt)
REVERT: C   35 TYR cc_start: 0.7822 (m-80) cc_final: 0.7557 (m-80)
REVERT: C   61 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7548 (ttm170)
  outliers start: 11
  outliers final: 9
  residues processed: 71
  average time/residue: 0.2189
  time to fit residues: 17.7970
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  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue   91 MET
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   61 ARG
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:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0870
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.135743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.112623 restraints weight = 4248.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.112735 restraints weight = 3119.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.113055 restraints weight = 3036.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.5182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2811  Z= 0.128
  Angle     :  0.603  13.803   3811  Z= 0.290
  Chirality :  0.039   0.173    400
  Planarity :  0.004   0.028    481
  Dihedral  :  3.969  17.758    385
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.93 %
    Favored  : 77.86 %
  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:  2.74 (0.44), residues: 338
  helix:  2.30 (0.37), residues: 180
  sheet:  1.71 (0.62), residues: 52
  loop :  1.17 (0.65), residues: 106

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   0.020   0.001   TYR A 100 
 ARG   0.006   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  181)
  hydrogen bonds       : angle       4.15407 (  510)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       0.57674 (    2)
  covalent geometry    : bond        0.00296 ( 2810)
  covalent geometry    : angle       0.60279 ( 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
  75 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   46 MET cc_start: 0.6828 (tpp) cc_final: 0.6411 (tmm)
REVERT: A   57 MET cc_start: 0.7079 (tpp) cc_final: 0.6678 (tpt)
REVERT: A   70 ARG cc_start: 0.6974 (mtt180) cc_final: 0.6460 (mmm160)
REVERT: A   74 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7444 (ttt180)
REVERT: C   35 TYR cc_start: 0.7841 (m-80) cc_final: 0.7560 (m-80)
REVERT: C   61 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7567 (ttm170)
  outliers start: 9
  outliers final: 8
  residues processed: 70
  average time/residue: 0.2194
  time to fit residues: 17.4920
Evaluate side-chains
  75 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 PHE
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   61 ARG
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:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0870
   chunk 5 optimal weight:    0.4980
   chunk 25 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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 = 0.3773 r_free = 0.3773 target = 0.136547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.113460 restraints weight = 4256.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.113407 restraints weight = 3308.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.113655 restraints weight = 3251.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.5245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2811  Z= 0.121
  Angle     :  0.592  13.569   3811  Z= 0.285
  Chirality :  0.039   0.203    400
  Planarity :  0.004   0.039    481
  Dihedral  :  3.749  12.576    385
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 18.93 %
    Favored  : 77.50 %
  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:  2.78 (0.45), residues: 338
  helix:  2.29 (0.37), residues: 181
  sheet:  1.86 (0.63), residues: 52
  loop :  1.19 (0.66), residues: 105

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   0.018   0.001   TYR A 100 
 ARG   0.006   0.000   ARG C  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  181)
  hydrogen bonds       : angle       4.14227 (  510)
  SS BOND              : bond        0.00198 (    1)
  SS BOND              : angle       0.55443 (    2)
  covalent geometry    : bond        0.00276 ( 2810)
  covalent geometry    : angle       0.59188 ( 3809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1612.59 seconds
wall clock time: 28 minutes 57.73 seconds (1737.73 seconds total)