Starting phenix.real_space_refine
on Tue Feb  3 12:55:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pm9_71729/02_2026/9pm9_71729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pm9_71729/02_2026/9pm9_71729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pm9_71729/02_2026/9pm9_71729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pm9_71729/02_2026/9pm9_71729.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pm9_71729/02_2026/9pm9_71729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pm9_71729/02_2026/9pm9_71729.map"
  }
  resolution = 2.75
  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=   0.003 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      12      5.16       5
     C    1558      2.51       5
     N     440      2.21       5
     O     502      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2515
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 2483
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2483
          Classifications: {'peptide': 326}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 314}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'G2P': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.52, per 1000 atoms: 0.21
  Number of scatterers: 2515
  At special positions: 0
  Unit cell: (59.184, 60.828, 96.996, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P       3     15.00
     O     502      8.00
     N     440      7.00
     C    1558      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        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: 0.19
  Conformation dependent library (CDL) restraints added in 61.7 milliseconds
  

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  590

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 1 sheets defined
      45.7% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'C' and resid 12 through 20
    Processing helix  chain 'C' and resid 22 through 28
    Processing helix  chain 'C' and resid 49 through 51
      No H-bonds generated for 'chain 'C' and resid 49 through 51'
    Processing helix  chain 'C' and resid 74 through 89
      Proline residue:  C  83  - end of helix
    Processing helix  chain 'C' and resid 105 through 121
      Proline residue:  C 111  - end of helix
    Processing helix  chain 'C' and resid 134 through 156
      removed outlier: 3.518A  pdb=" N   LYS C 156 " --> pdb=" O   ALA C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 171
    Processing helix  chain 'C' and resid 172 through 191
    Processing helix  chain 'C' and resid 199 through 208
    Processing helix  chain 'C' and resid 209 through 212
    Processing helix  chain 'C' and resid 228 through 232
      removed outlier: 3.653A  pdb=" N   LYS C 232 " --> pdb=" O   GLU C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 303
      removed outlier: 3.625A  pdb=" N   ALA C 303 " --> pdb=" O   GLU C 299 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 318
    Processing sheet with id=AA1, first strand: chain 'C' and resid 53 through 55
      removed outlier: 8.153A  pdb=" N   TYR C  54 " --> pdb=" O   MET C  33 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   TYR C  35 " --> pdb=" O   TYR C  54 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   VAL C   6 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   THR C  34 " --> pdb=" O   VAL C   6 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   ILE C   8 " --> pdb=" O   THR C  34 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL C  36 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   ALA C  10 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   HIS C   7 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   VAL C  98 " --> pdb=" O   HIS C   7 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   TRP C   9 " --> pdb=" O   VAL C  98 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   SER C 100 " --> pdb=" O   TRP C   9 " (cutoff:3.500A)
      removed outlier: 8.671A  pdb=" N   VAL C  11 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ASN C  95 " --> pdb=" O   VAL C 125 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   CYS C 127 " --> pdb=" O   ASN C  95 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL C  97 " --> pdb=" O   CYS C 127 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   VAL C 129 " --> pdb=" O   VAL C  97 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   PHE C  99 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ILE C 160 " --> pdb=" O   VAL C 124 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   TYR C 163 " --> pdb=" O   LEU C 222 " (cutoff:3.500A)
      removed outlier: 8.940A  pdb=" N   THR C 224 " --> pdb=" O   TYR C 163 " (cutoff:3.500A)
      removed outlier: 13.574A  pdb=" N   MET C 165 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 18.689A  pdb=" N   MET C 226 " --> pdb=" O   MET C 165 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA C 239 " --> pdb=" O   LEU C 278 " (cutoff:3.500A)

    115 hydrogen bonds defined for protein.
    330 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: 0.21

  Time building geometry restraints manager: 0.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 862
        1.35 -     1.47: 574
        1.47 -     1.60: 1101
        1.60 -     1.72: 3
        1.72 -     1.85: 19
  Bond restraints: 2559
  Sorted by residual:
  bond pdb=" CA  HIS C 209 "
       pdb=" C   HIS C 209 "
    ideal  model  delta    sigma   weight residual
    1.522  1.529 -0.007 1.26e-02 6.30e+03 3.39e-01
  bond pdb=" C   HIS C 209 "
       pdb=" N   PRO C 210 "
    ideal  model  delta    sigma   weight residual
    1.336  1.342 -0.006 1.08e-02 8.57e+03 3.36e-01
  bond pdb=" CB  PRO C 210 "
       pdb=" CG  PRO C 210 "
    ideal  model  delta    sigma   weight residual
    1.492  1.465  0.027 5.00e-02 4.00e+02 2.93e-01
  bond pdb=" N   ASP C 247 "
       pdb=" CA  ASP C 247 "
    ideal  model  delta    sigma   weight residual
    1.460  1.467 -0.007 1.42e-02 4.96e+03 2.68e-01
  bond pdb=" C   ILE C  82 "
       pdb=" N   PRO C  83 "
    ideal  model  delta    sigma   weight residual
    1.335  1.341 -0.007 1.28e-02 6.10e+03 2.59e-01
  ... (remaining 2554 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 3406
        1.08 -     2.16: 46
        2.16 -     3.24: 12
        3.24 -     4.32: 1
        4.32 -     5.40: 2
  Bond angle restraints: 3467
  Sorted by residual:
  angle pdb=" C   LYS C 246 "
        pdb=" N   ASP C 247 "
        pdb=" CA  ASP C 247 "
      ideal   model   delta    sigma   weight residual
     122.82  125.02   -2.20 1.42e+00 4.96e-01 2.41e+00
  angle pdb=" C   HIS C 209 "
        pdb=" N   PRO C 210 "
        pdb=" CD  PRO C 210 "
      ideal   model   delta    sigma   weight residual
     125.00  130.40   -5.40 4.10e+00 5.95e-02 1.73e+00
  angle pdb=" CA  HIS C 209 "
        pdb=" C   HIS C 209 "
        pdb=" N   PRO C 210 "
      ideal   model   delta    sigma   weight residual
     120.93  122.29   -1.36 1.06e+00 8.90e-01 1.65e+00
  angle pdb=" N   HIS C 209 "
        pdb=" CA  HIS C 209 "
        pdb=" C   HIS C 209 "
      ideal   model   delta    sigma   weight residual
     113.16  114.75   -1.59 1.42e+00 4.96e-01 1.25e+00
  angle pdb=" C   ILE C  82 "
        pdb=" N   PRO C  83 "
        pdb=" CD  PRO C  83 "
      ideal   model   delta    sigma   weight residual
     125.00  129.51   -4.51 4.10e+00 5.95e-02 1.21e+00
  ... (remaining 3462 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 1465
       17.31 -    34.62: 71
       34.62 -    51.93: 9
       51.93 -    69.24: 3
       69.24 -    86.55: 1
  Dihedral angle restraints: 1549
    sinusoidal: 627
      harmonic: 922
  Sorted by residual:
  dihedral pdb=" CB  GLU C  73 "
           pdb=" CG  GLU C  73 "
           pdb=" CD  GLU C  73 "
           pdb=" OE1 GLU C  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.55   86.55     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" N   GLN C   5 "
           pdb=" CA  GLN C   5 "
           pdb=" CB  GLN C   5 "
           pdb=" CG  GLN C   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.76   55.76     3      1.50e+01 4.44e-03 9.36e+00
  dihedral pdb=" N   ILE C 298 "
           pdb=" CA  ILE C 298 "
           pdb=" CB  ILE C 298 "
           pdb=" CG1 ILE C 298 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.56   47.56     3      1.50e+01 4.44e-03 8.51e+00
  ... (remaining 1546 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 248
       0.031 -    0.062: 98
       0.062 -    0.094: 18
       0.094 -    0.125: 20
       0.125 -    0.156: 1
  Chirality restraints: 385
  Sorted by residual:
  chirality pdb=" CA  HIS C 209 "
            pdb=" N   HIS C 209 "
            pdb=" C   HIS C 209 "
            pdb=" CB  HIS C 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.08e-01
  chirality pdb=" CA  VAL C 125 "
            pdb=" N   VAL C 125 "
            pdb=" C   VAL C 125 "
            pdb=" CB  VAL C 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.61e-01
  chirality pdb=" CA  ILE C 270 "
            pdb=" N   ILE C 270 "
            pdb=" C   ILE C 270 "
            pdb=" CB  ILE C 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 382 not shown)

  Planarity restraints: 455
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 244 "   -0.021 5.00e-02 4.00e+02   3.15e-02 1.59e+00
        pdb=" N   PRO C 245 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C 245 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 245 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 110 "   -0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO C 111 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C 111 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 111 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 268 "    0.017 5.00e-02 4.00e+02   2.58e-02 1.07e+00
        pdb=" N   PRO C 269 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO C 269 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 269 "    0.014 5.00e-02 4.00e+02
  ... (remaining 452 not shown)

  Histogram of nonbonded interaction distances:
        2.58 -     3.04: 1584
        3.04 -     3.51: 2537
        3.51 -     3.97: 3890
        3.97 -     4.44: 4716
        4.44 -     4.90: 7425
  Nonbonded interactions: 20152
  Sorted by model distance:
  nonbonded pdb=" C4  G2P C 401 "
            pdb=" N1  G2P C 401 "
     model   vdw
     2.576 2.672
  nonbonded pdb=" N   THR C 218 "
            pdb=" O   THR C 218 "
     model   vdw
     2.634 2.496
  nonbonded pdb=" O2' G2P C 401 "
            pdb=" O3' G2P C 401 "
     model   vdw
     2.660 2.432
  nonbonded pdb=" N   ALA C 239 "
            pdb=" O   ALA C 239 "
     model   vdw
     2.663 2.496
  nonbonded pdb=" N   HIS C  31 "
            pdb=" O   HIS C  31 "
     model   vdw
     2.676 2.496
  ... (remaining 20147 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.660
  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:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.930
  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:5.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
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      :  0.003   0.027   2559  Z= 0.114
  Angle     :  0.385   5.395   3467  Z= 0.202
  Chirality :  0.040   0.156    385
  Planarity :  0.003   0.032    455
  Dihedral  : 10.349  86.552    959
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  3.37 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.62 (0.48), residues: 324
  helix:  1.63 (0.45), residues: 139
  sheet:  1.28 (0.66), residues: 76
  loop :  0.31 (0.60), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 120 
 TYR   0.008   0.001   TYR C  35 
 PHE   0.006   0.001   PHE C 240 
 TRP   0.004   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 2559)
  covalent geometry    : angle       0.38529 ( 3467)
  hydrogen bonds       : bond        0.13381 (  115)
  hydrogen bonds       : angle       5.83011 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: C   57 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7421 (mttt)
REVERT: C   72 ASP cc_start: 0.8131 (t0) cc_final: 0.7889 (t0)
REVERT: C  119 GLU cc_start: 0.8644 (tt0) cc_final: 0.8276 (tt0)
REVERT: C  305 GLN cc_start: 0.8839 (mt0) cc_final: 0.8547 (tt0)
REVERT: C  325 LEU cc_start: 0.7487 (mt) cc_final: 0.7038 (pt)
  outliers start: 2
  outliers final: 2
  residues processed: 49
  average time/residue: 0.5582
  time to fit residues: 27.9732
Evaluate side-chains
  34 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  264 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C 209 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.104500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.087842 restraints weight = 4106.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.59
r_work: 0.3026 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2559  Z= 0.127
  Angle     :  0.445   5.365   3467  Z= 0.234
  Chirality :  0.042   0.156    385
  Planarity :  0.004   0.050    455
  Dihedral  :  7.900  66.234    384
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  7.87 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.49), residues: 324
  helix:  1.84 (0.45), residues: 145
  sheet:  1.52 (0.66), residues: 76
  loop :  0.24 (0.60), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  62 
 TYR   0.017   0.002   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.004   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2559)
  covalent geometry    : angle       0.44500 ( 3467)
  hydrogen bonds       : bond        0.03783 (  115)
  hydrogen bonds       : angle       4.49810 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.099 
Fit side-chains
REVERT: C   54 TYR cc_start: 0.8282 (t80) cc_final: 0.8080 (t80)
REVERT: C   57 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7371 (mttp)
REVERT: C   72 ASP cc_start: 0.8087 (t0) cc_final: 0.7858 (t0)
REVERT: C  119 GLU cc_start: 0.8619 (tt0) cc_final: 0.8258 (tt0)
REVERT: C  305 GLN cc_start: 0.8846 (mt0) cc_final: 0.8495 (tt0)
REVERT: C  325 LEU cc_start: 0.7595 (mt) cc_final: 0.7019 (pt)
  outliers start: 6
  outliers final: 5
  residues processed: 39
  average time/residue: 0.4167
  time to fit residues: 16.7013
Evaluate side-chains
  37 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 13 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.104100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.087325 restraints weight = 4108.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.60
r_work: 0.3027 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2559  Z= 0.141
  Angle     :  0.437   5.430   3467  Z= 0.230
  Chirality :  0.042   0.165    385
  Planarity :  0.004   0.034    455
  Dihedral  :  7.951  66.866    382
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  9.36 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.88 (0.48), residues: 324
  helix:  1.90 (0.45), residues: 145
  sheet:  1.45 (0.66), residues: 76
  loop :  0.24 (0.60), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  62 
 TYR   0.015   0.002   TYR C  54 
 PHE   0.009   0.001   PHE C 240 
 TRP   0.005   0.001   TRP C   9 
 HIS   0.005   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 2559)
  covalent geometry    : angle       0.43666 ( 3467)
  hydrogen bonds       : bond        0.03595 (  115)
  hydrogen bonds       : angle       4.27107 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.106 
Fit side-chains
REVERT: C   44 ARG cc_start: 0.8327 (mmt180) cc_final: 0.8052 (mmt90)
REVERT: C   57 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7404 (mttp)
REVERT: C   72 ASP cc_start: 0.8084 (t0) cc_final: 0.7861 (t0)
REVERT: C  119 GLU cc_start: 0.8600 (tt0) cc_final: 0.8244 (tt0)
REVERT: C  305 GLN cc_start: 0.8875 (mt0) cc_final: 0.8497 (tt0)
REVERT: C  325 LEU cc_start: 0.7641 (mt) cc_final: 0.7043 (pt)
  outliers start: 8
  outliers final: 5
  residues processed: 39
  average time/residue: 0.5224
  time to fit residues: 20.9253
Evaluate side-chains
  35 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 25 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   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 = 0.3422 r_free = 0.3422 target = 0.106176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.089442 restraints weight = 4115.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.59
r_work: 0.3052 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2559  Z= 0.103
  Angle     :  0.402   5.370   3467  Z= 0.213
  Chirality :  0.041   0.156    385
  Planarity :  0.005   0.068    455
  Dihedral  :  7.796  66.215    382
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 10.86 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  2.10 (0.49), residues: 324
  helix:  2.06 (0.45), residues: 147
  sheet:  1.60 (0.65), residues: 75
  loop :  0.32 (0.61), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  62 
 TYR   0.010   0.001   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.004   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 2559)
  covalent geometry    : angle       0.40222 ( 3467)
  hydrogen bonds       : bond        0.03139 (  115)
  hydrogen bonds       : angle       3.95814 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.108 
Fit side-chains
REVERT: C   44 ARG cc_start: 0.8321 (mmt180) cc_final: 0.8052 (mmt90)
REVERT: C   57 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7357 (mttp)
REVERT: C   72 ASP cc_start: 0.8059 (t0) cc_final: 0.7851 (t0)
REVERT: C  119 GLU cc_start: 0.8548 (tt0) cc_final: 0.8172 (tt0)
REVERT: C  226 MET cc_start: 0.8593 (mtm) cc_final: 0.8062 (mtm)
REVERT: C  305 GLN cc_start: 0.8854 (mt0) cc_final: 0.8502 (tt0)
REVERT: C  325 LEU cc_start: 0.7643 (mt) cc_final: 0.7099 (pt)
  outliers start: 7
  outliers final: 5
  residues processed: 41
  average time/residue: 0.5931
  time to fit residues: 24.9043
Evaluate side-chains
  36 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.105035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.088277 restraints weight = 4025.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.56
r_work: 0.3039 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2559  Z= 0.120
  Angle     :  0.409   5.399   3467  Z= 0.216
  Chirality :  0.042   0.160    385
  Planarity :  0.004   0.042    455
  Dihedral  :  7.834  66.416    382
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.11 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  2.10 (0.49), residues: 324
  helix:  2.09 (0.45), residues: 147
  sheet:  1.57 (0.65), residues: 75
  loop :  0.28 (0.60), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  62 
 TYR   0.016   0.002   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.004   0.001   TRP C   9 
 HIS   0.004   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 2559)
  covalent geometry    : angle       0.40947 ( 3467)
  hydrogen bonds       : bond        0.03217 (  115)
  hydrogen bonds       : angle       3.91550 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.103 
Fit side-chains
REVERT: C   44 ARG cc_start: 0.8318 (mmt180) cc_final: 0.8035 (mmt90)
REVERT: C   57 LYS cc_start: 0.7692 (mtmt) cc_final: 0.7316 (mttp)
REVERT: C   72 ASP cc_start: 0.8091 (t0) cc_final: 0.7869 (t0)
REVERT: C  119 GLU cc_start: 0.8552 (tt0) cc_final: 0.8194 (tt0)
REVERT: C  305 GLN cc_start: 0.8874 (mt0) cc_final: 0.8506 (tt0)
REVERT: C  325 LEU cc_start: 0.7652 (mt) cc_final: 0.7095 (pt)
  outliers start: 6
  outliers final: 4
  residues processed: 36
  average time/residue: 0.5552
  time to fit residues: 20.5144
Evaluate side-chains
  34 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.105188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.088423 restraints weight = 4071.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.59
r_work: 0.3043 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2559  Z= 0.114
  Angle     :  0.415   5.377   3467  Z= 0.218
  Chirality :  0.041   0.159    385
  Planarity :  0.005   0.082    455
  Dihedral  :  7.815  66.289    382
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.23 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.49), residues: 324
  helix:  2.14 (0.45), residues: 147
  sheet:  1.48 (0.65), residues: 75
  loop :  0.28 (0.61), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C  62 
 TYR   0.018   0.002   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.004   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 2559)
  covalent geometry    : angle       0.41487 ( 3467)
  hydrogen bonds       : bond        0.03135 (  115)
  hydrogen bonds       : angle       3.85762 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.115 
Fit side-chains
REVERT: C   44 ARG cc_start: 0.8284 (mmt180) cc_final: 0.8005 (mmt90)
REVERT: C   57 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7380 (mttp)
REVERT: C   72 ASP cc_start: 0.8084 (t0) cc_final: 0.7877 (t0)
REVERT: C  119 GLU cc_start: 0.8520 (tt0) cc_final: 0.8176 (tt0)
REVERT: C  305 GLN cc_start: 0.8840 (mt0) cc_final: 0.8496 (tt0)
REVERT: C  325 LEU cc_start: 0.7648 (mt) cc_final: 0.7130 (pt)
  outliers start: 5
  outliers final: 4
  residues processed: 37
  average time/residue: 0.5488
  time to fit residues: 20.8536
Evaluate side-chains
  35 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 12 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.105323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.088779 restraints weight = 4035.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.56
r_work: 0.3044 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2559  Z= 0.105
  Angle     :  0.403   5.364   3467  Z= 0.213
  Chirality :  0.041   0.158    385
  Planarity :  0.004   0.053    455
  Dihedral  :  7.739  65.886    382
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.36 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  2.09 (0.49), residues: 324
  helix:  2.18 (0.45), residues: 147
  sheet:  1.36 (0.64), residues: 75
  loop :  0.29 (0.61), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  62 
 TYR   0.024   0.002   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.003   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 2559)
  covalent geometry    : angle       0.40321 ( 3467)
  hydrogen bonds       : bond        0.03046 (  115)
  hydrogen bonds       : angle       3.77405 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.102 
Fit side-chains
REVERT: C   44 ARG cc_start: 0.8306 (mmt180) cc_final: 0.8000 (mmt90)
REVERT: C   57 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7328 (mttp)
REVERT: C   72 ASP cc_start: 0.8074 (t0) cc_final: 0.7857 (t70)
REVERT: C  119 GLU cc_start: 0.8509 (tt0) cc_final: 0.8140 (tt0)
REVERT: C  305 GLN cc_start: 0.8865 (mt0) cc_final: 0.8493 (tt0)
REVERT: C  325 LEU cc_start: 0.7698 (mt) cc_final: 0.7168 (pt)
  outliers start: 6
  outliers final: 5
  residues processed: 37
  average time/residue: 0.3851
  time to fit residues: 14.6352
Evaluate side-chains
  35 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0970
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.105165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.088440 restraints weight = 4097.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.57
r_work: 0.3053 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2559  Z= 0.119
  Angle     :  0.447   5.775   3467  Z= 0.234
  Chirality :  0.042   0.159    385
  Planarity :  0.005   0.085    455
  Dihedral  :  7.772  65.919    382
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.36 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  2.04 (0.48), residues: 324
  helix:  2.18 (0.45), residues: 147
  sheet:  1.28 (0.64), residues: 75
  loop :  0.24 (0.60), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG C  62 
 TYR   0.025   0.002   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.004   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2559)
  covalent geometry    : angle       0.44748 ( 3467)
  hydrogen bonds       : bond        0.03098 (  115)
  hydrogen bonds       : angle       3.77627 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.063 
Fit side-chains
REVERT: C   44 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7971 (mmt90)
REVERT: C   57 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7384 (mttp)
REVERT: C   72 ASP cc_start: 0.8059 (t0) cc_final: 0.7852 (t70)
REVERT: C  119 GLU cc_start: 0.8488 (tt0) cc_final: 0.8130 (tt0)
REVERT: C  305 GLN cc_start: 0.8835 (mt0) cc_final: 0.8492 (tt0)
REVERT: C  325 LEU cc_start: 0.7684 (mt) cc_final: 0.7159 (pt)
  outliers start: 6
  outliers final: 5
  residues processed: 36
  average time/residue: 0.4457
  time to fit residues: 16.4412
Evaluate side-chains
  35 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 15 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.105079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.088350 restraints weight = 4138.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.58
r_work: 0.3043 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2559  Z= 0.120
  Angle     :  0.439   6.222   3467  Z= 0.231
  Chirality :  0.042   0.159    385
  Planarity :  0.004   0.054    455
  Dihedral  :  7.749  65.961    382
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.73 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  2.00 (0.48), residues: 324
  helix:  2.18 (0.45), residues: 147
  sheet:  1.21 (0.64), residues: 75
  loop :  0.23 (0.61), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  62 
 TYR   0.028   0.002   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.003   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 2559)
  covalent geometry    : angle       0.43893 ( 3467)
  hydrogen bonds       : bond        0.03118 (  115)
  hydrogen bonds       : angle       3.77097 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.104 
Fit side-chains
REVERT: C   44 ARG cc_start: 0.8261 (mmt180) cc_final: 0.7934 (mmt90)
REVERT: C   57 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7387 (mttp)
REVERT: C   72 ASP cc_start: 0.8066 (t0) cc_final: 0.7850 (t0)
REVERT: C  119 GLU cc_start: 0.8511 (tt0) cc_final: 0.8153 (tt0)
REVERT: C  305 GLN cc_start: 0.8850 (mt0) cc_final: 0.8471 (tt0)
REVERT: C  325 LEU cc_start: 0.7681 (mt) cc_final: 0.7131 (pt)
  outliers start: 5
  outliers final: 5
  residues processed: 35
  average time/residue: 0.4121
  time to fit residues: 14.8359
Evaluate side-chains
  35 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0670
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7518

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.105259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.088402 restraints weight = 4133.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.60
r_work: 0.3032 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2559  Z= 0.122
  Angle     :  0.465   6.376   3467  Z= 0.239
  Chirality :  0.042   0.159    385
  Planarity :  0.005   0.090    455
  Dihedral  :  7.769  66.026    382
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.73 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.96 (0.48), residues: 324
  helix:  2.17 (0.45), residues: 147
  sheet:  1.17 (0.64), residues: 75
  loop :  0.19 (0.60), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG C  62 
 TYR   0.031   0.002   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.003   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2559)
  covalent geometry    : angle       0.46472 ( 3467)
  hydrogen bonds       : bond        0.03106 (  115)
  hydrogen bonds       : angle       3.76733 (  330)

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

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

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  648 Ramachandran restraints generated.
    324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.100 
Fit side-chains
REVERT: C   44 ARG cc_start: 0.8190 (mmt180) cc_final: 0.7830 (mmt90)
REVERT: C   57 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7337 (mttp)
REVERT: C   72 ASP cc_start: 0.8078 (t0) cc_final: 0.7860 (t70)
REVERT: C  119 GLU cc_start: 0.8528 (tt0) cc_final: 0.8158 (tt0)
REVERT: C  305 GLN cc_start: 0.8876 (mt0) cc_final: 0.8484 (tt0)
REVERT: C  325 LEU cc_start: 0.7668 (mt) cc_final: 0.7124 (pt)
  outliers start: 5
  outliers final: 5
  residues processed: 34
  average time/residue: 0.4070
  time to fit residues: 14.2035
Evaluate side-chains
  35 residues out of total 268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0980
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0770
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.6740

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.105509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.088747 restraints weight = 4099.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.59
r_work: 0.3041 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2559  Z= 0.113
  Angle     :  0.438   6.741   3467  Z= 0.230
  Chirality :  0.041   0.158    385
  Planarity :  0.004   0.057    455
  Dihedral  :  7.715  65.836    382
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.73 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.96 (0.48), residues: 324
  helix:  2.19 (0.45), residues: 147
  sheet:  1.13 (0.64), residues: 75
  loop :  0.18 (0.60), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  62 
 TYR   0.028   0.002   TYR C  54 
 PHE   0.008   0.001   PHE C 240 
 TRP   0.004   0.001   TRP C   9 
 HIS   0.003   0.001   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 2559)
  covalent geometry    : angle       0.43801 ( 3467)
  hydrogen bonds       : bond        0.03048 (  115)
  hydrogen bonds       : angle       3.73389 (  330)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1050.84 seconds
wall clock time: 18 minutes 40.64 seconds (1120.64 seconds total)