Starting phenix.real_space_refine
on Fri Aug 22 13:39:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5d_37286/08_2025/8w5d_37286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5d_37286/08_2025/8w5d_37286.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5d_37286/08_2025/8w5d_37286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5d_37286/08_2025/8w5d_37286.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5d_37286/08_2025/8w5d_37286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5d_37286/08_2025/8w5d_37286.map"
  }
  resolution = 4.3
  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=   0.019 sd=   0.087
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      10      5.16       5
     C    2152      2.51       5
     N     594      2.21       5
     O     675      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3431
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 869
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "C"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 944
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 8, 'TRANS': 118}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 674
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 6, 'TRANS': 83}
          Chain breaks: 2
  Restraints were copied for chains:
    c
  Time building chain proxies: 0.92, per 1000 atoms: 0.27
  Number of scatterers: 3431
  At special positions: 0
  Unit cell: (92.4, 79.2, 81.84, 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      10     16.00
     O     675      8.00
     N     594      7.00
     C    2152      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: 0.21
  Conformation dependent library (CDL) restraints added in 95.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  836

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 9 sheets defined
      12.1% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'H' and resid 31 through 33
      No H-bonds generated for 'chain 'H' and resid 31 through 33'
    Processing helix  chain 'c' and resid 101 through 116
      removed outlier: 3.820A  pdb=" N   ARG c 105 " --> pdb=" O   THR c 101 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 118 through 127
    Processing helix  chain 'C' and resid 101 through 116
      removed outlier: 3.820A  pdb=" N   ARG C 105 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 127
    Processing sheet with id=AA1, first strand: chain 'H' and resid 21 through 23
    Processing sheet with id=AA2, first strand: chain 'H' and resid 54 through 55
      removed outlier: 3.797A  pdb=" N   ILE H  54 " --> pdb=" O   VAL H  37 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 104 through 106
      removed outlier: 3.552A  pdb=" N   TYR H 105 " --> pdb=" O   THR C   7 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'c' and resid 22 through 26
      removed outlier: 4.995A  pdb=" N   SER c  34 " --> pdb=" O   ARG c  24 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   SER C  34 " --> pdb=" O   ARG C  24 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'c' and resid 72 through 74
      removed outlier: 7.610A  pdb=" N   THR c  72 " --> pdb=" O   THR c  85 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR c  85 " --> pdb=" O   THR c  72 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 74
      removed outlier: 7.610A  pdb=" N   THR C  72 " --> pdb=" O   THR C  85 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   THR C  85 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA8, first strand: chain 'L' and resid 52 through 53
      removed outlier: 3.923A  pdb=" N   LYS L  52 " --> pdb=" O   GLN L  44 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   GLN L  44 " --> pdb=" O   LYS L  52 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLN L  97 " --> pdb=" O   ASN L  41 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLN L  96 " --> pdb=" O   GLY L 106 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLY L 106 " --> pdb=" O   GLN L  96 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 71 through 72

    95 hydrogen bonds defined for protein.
    231 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: 0.41

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 788
        1.33 -     1.45: 730
        1.45 -     1.57: 1964
        1.57 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 3494
  Sorted by residual:
  bond pdb=" CA  SER L   3 "
       pdb=" C   SER L   3 "
    ideal  model  delta    sigma   weight residual
    1.522  1.480  0.042 1.24e-02 6.50e+03 1.14e+01
  bond pdb=" CA  ASP L   4 "
       pdb=" C   ASP L   4 "
    ideal  model  delta    sigma   weight residual
    1.522  1.481  0.041 1.24e-02 6.50e+03 1.07e+01
  bond pdb=" CA  ASP L   4 "
       pdb=" CB  ASP L   4 "
    ideal  model  delta    sigma   weight residual
    1.535  1.475  0.060 1.90e-02 2.77e+03 1.01e+01
  bond pdb=" CB  ASP L   4 "
       pdb=" CG  ASP L   4 "
    ideal  model  delta    sigma   weight residual
    1.516  1.449  0.067 2.50e-02 1.60e+03 7.17e+00
  bond pdb=" C   VAL L 101 "
       pdb=" N   PRO L 102 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.91e+00
  ... (remaining 3489 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.02: 4602
        3.02 -     6.05: 124
        6.05 -     9.07: 17
        9.07 -    12.10: 4
       12.10 -    15.12: 1
  Bond angle restraints: 4748
  Sorted by residual:
  angle pdb=" CA  LYS H  78 "
        pdb=" CB  LYS H  78 "
        pdb=" CG  LYS H  78 "
      ideal   model   delta    sigma   weight residual
     114.10  123.26   -9.16 2.00e+00 2.50e-01 2.10e+01
  angle pdb=" CA  LEU H  48 "
        pdb=" CB  LEU H  48 "
        pdb=" CG  LEU H  48 "
      ideal   model   delta    sigma   weight residual
     116.30  131.42  -15.12 3.50e+00 8.16e-02 1.87e+01
  angle pdb=" C   GLY c  12 "
        pdb=" N   LYS c  13 "
        pdb=" CA  LYS c  13 "
      ideal   model   delta    sigma   weight residual
     121.54  129.71   -8.17 1.91e+00 2.74e-01 1.83e+01
  angle pdb=" C   GLY C  12 "
        pdb=" N   LYS C  13 "
        pdb=" CA  LYS C  13 "
      ideal   model   delta    sigma   weight residual
     121.54  129.64   -8.10 1.91e+00 2.74e-01 1.80e+01
  angle pdb=" N   VAL L   6 "
        pdb=" CA  VAL L   6 "
        pdb=" C   VAL L   6 "
      ideal   model   delta    sigma   weight residual
     108.42  114.30   -5.88 1.43e+00 4.89e-01 1.69e+01
  ... (remaining 4743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.89: 1927
       14.89 -    29.77: 131
       29.77 -    44.66: 29
       44.66 -    59.54: 3
       59.54 -    74.43: 6
  Dihedral angle restraints: 2096
    sinusoidal: 798
      harmonic: 1298
  Sorted by residual:
  dihedral pdb=" CA  ASP c  14 "
           pdb=" C   ASP c  14 "
           pdb=" N   GLY c  15 "
           pdb=" CA  GLY c  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.24   30.76     0      5.00e+00 4.00e-02 3.78e+01
  dihedral pdb=" CA  ASP C  14 "
           pdb=" C   ASP C  14 "
           pdb=" N   GLY C  15 "
           pdb=" CA  GLY C  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.26   30.74     0      5.00e+00 4.00e-02 3.78e+01
  dihedral pdb=" CA  GLU H  49 "
           pdb=" C   GLU H  49 "
           pdb=" N   TRP H  50 "
           pdb=" CA  TRP H  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.08  -29.92     0      5.00e+00 4.00e-02 3.58e+01
  ... (remaining 2093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 359
       0.053 -    0.106: 125
       0.106 -    0.158: 52
       0.158 -    0.211: 4
       0.211 -    0.264: 4
  Chirality restraints: 544
  Sorted by residual:
  chirality pdb=" CG  LEU L  53 "
            pdb=" CB  LEU L  53 "
            pdb=" CD1 LEU L  53 "
            pdb=" CD2 LEU L  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  ILE L   5 "
            pdb=" N   ILE L   5 "
            pdb=" C   ILE L   5 "
            pdb=" CB  ILE L   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" CB  ILE C  68 "
            pdb=" CA  ILE C  68 "
            pdb=" CG1 ILE C  68 "
            pdb=" CG2 ILE C  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 541 not shown)

  Planarity restraints: 620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  39 "   -0.025 2.00e-02 2.50e+03   1.61e-02 6.51e+00
        pdb=" CG  TRP H  39 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  39 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  39 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  39 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  39 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  39 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  39 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  65 "    0.040 5.00e-02 4.00e+02   5.99e-02 5.74e+00
        pdb=" N   PRO L  66 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO L  66 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO L  66 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS L  83 "   -0.039 5.00e-02 4.00e+02   5.84e-02 5.47e+00
        pdb=" N   PRO L  84 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO L  84 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO L  84 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 617 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.49: 20
        2.49 -     3.09: 2354
        3.09 -     3.69: 4888
        3.69 -     4.30: 6389
        4.30 -     4.90: 10673
  Nonbonded interactions: 24324
  Sorted by model distance:
  nonbonded pdb=" CG2 VAL L   6 "
            pdb=" O   THR L  23 "
     model   vdw
     1.882 3.460
  nonbonded pdb=" CG2 VAL L   6 "
            pdb=" CA  ILE L  24 "
     model   vdw
     2.126 3.890
  nonbonded pdb=" CG2 VAL L   6 "
            pdb=" CD1 ILE L  24 "
     model   vdw
     2.195 3.880
  nonbonded pdb=" OG  SER H 102 "
            pdb=" O   ASN H 111 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER H  31 "
            pdb=" O   ASN c  10 "
     model   vdw
     2.287 3.040
  ... (remaining 24319 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'c'
}

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:             0.620
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.450
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
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   0.067   3494  Z= 0.340
  Angle     :  1.175  15.119   4748  Z= 0.627
  Chirality :  0.063   0.264    544
  Planarity :  0.008   0.060    620
  Dihedral  : 11.775  74.426   1260
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 18.31 %
    Favored  : 81.46 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.14 %
    Favored  : 92.06 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

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: -4.56 (0.32), residues: 437
  helix: -2.57 (0.52), residues: 46
  sheet: -2.12 (0.45), residues: 118
  loop : -3.76 (0.29), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  41 
 TYR   0.034   0.003   TYR H 112 
 PHE   0.032   0.004   PHE H 113 
 TRP   0.040   0.007   TRP H  39 
 HIS   0.011   0.004   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 ( 3494)
  covalent geometry    : angle       1.17477 ( 4748)
  hydrogen bonds       : bond        0.16497 (   95)
  hydrogen bonds       : angle       7.36503 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 154
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   42 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8691 (tm-30)
REVERT: H   48 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8653 (pp)
REVERT: H  105 TYR cc_start: 0.8231 (m-10) cc_final: 0.7856 (m-10)
REVERT: c   63 LYS cc_start: 0.8370 (mttt) cc_final: 0.8167 (mtpt)
REVERT: c   99 TYR cc_start: 0.7718 (m-10) cc_final: 0.7322 (m-80)
REVERT: C    2 LYS cc_start: 0.8728 (tptt) cc_final: 0.8206 (tptt)
REVERT: C   24 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7903 (mmt180)
REVERT: L   40 MET cc_start: 0.8598 (tpt) cc_final: 0.8290 (tpt)
REVERT: L   55 ILE cc_start: 0.7972 (pp) cc_final: 0.7733 (pt)
REVERT: L   80 LEU cc_start: 0.8590 (tp) cc_final: 0.8354 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 156
  average time/residue: 0.0753
  time to fit residues: 13.6556
Evaluate side-chains
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
H  76 ASN
c  22 ASN
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  69 GLN
C  22 ASN
** L  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  61 GLN
** L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.071968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.061398 restraints weight = 14443.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.063203 restraints weight = 8256.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.064479 restraints weight = 5458.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.065406 restraints weight = 3974.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.066022 restraints weight = 3115.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3494  Z= 0.169
  Angle     :  0.785   8.620   4748  Z= 0.408
  Chirality :  0.047   0.163    544
  Planarity :  0.006   0.078    620
  Dihedral  :  7.091  33.073    479
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.13 %
    Favored  : 87.87 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.91 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

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: -4.23 (0.33), residues: 437
  helix: -1.72 (0.63), residues: 48
  sheet: -1.92 (0.41), residues: 135
  loop : -3.72 (0.30), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  21 
 TYR   0.017   0.002   TYR L 103 
 PHE   0.027   0.002   PHE L  78 
 TRP   0.028   0.003   TRP H  39 
 HIS   0.007   0.002   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3494)
  covalent geometry    : angle       0.78511 ( 4748)
  hydrogen bonds       : bond        0.04048 (   95)
  hydrogen bonds       : angle       5.89476 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8831 (mt0) cc_final: 0.8509 (mt0)
REVERT: H   42 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: H   73 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8410 (ttp-110)
REVERT: H  105 TYR cc_start: 0.8785 (m-10) cc_final: 0.8326 (m-10)
REVERT: c   37 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8132 (tm-30)
REVERT: c   63 LYS cc_start: 0.8451 (mttt) cc_final: 0.8235 (tttt)
REVERT: c   69 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7396 (pp30)
REVERT: c   95 SER cc_start: 0.8834 (t) cc_final: 0.8557 (p)
REVERT: c  122 ILE cc_start: 0.8956 (pt) cc_final: 0.8575 (pt)
REVERT: c  127 GLN cc_start: 0.8750 (mp10) cc_final: 0.8228 (mp10)
REVERT: C    2 LYS cc_start: 0.8418 (tptt) cc_final: 0.8150 (tptt)
REVERT: C   11 ILE cc_start: 0.9373 (pt) cc_final: 0.9153 (pt)
REVERT: C   24 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8104 (mmt180)
REVERT: L   60 ASN cc_start: 0.8639 (m110) cc_final: 0.8184 (m110)
REVERT: L   80 LEU cc_start: 0.8240 (tp) cc_final: 0.8037 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0682
  time to fit residues: 9.4325
Evaluate side-chains
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 39 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
H 103 GLN
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.069398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.058910 restraints weight = 14736.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.060662 restraints weight = 8591.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.061890 restraints weight = 5768.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.062754 restraints weight = 4260.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.063368 restraints weight = 3367.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3494  Z= 0.215
  Angle     :  0.779   9.606   4748  Z= 0.403
  Chirality :  0.046   0.139    544
  Planarity :  0.005   0.045    620
  Dihedral  :  6.791  37.113    479
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.19 %
    Favored  : 85.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.89 (0.35), residues: 437
  helix: -1.51 (0.67), residues: 48
  sheet: -1.63 (0.45), residues: 135
  loop : -3.52 (0.31), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  21 
 TYR   0.022   0.002   TYR L 103 
 PHE   0.026   0.002   PHE L  78 
 TRP   0.014   0.003   TRP H  55 
 HIS   0.006   0.002   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 3494)
  covalent geometry    : angle       0.77912 ( 4748)
  hydrogen bonds       : bond        0.04103 (   95)
  hydrogen bonds       : angle       5.69688 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8733 (mt0) cc_final: 0.8467 (mt0)
REVERT: H   42 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8930 (tm-30)
REVERT: H   60 THR cc_start: 0.8741 (p) cc_final: 0.8395 (p)
REVERT: H   73 ARG cc_start: 0.8830 (ttp-110) cc_final: 0.8127 (ttp-110)
REVERT: H   75 ASP cc_start: 0.8972 (m-30) cc_final: 0.8745 (m-30)
REVERT: c   13 LYS cc_start: 0.9560 (ttmt) cc_final: 0.9192 (ptpt)
REVERT: c   37 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8042 (tm-30)
REVERT: c   46 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8241 (mmtt)
REVERT: c   65 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8230 (tm-30)
REVERT: c   95 SER cc_start: 0.8876 (t) cc_final: 0.8664 (p)
REVERT: c  122 ILE cc_start: 0.8972 (pt) cc_final: 0.8650 (pt)
REVERT: c  127 GLN cc_start: 0.8915 (mp10) cc_final: 0.8301 (mp10)
REVERT: C    2 LYS cc_start: 0.8336 (tptt) cc_final: 0.8099 (tptt)
REVERT: C   11 ILE cc_start: 0.9467 (pt) cc_final: 0.8984 (pt)
REVERT: C   37 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8617 (tm-30)
REVERT: C   46 LYS cc_start: 0.8734 (mptt) cc_final: 0.8122 (mtmt)
REVERT: C  111 GLU cc_start: 0.9160 (pt0) cc_final: 0.8844 (pt0)
REVERT: L   60 ASN cc_start: 0.8714 (m110) cc_final: 0.8068 (m110)
REVERT: L   80 LEU cc_start: 0.8333 (tp) cc_final: 0.7942 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0643
  time to fit residues: 8.7618
Evaluate side-chains
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 34 optimal weight:   20.0000
   chunk 42 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    6.7588

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

Flipped N/Q/H residues before XYZ refinement:
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  69 GLN ** 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 = 0.3059 r_free = 0.3059 target = 0.067240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.057179 restraints weight = 14894.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.058859 restraints weight = 8493.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.060046 restraints weight = 5638.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.060863 restraints weight = 4139.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.061466 restraints weight = 3284.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   3494  Z= 0.294
  Angle     :  0.821  10.582   4748  Z= 0.426
  Chirality :  0.048   0.142    544
  Planarity :  0.006   0.044    620
  Dihedral  :  7.143  38.996    479
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.10 %
    Favored  : 84.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.71 %

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: -3.88 (0.36), residues: 437
  helix: -1.73 (0.62), residues: 48
  sheet: -1.71 (0.44), residues: 139
  loop : -3.42 (0.33), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG c 109 
 TYR   0.014   0.002   TYR H  35 
 PHE   0.023   0.002   PHE L  78 
 TRP   0.016   0.003   TRP H  55 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 3494)
  covalent geometry    : angle       0.82106 ( 4748)
  hydrogen bonds       : bond        0.04095 (   95)
  hydrogen bonds       : angle       5.83648 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    9 GLN cc_start: 0.8104 (tp40) cc_final: 0.7862 (tt0)
REVERT: H   19 GLN cc_start: 0.8623 (mt0) cc_final: 0.8292 (mt0)
REVERT: H   50 TRP cc_start: 0.8137 (p-90) cc_final: 0.7707 (p-90)
REVERT: H   71 SER cc_start: 0.9247 (m) cc_final: 0.8738 (p)
REVERT: H   75 ASP cc_start: 0.9096 (m-30) cc_final: 0.8840 (m-30)
REVERT: H   80 GLN cc_start: 0.9158 (mm110) cc_final: 0.8864 (mm-40)
REVERT: H   84 LYS cc_start: 0.9405 (ttpp) cc_final: 0.9181 (tptp)
REVERT: H  101 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: H  103 GLN cc_start: 0.8570 (tp-100) cc_final: 0.7808 (tp40)
REVERT: c   13 LYS cc_start: 0.9665 (ttmt) cc_final: 0.9250 (ptpt)
REVERT: c   37 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: c   65 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8107 (tm-30)
REVERT: c   67 LYS cc_start: 0.9106 (ttmm) cc_final: 0.8703 (ttmm)
REVERT: C    2 LYS cc_start: 0.8400 (tptt) cc_final: 0.8161 (tptt)
REVERT: C   10 ASN cc_start: 0.9215 (m-40) cc_final: 0.8698 (p0)
REVERT: C   37 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8521 (tm-30)
REVERT: C   46 LYS cc_start: 0.8834 (mptt) cc_final: 0.8456 (mttt)
REVERT: C   70 ASN cc_start: 0.9152 (m-40) cc_final: 0.8912 (m-40)
REVERT: C  101 THR cc_start: 0.9545 (p) cc_final: 0.9292 (t)
REVERT: C  111 GLU cc_start: 0.9207 (pt0) cc_final: 0.8779 (pt0)
REVERT: L   60 ASN cc_start: 0.8718 (m110) cc_final: 0.8392 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0657
  time to fit residues: 8.3388
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  10 ASN
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.069249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.059071 restraints weight = 14827.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.060819 restraints weight = 8585.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.062029 restraints weight = 5712.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.062858 restraints weight = 4188.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.063512 restraints weight = 3312.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.5092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3494  Z= 0.176
  Angle     :  0.772   9.451   4748  Z= 0.395
  Chirality :  0.047   0.199    544
  Planarity :  0.005   0.041    620
  Dihedral  :  6.700  37.520    479
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.96 %
    Favored  : 86.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

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: -3.55 (0.37), residues: 437
  helix: -0.88 (0.70), residues: 48
  sheet: -1.63 (0.45), residues: 139
  loop : -3.24 (0.33), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  21 
 TYR   0.018   0.001   TYR L 103 
 PHE   0.018   0.002   PHE L  78 
 TRP   0.012   0.002   TRP H  55 
 HIS   0.004   0.001   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3494)
  covalent geometry    : angle       0.77224 ( 4748)
  hydrogen bonds       : bond        0.03793 (   95)
  hydrogen bonds       : angle       5.48455 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8658 (mt0) cc_final: 0.8288 (mt0)
REVERT: H   42 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8981 (tm-30)
REVERT: H   50 TRP cc_start: 0.7903 (p-90) cc_final: 0.7642 (p-90)
REVERT: H   71 SER cc_start: 0.9288 (m) cc_final: 0.8719 (p)
REVERT: H   80 GLN cc_start: 0.9167 (mm110) cc_final: 0.8876 (mm-40)
REVERT: H   84 LYS cc_start: 0.9288 (ttpp) cc_final: 0.9076 (tptp)
REVERT: H  101 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: c   13 LYS cc_start: 0.9689 (ttmt) cc_final: 0.9251 (ptpt)
REVERT: c   37 GLN cc_start: 0.8647 (tm-30) cc_final: 0.7980 (tm-30)
REVERT: c   46 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8295 (mmmt)
REVERT: c   65 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: c   67 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8684 (ttmm)
REVERT: c  103 GLU cc_start: 0.9258 (tp30) cc_final: 0.9009 (tp30)
REVERT: C   11 ILE cc_start: 0.9466 (pt) cc_final: 0.9113 (pt)
REVERT: C   37 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8696 (tm-30)
REVERT: C   46 LYS cc_start: 0.8837 (mptt) cc_final: 0.8550 (mtmt)
REVERT: C  111 GLU cc_start: 0.9191 (pt0) cc_final: 0.8772 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0608
  time to fit residues: 7.8435
Evaluate side-chains
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 30 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 15 optimal weight:    0.1980
   chunk 32 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    3.4386

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

Flipped N/Q/H residues before XYZ refinement:
H 103 GLN
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.070565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.059978 restraints weight = 14427.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.061699 restraints weight = 8300.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.062914 restraints weight = 5581.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.063770 restraints weight = 4141.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.064369 restraints weight = 3302.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.5263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3494  Z= 0.175
  Angle     :  0.788   9.658   4748  Z= 0.398
  Chirality :  0.047   0.191    544
  Planarity :  0.004   0.028    620
  Dihedral  :  6.641  35.526    479
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.19 %
    Favored  : 85.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

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: -3.51 (0.37), residues: 437
  helix: -1.34 (0.67), residues: 48
  sheet: -1.52 (0.46), residues: 139
  loop : -3.16 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  73 
 TYR   0.015   0.001   TYR L 103 
 PHE   0.015   0.002   PHE L  78 
 TRP   0.010   0.002   TRP H  55 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3494)
  covalent geometry    : angle       0.78787 ( 4748)
  hydrogen bonds       : bond        0.03623 (   95)
  hydrogen bonds       : angle       5.50697 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8687 (mt0) cc_final: 0.8248 (mt0)
REVERT: H   42 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8987 (tm-30)
REVERT: H   50 TRP cc_start: 0.7821 (p-90) cc_final: 0.7599 (p-90)
REVERT: H   71 SER cc_start: 0.9312 (m) cc_final: 0.8731 (p)
REVERT: H   80 GLN cc_start: 0.9073 (mm110) cc_final: 0.8695 (mm-40)
REVERT: H   84 LYS cc_start: 0.9305 (ttpp) cc_final: 0.9050 (tptp)
REVERT: H  105 TYR cc_start: 0.8543 (m-10) cc_final: 0.8184 (m-10)
REVERT: H  108 ASN cc_start: 0.8286 (t0) cc_final: 0.7773 (t0)
REVERT: c   13 LYS cc_start: 0.9688 (ttmt) cc_final: 0.9256 (ptpt)
REVERT: c   37 GLN cc_start: 0.8603 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: c   46 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8183 (mmmt)
REVERT: c   65 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: c   67 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8687 (ttmm)
REVERT: C   11 ILE cc_start: 0.9349 (pt) cc_final: 0.8972 (pt)
REVERT: C   37 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8693 (tm-30)
REVERT: C   46 LYS cc_start: 0.8902 (mptt) cc_final: 0.8567 (mtmt)
REVERT: C   70 ASN cc_start: 0.9020 (m-40) cc_final: 0.8815 (m-40)
REVERT: C  111 GLU cc_start: 0.9122 (pt0) cc_final: 0.8638 (pt0)
REVERT: L   99 LYS cc_start: 0.8432 (mmmm) cc_final: 0.7937 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0730
  time to fit residues: 9.0213
Evaluate side-chains
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 15 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0170
   chunk 40 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 24 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.8824

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

Flipped N/Q/H residues before XYZ refinement:
H  16 GLN
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.073296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.062860 restraints weight = 14734.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.064673 restraints weight = 8470.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.065922 restraints weight = 5625.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.066834 restraints weight = 4123.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.067473 restraints weight = 3237.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.5496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3494  Z= 0.134
  Angle     :  0.764   9.020   4748  Z= 0.388
  Chirality :  0.047   0.181    544
  Planarity :  0.004   0.027    620
  Dihedral  :  6.363  35.320    479
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.59 %
    Favored  : 87.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.20 (0.38), residues: 437
  helix: -1.09 (0.70), residues: 48
  sheet: -1.31 (0.46), residues: 139
  loop : -2.95 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  73 
 TYR   0.009   0.001   TYR H  35 
 PHE   0.022   0.002   PHE H 113 
 TRP   0.013   0.002   TRP H 110 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3494)
  covalent geometry    : angle       0.76354 ( 4748)
  hydrogen bonds       : bond        0.03477 (   95)
  hydrogen bonds       : angle       5.35121 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   42 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8914 (tm-30)
REVERT: H   60 THR cc_start: 0.8756 (p) cc_final: 0.8402 (p)
REVERT: H   71 SER cc_start: 0.9311 (m) cc_final: 0.8695 (p)
REVERT: H   73 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.7958 (ttp-110)
REVERT: H   80 GLN cc_start: 0.8795 (mm110) cc_final: 0.8374 (mm-40)
REVERT: H   84 LYS cc_start: 0.9226 (ttpp) cc_final: 0.9017 (tptp)
REVERT: H  108 ASN cc_start: 0.8226 (t0) cc_final: 0.7986 (t0)
REVERT: c   13 LYS cc_start: 0.9633 (ttmt) cc_final: 0.9153 (ptpt)
REVERT: c   14 ASP cc_start: 0.8588 (p0) cc_final: 0.8307 (p0)
REVERT: c   65 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: c  109 ARG cc_start: 0.9329 (ttp80) cc_final: 0.8859 (tmm-80)
REVERT: C   37 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8826 (tm-30)
REVERT: C   46 LYS cc_start: 0.8921 (mptt) cc_final: 0.8577 (mtmt)
REVERT: C  111 GLU cc_start: 0.9071 (pt0) cc_final: 0.8708 (pt0)
REVERT: L   40 MET cc_start: 0.9259 (tpt) cc_final: 0.8802 (tpt)
REVERT: L   99 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8161 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0647
  time to fit residues: 7.9432
Evaluate side-chains
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:   20.0000
   chunk 39 optimal weight:    0.5980
   chunk 11 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 24 optimal weight:    0.5980
   chunk 16 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.5982

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

Flipped N/Q/H residues before XYZ refinement:
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  69 GLN
** L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.074044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.063426 restraints weight = 14484.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.065246 restraints weight = 8362.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.066555 restraints weight = 5586.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.067492 restraints weight = 4084.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.068175 restraints weight = 3201.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.5675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3494  Z= 0.127
  Angle     :  0.767   9.057   4748  Z= 0.387
  Chirality :  0.047   0.173    544
  Planarity :  0.004   0.026    620
  Dihedral  :  6.104  33.669    479
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.27 %
    Favored  : 86.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -2.88 (0.40), residues: 437
  helix: -0.94 (0.72), residues: 48
  sheet: -1.12 (0.46), residues: 149
  loop : -2.75 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  73 
 TYR   0.014   0.001   TYR L 103 
 PHE   0.026   0.002   PHE H 113 
 TRP   0.014   0.002   TRP H  50 
 HIS   0.004   0.002   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3494)
  covalent geometry    : angle       0.76737 ( 4748)
  hydrogen bonds       : bond        0.03465 (   95)
  hydrogen bonds       : angle       5.31917 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   54 ILE cc_start: 0.9015 (pt) cc_final: 0.8056 (mm)
REVERT: H   71 SER cc_start: 0.9344 (m) cc_final: 0.8756 (p)
REVERT: H   73 ARG cc_start: 0.8763 (ttp-110) cc_final: 0.7991 (ttp-110)
REVERT: H   74 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8702 (ttmt)
REVERT: H   75 ASP cc_start: 0.8967 (m-30) cc_final: 0.8501 (m-30)
REVERT: H   80 GLN cc_start: 0.8827 (mm110) cc_final: 0.8339 (mm-40)
REVERT: H   84 LYS cc_start: 0.9261 (ttpp) cc_final: 0.9034 (tptp)
REVERT: H  108 ASN cc_start: 0.8158 (t0) cc_final: 0.7920 (t0)
REVERT: c   13 LYS cc_start: 0.9613 (ttmt) cc_final: 0.8745 (ptpt)
REVERT: c   14 ASP cc_start: 0.8493 (p0) cc_final: 0.8188 (p0)
REVERT: c   65 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8262 (tm-30)
REVERT: c  109 ARG cc_start: 0.9290 (ttp80) cc_final: 0.8818 (tmm-80)
REVERT: C   11 ILE cc_start: 0.9075 (pt) cc_final: 0.8654 (pt)
REVERT: C   37 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8838 (tm-30)
REVERT: C   45 GLU cc_start: 0.7856 (pt0) cc_final: 0.7266 (pt0)
REVERT: C  103 GLU cc_start: 0.9363 (pm20) cc_final: 0.9109 (pm20)
REVERT: C  111 GLU cc_start: 0.9068 (pt0) cc_final: 0.8713 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0591
  time to fit residues: 7.2926
Evaluate side-chains
  88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0270
   chunk 2 optimal weight:    9.9990
   overall best weight:    4.6046

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

Flipped N/Q/H residues before XYZ refinement:
H  79 ASN
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.072091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.061749 restraints weight = 14889.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.063500 restraints weight = 8486.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.064727 restraints weight = 5643.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.065562 restraints weight = 4160.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.066200 restraints weight = 3302.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.5819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   3494  Z= 0.212
  Angle     :  0.812   9.592   4748  Z= 0.415
  Chirality :  0.048   0.179    544
  Planarity :  0.004   0.025    620
  Dihedral  :  6.329  35.421    479
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.19 %
    Favored  : 85.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.15 (0.38), residues: 437
  helix: -1.11 (0.70), residues: 48
  sheet: -1.35 (0.46), residues: 139
  loop : -2.84 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  73 
 TYR   0.017   0.002   TYR H 112 
 PHE   0.023   0.002   PHE H 113 
 TRP   0.033   0.004   TRP L  42 
 HIS   0.004   0.001   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 3494)
  covalent geometry    : angle       0.81235 ( 4748)
  hydrogen bonds       : bond        0.03635 (   95)
  hydrogen bonds       : angle       5.49443 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 THR cc_start: 0.8617 (p) cc_final: 0.8253 (p)
REVERT: H   71 SER cc_start: 0.9422 (m) cc_final: 0.8838 (p)
REVERT: H   80 GLN cc_start: 0.8793 (mm110) cc_final: 0.8363 (mm-40)
REVERT: H   84 LYS cc_start: 0.9315 (ttpp) cc_final: 0.9086 (tptp)
REVERT: H  105 TYR cc_start: 0.8694 (m-10) cc_final: 0.8452 (m-10)
REVERT: H  108 ASN cc_start: 0.8285 (t0) cc_final: 0.7997 (t0)
REVERT: c   14 ASP cc_start: 0.8621 (p0) cc_final: 0.8275 (p0)
REVERT: c   65 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: C   37 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8700 (tm-30)
REVERT: C   45 GLU cc_start: 0.7898 (pt0) cc_final: 0.7386 (pt0)
REVERT: C  111 GLU cc_start: 0.9088 (pt0) cc_final: 0.8636 (pt0)
REVERT: L   99 LYS cc_start: 0.8193 (mmmm) cc_final: 0.6670 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0641
  time to fit residues: 7.5622
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0670
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0270
   chunk 11 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0370
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    0.4254

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

Flipped N/Q/H residues before XYZ refinement:
H  79 ASN
H  80 GLN
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  69 GLN
L  81 ASN
** L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.076093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.065624 restraints weight = 13965.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.067448 restraints weight = 7896.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.068734 restraints weight = 5206.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.069603 restraints weight = 3796.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.070282 restraints weight = 2990.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.6033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3494  Z= 0.127
  Angle     :  0.810   9.911   4748  Z= 0.405
  Chirality :  0.048   0.162    544
  Planarity :  0.004   0.029    620
  Dihedral  :  5.962  32.138    479
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.36 %
    Favored  : 87.64 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.26 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -2.84 (0.39), residues: 437
  helix: -0.89 (0.71), residues: 48
  sheet: -1.16 (0.44), residues: 149
  loop : -2.66 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  73 
 TYR   0.021   0.001   TYR L 103 
 PHE   0.026   0.002   PHE H 113 
 TRP   0.016   0.002   TRP L  42 
 HIS   0.004   0.001   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3494)
  covalent geometry    : angle       0.80985 ( 4748)
  hydrogen bonds       : bond        0.03310 (   95)
  hydrogen bonds       : angle       5.24562 (  231)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   42 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8869 (tm-30)
REVERT: H   54 ILE cc_start: 0.8826 (pt) cc_final: 0.7926 (mm)
REVERT: H   71 SER cc_start: 0.9339 (m) cc_final: 0.8670 (p)
REVERT: H   73 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8039 (ttp-110)
REVERT: H   80 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8254 (mm-40)
REVERT: H   84 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8942 (tptp)
REVERT: H   89 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8067 (tm-30)
REVERT: H  108 ASN cc_start: 0.8171 (t0) cc_final: 0.7864 (t0)
REVERT: c   14 ASP cc_start: 0.8508 (p0) cc_final: 0.8264 (p0)
REVERT: c   65 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: C   37 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8950 (tm-30)
REVERT: C   46 LYS cc_start: 0.9163 (mptt) cc_final: 0.8580 (mtmt)
REVERT: C   47 ARG cc_start: 0.8753 (mtm110) cc_final: 0.8522 (ttm110)
REVERT: C   70 ASN cc_start: 0.9004 (m110) cc_final: 0.8544 (m-40)
REVERT: C  111 GLU cc_start: 0.9105 (pt0) cc_final: 0.8657 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0592
  time to fit residues: 7.8427
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:   10.0000
   chunk 39 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    3.2984

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

Flipped N/Q/H residues before XYZ refinement:
H  79 ASN
** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  70 ASN
L  81 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.074169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.063883 restraints weight = 14741.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.065624 restraints weight = 8534.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.066884 restraints weight = 5695.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.067730 restraints weight = 4178.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.068409 restraints weight = 3301.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.6284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3494  Z= 0.178
  Angle     :  0.826   9.158   4748  Z= 0.423
  Chirality :  0.049   0.170    544
  Planarity :  0.005   0.040    620
  Dihedral  :  6.062  32.347    479
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.36 %
    Favored  : 87.64 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.00 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -2.96 (0.39), residues: 437
  helix: -0.96 (0.71), residues: 48
  sheet: -1.34 (0.43), residues: 149
  loop : -2.67 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  73 
 TYR   0.019   0.002   TYR L 103 
 PHE   0.032   0.002   PHE H 113 
 TRP   0.035   0.005   TRP H 110 
 HIS   0.003   0.001   HIS L  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 3494)
  covalent geometry    : angle       0.82557 ( 4748)
  hydrogen bonds       : bond        0.03289 (   95)
  hydrogen bonds       : angle       5.29588 (  231)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 682.77 seconds
wall clock time: 12 minutes 26.90 seconds (746.90 seconds total)