Starting phenix.real_space_refine
on Wed Sep 17 03:16:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gix_51380/09_2025/9gix_51380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gix_51380/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gix_51380/09_2025/9gix_51380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gix_51380/09_2025/9gix_51380.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gix_51380/09_2025/9gix_51380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gix_51380/09_2025/9gix_51380.map"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.74, per 1000 atoms: 0.27
  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: 0.16
  Conformation dependent library (CDL) restraints added in 88.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.11
  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: 0.35

  Time building geometry restraints manager: 0.23 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:             4.680
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.140
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.900
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.002   ARG C 112 
 TYR   0.023   0.004   TYR A  64 
 PHE   0.013   0.002   PHE B  43 
 TRP   0.022   0.005   TRP A  36 
 HIS   0.008   0.002   HIS A  86 

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

*********************** 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  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.6015 (ttp-170) cc_final: 0.5766 (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: 0.5900 (mmm160)
REVERT: A   74 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.6783 (mtt180)
REVERT: B   19 LYS cc_start: 0.7844 (tttt) cc_final: 0.7132 (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: 0.7440 (mmm)
REVERT: B   60 MET cc_start: 0.6768 (mtm) cc_final: 0.6351 (mtt)
REVERT: C   35 TYR cc_start: 0.7125 (m-80) cc_final: 0.6812 (m-80)
REVERT: C   42 MET cc_start: 0.8517 (mmm) cc_final: 0.8133 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1239
  time to fit residues: 12.9285
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  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3804 r_free = 0.3804 target = 0.138439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.114722 restraints weight = 4445.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.114653 restraints weight = 3268.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114711 restraints weight = 3379.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.115541 restraints weight = 2855.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.115601 restraints weight = 2619.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2811  Z= 0.140
  Angle     :  0.581   7.229   3811  Z= 0.310
  Chirality :  0.040   0.139    400
  Planarity :  0.004   0.035    481
  Dihedral  :  4.480  16.661    385
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 11.79 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.44), residues: 338
  helix:  1.46 (0.36), residues: 183
  sheet:  0.96 (0.72), residues: 45
  loop :  1.72 (0.64), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  99 
 TYR   0.012   0.001   TYR A  64 
 PHE   0.013   0.001   PHE C  32 
 TRP   0.013   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 2810)
  covalent geometry    : angle       0.58084 ( 3809)
  SS BOND              : bond        0.00222 (    1)
  SS BOND              : angle       0.19968 (    2)
  hydrogen bonds       : bond        0.04847 (  181)
  hydrogen bonds       : angle       4.46259 (  510)

*********************** 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  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7059 (mtt180)
REVERT: A  104 TYR cc_start: 0.6065 (m-80) cc_final: 0.5747 (m-10)
REVERT: B   19 LYS cc_start: 0.7468 (tttt) cc_final: 0.7245 (mtpt)
REVERT: C   35 TYR cc_start: 0.7678 (m-80) cc_final: 0.7356 (m-80)
REVERT: C   42 MET cc_start: 0.8533 (mmm) cc_final: 0.8084 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0954
  time to fit residues: 7.1640
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  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 3 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3732 r_free = 0.3732 target = 0.134407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.110384 restraints weight = 4266.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.110557 restraints weight = 3068.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.110790 restraints weight = 2981.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.111413 restraints weight = 2636.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.111551 restraints weight = 2477.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2811  Z= 0.173
  Angle     :  0.566   7.932   3811  Z= 0.300
  Chirality :  0.042   0.141    400
  Planarity :  0.004   0.034    481
  Dihedral  :  4.317  14.878    385
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.36 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.45), residues: 338
  helix:  1.61 (0.36), residues: 183
  sheet:  1.47 (0.67), residues: 52
  loop :  1.59 (0.68), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A   9 
 TYR   0.013   0.002   TYR A 104 
 PHE   0.017   0.002   PHE A  71 
 TRP   0.010   0.001   TRP A  36 
 HIS   0.004   0.002   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 2810)
  covalent geometry    : angle       0.56574 ( 3809)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.15675 (    2)
  hydrogen bonds       : bond        0.04669 (  181)
  hydrogen bonds       : angle       4.39926 (  510)

*********************** 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  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7157 (tpp) cc_final: 0.6569 (tpt)
REVERT: A   74 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.7035 (mtt180)
REVERT: A  104 TYR cc_start: 0.5947 (m-80) cc_final: 0.5468 (m-80)
REVERT: B   19 LYS cc_start: 0.7580 (tttt) cc_final: 0.7285 (mtpt)
REVERT: B   84 ARG cc_start: 0.7628 (tmt170) cc_final: 0.7121 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7702 (m-80) cc_final: 0.7305 (m-80)
REVERT: C   42 MET cc_start: 0.8479 (mmm) cc_final: 0.8262 (mmt)
  outliers start: 5
  outliers final: 3
  residues processed: 71
  average time/residue: 0.0978
  time to fit residues: 7.8323
Evaluate side-chains
  67 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
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  115 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0570
   chunk 7 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.135922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.111518 restraints weight = 4370.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.112332 restraints weight = 3981.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.112656 restraints weight = 3494.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.112998 restraints weight = 3331.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113102 restraints weight = 3010.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.4338

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= 0.140
  Angle     :  0.561  13.621   3811  Z= 0.282
  Chirality :  0.039   0.144    400
  Planarity :  0.004   0.030    481
  Dihedral  :  4.066  14.294    385
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.45), residues: 338
  helix:  1.78 (0.36), residues: 185
  sheet:  1.10 (0.70), residues: 45
  loop :  1.43 (0.65), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  53 
 TYR   0.012   0.001   TYR A  64 
 PHE   0.011   0.001   PHE A  71 
 TRP   0.007   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 2810)
  covalent geometry    : angle       0.56161 ( 3809)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       0.17977 (    2)
  hydrogen bonds       : bond        0.04137 (  181)
  hydrogen bonds       : angle       4.29552 (  510)

*********************** 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
  73 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 MET cc_start: 0.7143 (tpp) cc_final: 0.6665 (tpt)
REVERT: A   74 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.7226 (ttt180)
REVERT: B   84 ARG cc_start: 0.7522 (tmt170) cc_final: 0.7066 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7774 (m-80) cc_final: 0.7412 (m-80)
REVERT: C   42 MET cc_start: 0.8471 (mmm) cc_final: 0.8249 (mmt)
  outliers start: 7
  outliers final: 6
  residues processed: 69
  average time/residue: 0.0927
  time to fit residues: 7.3201
Evaluate side-chains
  65 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
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 C residue   21 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 27 optimal weight:    0.1980
   chunk 24 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.136073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.109988 restraints weight = 4264.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.112087 restraints weight = 3077.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113228 restraints weight = 2508.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.113736 restraints weight = 2231.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.113736 restraints weight = 2107.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.4581

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= 0.133
  Angle     :  0.539  11.260   3811  Z= 0.270
  Chirality :  0.039   0.141    400
  Planarity :  0.004   0.028    481
  Dihedral  :  3.956  13.459    385
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.45), residues: 338
  helix:  2.01 (0.36), residues: 185
  sheet:  1.27 (0.69), residues: 45
  loop :  1.30 (0.66), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  53 
 TYR   0.011   0.001   TYR A  64 
 PHE   0.012   0.001   PHE A  71 
 TRP   0.007   0.001   TRP A  36 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 2810)
  covalent geometry    : angle       0.53883 ( 3809)
  SS BOND              : bond        0.00066 (    1)
  SS BOND              : angle       0.08366 (    2)
  hydrogen bonds       : bond        0.03967 (  181)
  hydrogen bonds       : angle       4.30545 (  510)

*********************** 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
  72 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.7048 (tmm) cc_final: 0.6782 (tmm)
REVERT: A   57 MET cc_start: 0.7155 (tpp) cc_final: 0.6704 (tpt)
REVERT: A   74 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.7446 (ttt180)
REVERT: B   84 ARG cc_start: 0.7492 (tmt170) cc_final: 0.7068 (tpt-90)
REVERT: C   35 TYR cc_start: 0.7769 (m-80) cc_final: 0.7442 (m-80)
REVERT: C   42 MET cc_start: 0.8416 (mmm) cc_final: 0.8142 (mmt)
  outliers start: 10
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0880
  time to fit residues: 6.5931
Evaluate side-chains
  68 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
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   22 LEU
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0970
   chunk 10 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.136892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113133 restraints weight = 4370.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.112981 restraints weight = 3382.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.113314 restraints weight = 3359.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.113764 restraints weight = 2950.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113979 restraints weight = 2800.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.4790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2811  Z= 0.121
  Angle     :  0.550  15.418   3811  Z= 0.268
  Chirality :  0.039   0.142    400
  Planarity :  0.004   0.026    481
  Dihedral  :  3.797  13.148    385
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.45), residues: 338
  helix:  2.24 (0.37), residues: 180
  sheet:  1.55 (0.68), residues: 45
  loop :  1.31 (0.65), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  53 
 TYR   0.009   0.001   TYR A  64 
 PHE   0.010   0.001   PHE A  71 
 TRP   0.006   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2810)
  covalent geometry    : angle       0.55052 ( 3809)
  SS BOND              : bond        0.00080 (    1)
  SS BOND              : angle       0.13099 (    2)
  hydrogen bonds       : bond        0.03781 (  181)
  hydrogen bonds       : angle       4.21962 (  510)

*********************** 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: 10
    poor density    : 65
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.7107 (tmm) cc_final: 0.6807 (tmm)
REVERT: A   57 MET cc_start: 0.7146 (tpp) cc_final: 0.6714 (tpt)
REVERT: A   74 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.7025 (mtt180)
REVERT: C   35 TYR cc_start: 0.7805 (m-80) cc_final: 0.7512 (m-80)
REVERT: C   42 MET cc_start: 0.8426 (mmm) cc_final: 0.8130 (mmt)
  outliers start: 10
  outliers final: 7
  residues processed: 68
  average time/residue: 0.0884
  time to fit residues: 6.8908
Evaluate side-chains
  70 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
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   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   76 MET
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 5 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 15 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:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.135495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.112682 restraints weight = 4241.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.112022 restraints weight = 3912.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.112329 restraints weight = 3991.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.112581 restraints weight = 3416.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.112890 restraints weight = 3246.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.4907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2811  Z= 0.153
  Angle     :  0.577  14.419   3811  Z= 0.284
  Chirality :  0.041   0.177    400
  Planarity :  0.004   0.028    481
  Dihedral  :  3.882  13.806    385
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.50 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.45), residues: 338
  helix:  2.17 (0.37), residues: 180
  sheet:  1.46 (0.63), residues: 52
  loop :  1.25 (0.68), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A   9 
 TYR   0.012   0.001   TYR A  64 
 PHE   0.015   0.001   PHE A  71 
 TRP   0.007   0.001   TRP A  30 
 HIS   0.003   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 2810)
  covalent geometry    : angle       0.57666 ( 3809)
  SS BOND              : bond        0.00117 (    1)
  SS BOND              : angle       0.12117 (    2)
  hydrogen bonds       : bond        0.04138 (  181)
  hydrogen bonds       : angle       4.29705 (  510)

*********************** 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
  74 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A   11 MET cc_start: 0.7120 (tmm) cc_final: 0.6807 (tmm)
REVERT: A   57 MET cc_start: 0.7198 (tpp) cc_final: 0.6780 (tpt)
REVERT: A   74 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.7327 (ttt180)
REVERT: C   35 TYR cc_start: 0.7801 (m-80) cc_final: 0.7520 (m-80)
REVERT: C   42 MET cc_start: 0.8411 (mmm) cc_final: 0.8142 (mmt)
  outliers start: 11
  outliers final: 10
  residues processed: 65
  average time/residue: 0.0934
  time to fit residues: 7.0169
Evaluate side-chains
  72 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
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   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 15 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0030
   chunk 28 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.136297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113208 restraints weight = 4309.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.112848 restraints weight = 3719.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.112873 restraints weight = 4113.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113822 restraints weight = 3417.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113826 restraints weight = 3019.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.5039

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= 0.132
  Angle     :  0.554  13.211   3811  Z= 0.274
  Chirality :  0.040   0.157    400
  Planarity :  0.004   0.031    481
  Dihedral  :  3.800  12.856    385
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.45), residues: 338
  helix:  2.27 (0.37), residues: 180
  sheet:  1.45 (0.67), residues: 45
  loop :  1.08 (0.63), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   9 
 TYR   0.011   0.001   TYR A  64 
 PHE   0.012   0.001   PHE A  71 
 TRP   0.007   0.001   TRP B  94 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 2810)
  covalent geometry    : angle       0.55422 ( 3809)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       0.31877 (    2)
  hydrogen bonds       : bond        0.03878 (  181)
  hydrogen bonds       : angle       4.20570 (  510)

*********************** 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
  75 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   11 MET cc_start: 0.7118 (tmm) cc_final: 0.6775 (tmm)
REVERT: A   57 MET cc_start: 0.7143 (tpp) cc_final: 0.6740 (tpt)
REVERT: A   74 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.7359 (ttt180)
REVERT: C   35 TYR cc_start: 0.7771 (m-80) cc_final: 0.7492 (m-80)
REVERT: C   42 MET cc_start: 0.8440 (mmm) cc_final: 0.8147 (mmt)
REVERT: C   61 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7630 (ttm170)
  outliers start: 11
  outliers final: 9
  residues processed: 67
  average time/residue: 0.1064
  time to fit residues: 8.0749
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  : 0.102 
-------------------------------------------------------------------------------
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   88 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   61 ARG
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 7 optimal weight:    0.4980
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0070
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.135907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.112338 restraints weight = 4286.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.112451 restraints weight = 3229.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.112707 restraints weight = 3105.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.113487 restraints weight = 2754.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.113585 restraints weight = 2543.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.5131

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= 0.121
  Angle     :  0.552  12.953   3811  Z= 0.271
  Chirality :  0.039   0.154    400
  Planarity :  0.003   0.030    481
  Dihedral  :  3.779  13.599    385
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.45), residues: 338
  helix:  2.30 (0.37), residues: 181
  sheet:  1.43 (0.62), residues: 52
  loop :  1.20 (0.67), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   9 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.011   0.001   PHE A  71 
 TRP   0.006   0.001   TRP B  94 
 HIS   0.002   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 2810)
  covalent geometry    : angle       0.55243 ( 3809)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       0.28708 (    2)
  hydrogen bonds       : bond        0.03749 (  181)
  hydrogen bonds       : angle       4.13855 (  510)

*********************** 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
  77 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.7126 (tmm) cc_final: 0.6797 (tmm)
REVERT: A   57 MET cc_start: 0.7117 (tpp) cc_final: 0.6728 (tpt)
REVERT: A   74 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.7502 (ttt180)
REVERT: C   35 TYR cc_start: 0.7800 (m-80) cc_final: 0.7527 (m-80)
REVERT: C   42 MET cc_start: 0.8468 (mmm) cc_final: 0.8222 (mmt)
REVERT: C   61 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7655 (ttm170)
REVERT: C   90 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7728 (tm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0950
  time to fit residues: 7.5838
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  : 0.181 
-------------------------------------------------------------------------------
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   54 CYS
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   76 MET
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain C residue   21 LEU
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:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 2 optimal weight:    0.1980
   chunk 17 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN
C   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.136330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.112537 restraints weight = 4214.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.112758 restraints weight = 3180.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.112983 restraints weight = 3038.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.113753 restraints weight = 2733.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113819 restraints weight = 2523.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
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   0.027   2811  Z= 0.119
  Angle     :  0.572  16.018   3811  Z= 0.274
  Chirality :  0.039   0.154    400
  Planarity :  0.003   0.030    481
  Dihedral  :  3.716  13.351    385
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.79 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.45), residues: 338
  helix:  2.32 (0.37), residues: 181
  sheet:  1.53 (0.62), residues: 52
  loop :  1.20 (0.67), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   9 
 TYR   0.009   0.001   TYR A  64 
 PHE   0.010   0.001   PHE A  71 
 TRP   0.006   0.001   TRP B  94 
 HIS   0.003   0.001   HIS B  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2810)
  covalent geometry    : angle       0.57252 ( 3809)
  SS BOND              : bond        0.00140 (    1)
  SS BOND              : angle       0.29938 (    2)
  hydrogen bonds       : bond        0.03655 (  181)
  hydrogen bonds       : angle       4.12986 (  510)

********************** 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: 10
    poor density    : 65
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   11 MET cc_start: 0.7110 (tmm) cc_final: 0.6784 (tmm)
REVERT: A   57 MET cc_start: 0.7119 (tpp) cc_final: 0.6733 (tpt)
REVERT: A   74 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.7474 (ttt180)
REVERT: C   35 TYR cc_start: 0.7792 (m-80) cc_final: 0.7529 (m-80)
REVERT: C   42 MET cc_start: 0.8489 (mmm) cc_final: 0.8252 (mmt)
REVERT: C   61 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7666 (ttm170)
  outliers start: 10
  outliers final: 9
  residues processed: 68
  average time/residue: 0.0989
  time to fit residues: 7.6683
Evaluate side-chains
  74 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
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   88 VAL
Chi-restraints excluded: chain C residue   21 LEU
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 15 optimal weight:    0.0030
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5590

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.136252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.112078 restraints weight = 4193.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.112162 restraints weight = 3050.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.112423 restraints weight = 2941.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.113402 restraints weight = 2611.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113486 restraints weight = 2411.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.5294

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= 0.122
  Angle     :  0.581  16.084   3811  Z= 0.278
  Chirality :  0.040   0.154    400
  Planarity :  0.004   0.030    481
  Dihedral  :  3.755  13.658    385
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.45), residues: 338
  helix:  2.34 (0.37), residues: 181
  sheet:  1.48 (0.63), residues: 52
  loop :  1.19 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   9 
 TYR   0.010   0.001   TYR A  64 
 PHE   0.011   0.001   PHE A  71 
 TRP   0.006   0.001   TRP B  94 
 HIS   0.002   0.001   HIS B  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 2810)
  covalent geometry    : angle       0.58116 ( 3809)
  SS BOND              : bond        0.00193 (    1)
  SS BOND              : angle       0.39752 (    2)
  hydrogen bonds       : bond        0.03659 (  181)
  hydrogen bonds       : angle       4.15021 (  510)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 868.92 seconds
wall clock time: 15 minutes 41.22 seconds (941.22 seconds total)