Starting phenix.real_space_refine
on Fri May  9 18:34:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5d_37286/05_2025/8w5d_37286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5d_37286/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5d_37286/05_2025/8w5d_37286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5d_37286/05_2025/8w5d_37286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5d_37286/05_2025/8w5d_37286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5d_37286/05_2025/8w5d_37286.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.019 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.72, per 1000 atoms: 0.79
  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: 0.75
  Conformation dependent library (CDL) restraints added in 401.1 milliseconds
  

  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: 0.43
  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: 0.95

  Time building geometry restraints manager: 0.89 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:             0.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.570
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:3.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.580
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.040   0.007   TRP H  39 
 HIS   0.011   0.004   HIS H  38 
 PHE   0.032   0.004   PHE H 113 
 TYR   0.034   0.003   TYR H 112 
 ARG   0.008   0.001   ARG H  41 

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

*********************** 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  : 0.402 
Fit side-chains
   revert: symmetry clash
   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: 0.8168 (mtpt)
REVERT: C    2 LYS cc_start: 0.8728 (tptt) cc_final: 0.8207 (tptt)
REVERT: C   24 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7902 (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: 0.8355 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 156
  average time/residue: 0.1994
  time to fit residues: 35.8446
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  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:   40.0000
   chunk 33 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H  38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3126 r_free = 0.3126 target = 0.069758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.059261 restraints weight = 14770.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.061017 restraints weight = 8500.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.062252 restraints weight = 5674.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3494  Z= 0.230
  Angle     :  0.817   9.380   4748  Z= 0.426
  Chirality :  0.047   0.166    544
  Planarity :  0.007   0.074    620
  Dihedral  :  7.292  33.603    479
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.04 %
    Favored  : 86.96 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.44 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.25 (0.33), residues: 437
  helix: -1.76 (0.64), residues: 48
  sheet: -1.99 (0.41), residues: 135
  loop : -3.70 (0.30), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP H  39 
 HIS   0.007   0.002   HIS H  38 
 PHE   0.029   0.003   PHE L  78 
 TYR   0.016   0.002   TYR L 103 
 ARG   0.013   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04203 (   95)
  hydrogen bonds       : angle       5.97315 (  231)
  covalent geometry    : bond        0.00508 ( 3494)
  covalent geometry    : angle       0.81747 ( 4748)

*********************** 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  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8864 (mt0) cc_final: 0.8476 (mt0)
REVERT: H   42 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8919 (tm-30)
REVERT: H   73 ARG cc_start: 0.8767 (ttp-110) cc_final: 0.8526 (ttp-110)
REVERT: H   75 ASP cc_start: 0.8976 (m-30) cc_final: 0.8771 (m-30)
REVERT: H  105 TYR cc_start: 0.8950 (m-10) cc_final: 0.8393 (m-10)
REVERT: c   13 LYS cc_start: 0.9411 (ttmm) cc_final: 0.9123 (ttmm)
REVERT: c   37 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: c   69 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7432 (pp30)
REVERT: c   95 SER cc_start: 0.8842 (t) cc_final: 0.8597 (p)
REVERT: c  122 ILE cc_start: 0.8976 (pt) cc_final: 0.8625 (pt)
REVERT: c  127 GLN cc_start: 0.8837 (mp10) cc_final: 0.8311 (mp10)
REVERT: C   11 ILE cc_start: 0.9439 (pt) cc_final: 0.9113 (pt)
REVERT: C   19 LEU cc_start: 0.8793 (tp) cc_final: 0.8591 (tp)
REVERT: C   37 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8600 (tm-30)
REVERT: L   60 ASN cc_start: 0.8768 (m110) cc_final: 0.8152 (m110)
REVERT: L   80 LEU cc_start: 0.8431 (tp) cc_final: 0.8228 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1575
  time to fit residues: 21.7110
Evaluate side-chains
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 17 optimal weight:   40.0000
   chunk 3 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.3084 r_free = 0.3084 target = 0.068758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.058610 restraints weight = 14363.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.060335 restraints weight = 8375.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.061508 restraints weight = 5597.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3494  Z= 0.241
  Angle     :  0.798   9.888   4748  Z= 0.416
  Chirality :  0.047   0.137    544
  Planarity :  0.006   0.045    620
  Dihedral  :  7.012  37.505    479
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.33 %
    Favored  : 84.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.71 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.92 (0.35), residues: 437
  helix: -1.61 (0.66), residues: 48
  sheet: -1.59 (0.47), residues: 126
  loop : -3.52 (0.31), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP H  55 
 HIS   0.006   0.002   HIS H  38 
 PHE   0.026   0.002   PHE L  78 
 TYR   0.019   0.002   TYR L 103 
 ARG   0.005   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (   95)
  hydrogen bonds       : angle       5.83239 (  231)
  covalent geometry    : bond        0.00521 ( 3494)
  covalent geometry    : angle       0.79831 ( 4748)

*********************** 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
  107 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8783 (mt0) cc_final: 0.8521 (mt0)
REVERT: H   73 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.8200 (ttp-110)
REVERT: H   75 ASP cc_start: 0.9062 (m-30) cc_final: 0.8819 (m-30)
REVERT: H  105 TYR cc_start: 0.9190 (m-80) cc_final: 0.8492 (m-10)
REVERT: c   37 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: c   65 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8012 (tm-30)
REVERT: c   67 LYS cc_start: 0.9043 (ttmm) cc_final: 0.8632 (ttmm)
REVERT: c   95 SER cc_start: 0.8924 (t) cc_final: 0.8722 (p)
REVERT: c  122 ILE cc_start: 0.8955 (pt) cc_final: 0.8681 (pt)
REVERT: c  127 GLN cc_start: 0.8971 (mp10) cc_final: 0.8334 (mp10)
REVERT: C   11 ILE cc_start: 0.9450 (pt) cc_final: 0.8986 (pt)
REVERT: C  111 GLU cc_start: 0.9126 (pt0) cc_final: 0.8815 (pt0)
REVERT: L   27 ARG cc_start: 0.8478 (ptp-170) cc_final: 0.8220 (ptp-170)
REVERT: L   80 LEU cc_start: 0.8464 (tp) cc_final: 0.8149 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1685
  time to fit residues: 21.7495
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  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 4 optimal weight:    0.0270
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 6 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.0440

-------------------------------------------------------------------------------
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**
** H 108 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**
C  69 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.072156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.061763 restraints weight = 14333.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.063544 restraints weight = 8251.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.064801 restraints weight = 5480.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.4575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3494  Z= 0.120
  Angle     :  0.739   8.468   4748  Z= 0.378
  Chirality :  0.047   0.170    544
  Planarity :  0.005   0.043    620
  Dihedral  :  6.449  36.518    479
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.47 (0.37), residues: 437
  helix: -1.24 (0.72), residues: 48
  sheet: -1.34 (0.44), residues: 145
  loop : -3.29 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP H 110 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.018   0.002   PHE L  78 
 TYR   0.010   0.001   TYR L 103 
 ARG   0.003   0.000   ARG H 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03545 (   95)
  hydrogen bonds       : angle       5.46971 (  231)
  covalent geometry    : bond        0.00263 ( 3494)
  covalent geometry    : angle       0.73945 ( 4748)

*********************** 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
  110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8567 (mt0) cc_final: 0.8290 (mt0)
REVERT: H   32 LEU cc_start: 0.9184 (tp) cc_final: 0.8686 (tp)
REVERT: H   39 TRP cc_start: 0.8799 (m100) cc_final: 0.7916 (m100)
REVERT: H   42 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8751 (tm-30)
REVERT: H   50 TRP cc_start: 0.7822 (p-90) cc_final: 0.7492 (p-90)
REVERT: H   71 SER cc_start: 0.9244 (m) cc_final: 0.8776 (p)
REVERT: H   73 ARG cc_start: 0.8770 (ttp-110) cc_final: 0.8149 (ttp-110)
REVERT: H   80 GLN cc_start: 0.9028 (mm110) cc_final: 0.8784 (mm-40)
REVERT: H   84 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8901 (tmtt)
REVERT: H  101 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8278 (tm-30)
REVERT: H  105 TYR cc_start: 0.8984 (m-80) cc_final: 0.8552 (m-10)
REVERT: H  108 ASN cc_start: 0.9232 (m-40) cc_final: 0.8800 (t0)
REVERT: c   37 GLN cc_start: 0.8739 (tm-30) cc_final: 0.7992 (tm-30)
REVERT: c   65 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: c   67 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8678 (ttmm)
REVERT: c   95 SER cc_start: 0.8887 (t) cc_final: 0.8638 (p)
REVERT: c  103 GLU cc_start: 0.9374 (tp30) cc_final: 0.9111 (tp30)
REVERT: c  122 ILE cc_start: 0.8874 (pt) cc_final: 0.8571 (pt)
REVERT: c  127 GLN cc_start: 0.8870 (mp10) cc_final: 0.8297 (mp10)
REVERT: C   11 ILE cc_start: 0.9361 (pt) cc_final: 0.8954 (pt)
REVERT: C  111 GLU cc_start: 0.9186 (pt0) cc_final: 0.8840 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1533
  time to fit residues: 20.4074
Evaluate side-chains
  84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0370
   chunk 29 optimal weight:    0.3980
   chunk 15 optimal weight:    0.5980
   chunk 24 optimal weight:    0.1980
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.4058

-------------------------------------------------------------------------------
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  10 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 = 0.3224 r_free = 0.3224 target = 0.075075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.064604 restraints weight = 14467.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.066464 restraints weight = 8191.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.067729 restraints weight = 5409.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.4964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3494  Z= 0.115
  Angle     :  0.742   8.665   4748  Z= 0.376
  Chirality :  0.046   0.148    544
  Planarity :  0.004   0.041    620
  Dihedral  :  6.101  33.764    479
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.36 %
    Favored  : 87.64 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.12 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.38), residues: 437
  helix: -1.13 (0.74), residues: 48
  sheet: -1.12 (0.44), residues: 145
  loop : -3.00 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H 110 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.014   0.001   PHE L  78 
 TYR   0.015   0.001   TYR L 103 
 ARG   0.003   0.000   ARG c 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03348 (   95)
  hydrogen bonds       : angle       5.47154 (  231)
  covalent geometry    : bond        0.00247 ( 3494)
  covalent geometry    : angle       0.74221 ( 4748)

*********************** 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
  109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8434 (mt0) cc_final: 0.8160 (mt0)
REVERT: H   39 TRP cc_start: 0.8655 (m100) cc_final: 0.7814 (m100)
REVERT: H   71 SER cc_start: 0.9238 (m) cc_final: 0.8625 (p)
REVERT: H   73 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8113 (ttp-110)
REVERT: H   75 ASP cc_start: 0.8756 (m-30) cc_final: 0.8547 (m-30)
REVERT: H   80 GLN cc_start: 0.8626 (mm110) cc_final: 0.8261 (mm-40)
REVERT: H   84 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8726 (tmtt)
REVERT: H  105 TYR cc_start: 0.8967 (m-80) cc_final: 0.8525 (m-10)
REVERT: c   13 LYS cc_start: 0.9407 (ttmt) cc_final: 0.9104 (ptpt)
REVERT: c   14 ASP cc_start: 0.8732 (p0) cc_final: 0.8449 (p0)
REVERT: c   37 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7908 (tm-30)
REVERT: c   65 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8096 (tm-30)
REVERT: c   67 LYS cc_start: 0.9093 (ttmm) cc_final: 0.8697 (ttmm)
REVERT: c   95 SER cc_start: 0.8865 (t) cc_final: 0.8593 (p)
REVERT: c  122 ILE cc_start: 0.8878 (pt) cc_final: 0.8584 (pt)
REVERT: c  127 GLN cc_start: 0.8822 (mp10) cc_final: 0.8241 (mp10)
REVERT: C   11 ILE cc_start: 0.9200 (pt) cc_final: 0.8750 (pt)
REVERT: C   53 SER cc_start: 0.9387 (t) cc_final: 0.8809 (p)
REVERT: C   69 GLN cc_start: 0.8975 (mt0) cc_final: 0.8588 (mt0)
REVERT: C  111 GLU cc_start: 0.9222 (pt0) cc_final: 0.8917 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1594
  time to fit residues: 20.9725
Evaluate side-chains
  90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 24 optimal weight:    0.6980
   chunk 34 optimal weight:    0.2980
   chunk 41 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
** H  79 ASN ** 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  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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.073653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.063104 restraints weight = 14637.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.064938 restraints weight = 8265.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.066179 restraints weight = 5463.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.5125

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= 0.135
  Angle     :  0.736   8.673   4748  Z= 0.377
  Chirality :  0.046   0.204    544
  Planarity :  0.004   0.051    620
  Dihedral  :  6.118  34.744    479
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.59 %
    Favored  : 87.41 %
  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 : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.38), residues: 437
  helix: -1.22 (0.72), residues: 48
  sheet: -1.09 (0.45), residues: 145
  loop : -2.95 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 110 
 HIS   0.008   0.003   HIS L  83 
 PHE   0.026   0.002   PHE H 113 
 TYR   0.019   0.002   TYR L 103 
 ARG   0.009   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (   95)
  hydrogen bonds       : angle       5.34979 (  231)
  covalent geometry    : bond        0.00294 ( 3494)
  covalent geometry    : angle       0.73628 ( 4748)

*********************** 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
  104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8619 (mt0) cc_final: 0.8261 (mt0)
REVERT: H   71 SER cc_start: 0.9294 (m) cc_final: 0.8622 (p)
REVERT: H   73 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8412 (ttp-110)
REVERT: H   80 GLN cc_start: 0.8776 (mm110) cc_final: 0.8396 (mm-40)
REVERT: H   84 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8754 (tmtt)
REVERT: H   89 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8123 (tm-30)
REVERT: H  105 TYR cc_start: 0.8922 (m-80) cc_final: 0.8555 (m-10)
REVERT: c   13 LYS cc_start: 0.9344 (ttmt) cc_final: 0.9025 (ptpt)
REVERT: c   14 ASP cc_start: 0.8773 (p0) cc_final: 0.8490 (p0)
REVERT: c   37 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: c   65 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: c   67 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8674 (ttmm)
REVERT: c   95 SER cc_start: 0.8877 (t) cc_final: 0.8548 (p)
REVERT: c  122 ILE cc_start: 0.8871 (pt) cc_final: 0.8554 (pt)
REVERT: c  127 GLN cc_start: 0.8951 (mp10) cc_final: 0.8331 (mp10)
REVERT: C   11 ILE cc_start: 0.9289 (pt) cc_final: 0.8997 (pt)
REVERT: C   37 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: C   46 LYS cc_start: 0.8766 (mptt) cc_final: 0.8185 (mtmt)
REVERT: C   69 GLN cc_start: 0.9026 (mt0) cc_final: 0.8669 (mt0)
REVERT: C   70 ASN cc_start: 0.9092 (m-40) cc_final: 0.8858 (m-40)
REVERT: C  111 GLU cc_start: 0.9222 (pt0) cc_final: 0.8854 (pt0)
REVERT: L   99 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7894 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1596
  time to fit residues: 19.9385
Evaluate side-chains
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 17 optimal weight:   50.0000
   chunk 1 optimal weight:   10.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** H  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 108 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  61 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 = 0.3161 r_free = 0.3161 target = 0.072362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.061691 restraints weight = 14275.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.063483 restraints weight = 8057.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.064757 restraints weight = 5322.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.5315

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= 0.148
  Angle     :  0.756   8.786   4748  Z= 0.384
  Chirality :  0.046   0.156    544
  Planarity :  0.004   0.043    620
  Dihedral  :  6.225  35.146    479
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.39), residues: 437
  helix: -1.12 (0.73), residues: 48
  sheet: -1.08 (0.44), residues: 149
  loop : -2.91 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 110 
 HIS   0.005   0.002   HIS L  83 
 PHE   0.026   0.002   PHE H 113 
 TYR   0.012   0.001   TYR L 103 
 ARG   0.005   0.000   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03489 (   95)
  hydrogen bonds       : angle       5.32362 (  231)
  covalent geometry    : bond        0.00325 ( 3494)
  covalent geometry    : angle       0.75610 ( 4748)

*********************** 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
  106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8651 (mt0) cc_final: 0.8240 (mt0)
REVERT: H   71 SER cc_start: 0.9342 (m) cc_final: 0.8822 (p)
REVERT: H   73 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8446 (ttp-110)
REVERT: H   75 ASP cc_start: 0.8919 (m-30) cc_final: 0.8703 (m-30)
REVERT: H   80 GLN cc_start: 0.8837 (mm110) cc_final: 0.8429 (mm-40)
REVERT: H  105 TYR cc_start: 0.8964 (m-80) cc_final: 0.8568 (m-10)
REVERT: c   14 ASP cc_start: 0.8807 (p0) cc_final: 0.8587 (p0)
REVERT: c   37 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: c   65 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: c   67 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8590 (ttmm)
REVERT: C   11 ILE cc_start: 0.9238 (pt) cc_final: 0.8999 (pt)
REVERT: C   19 LEU cc_start: 0.8826 (tp) cc_final: 0.8592 (tt)
REVERT: C   37 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8627 (tm-30)
REVERT: C   69 GLN cc_start: 0.9019 (mt0) cc_final: 0.8682 (mt0)
REVERT: C  111 GLU cc_start: 0.9234 (pt0) cc_final: 0.8929 (pt0)
REVERT: L   40 MET cc_start: 0.9306 (tpt) cc_final: 0.8927 (tpt)
REVERT: L   99 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8183 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1577
  time to fit residues: 20.1052
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  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 10 optimal weight:   20.0000
   chunk 13 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 40 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
H  16 GLN
** H  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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  81 ASN
** L  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.070649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.060155 restraints weight = 14438.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.061964 restraints weight = 8105.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.063252 restraints weight = 5340.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.5526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3494  Z= 0.220
  Angle     :  0.797   9.229   4748  Z= 0.406
  Chirality :  0.048   0.221    544
  Planarity :  0.004   0.038    620
  Dihedral  :  6.484  36.347    479
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 15.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.65 %
    Favored  : 85.35 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.85 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.38), residues: 437
  helix: -1.37 (0.68), residues: 48
  sheet: -1.24 (0.44), residues: 149
  loop : -2.89 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP H  55 
 HIS   0.006   0.003   HIS L  83 
 PHE   0.020   0.002   PHE H 113 
 TYR   0.014   0.002   TYR L 103 
 ARG   0.004   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (   95)
  hydrogen bonds       : angle       5.42999 (  231)
  covalent geometry    : bond        0.00478 ( 3494)
  covalent geometry    : angle       0.79732 ( 4748)

*********************** 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
  100 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8734 (mt0) cc_final: 0.8339 (mt0)
REVERT: H   32 LEU cc_start: 0.9231 (tp) cc_final: 0.8999 (tp)
REVERT: H   60 THR cc_start: 0.8865 (p) cc_final: 0.8617 (p)
REVERT: H   71 SER cc_start: 0.9405 (m) cc_final: 0.8755 (p)
REVERT: H   73 ARG cc_start: 0.8857 (ttp-110) cc_final: 0.8601 (ttp-110)
REVERT: H   80 GLN cc_start: 0.8952 (mm110) cc_final: 0.8433 (mm-40)
REVERT: H  105 TYR cc_start: 0.9064 (m-80) cc_final: 0.8627 (m-10)
REVERT: c   46 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8199 (mmmt)
REVERT: c   65 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8170 (tm-30)
REVERT: c   67 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8612 (ttmm)
REVERT: C   37 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8793 (tm-30)
REVERT: C   46 LYS cc_start: 0.8860 (mptt) cc_final: 0.8087 (mtmt)
REVERT: C   69 GLN cc_start: 0.8974 (mt0) cc_final: 0.8604 (mt0)
REVERT: C   70 ASN cc_start: 0.9164 (m-40) cc_final: 0.8819 (m-40)
REVERT: C  111 GLU cc_start: 0.9248 (pt0) cc_final: 0.8825 (pt0)
REVERT: L   99 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8197 (mmmm)
  outliers start: 1
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1622
  time to fit residues: 19.3076
Evaluate side-chains
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   overall best weight:    5.9988

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.069665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.059122 restraints weight = 13975.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.060918 restraints weight = 7692.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.062193 restraints weight = 5026.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.5817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   3494  Z= 0.260
  Angle     :  0.850  10.138   4748  Z= 0.434
  Chirality :  0.049   0.227    544
  Planarity :  0.005   0.049    620
  Dihedral  :  6.750  36.458    479
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.87 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.85 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.71 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.16 (0.38), residues: 437
  helix: -1.40 (0.65), residues: 48
  sheet: -1.39 (0.43), residues: 149
  loop : -2.80 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP H  55 
 HIS   0.007   0.003   HIS L  83 
 PHE   0.025   0.002   PHE H 113 
 TYR   0.017   0.002   TYR L 103 
 ARG   0.007   0.001   ARG c  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03942 (   95)
  hydrogen bonds       : angle       5.61419 (  231)
  covalent geometry    : bond        0.00564 ( 3494)
  covalent geometry    : angle       0.84975 ( 4748)

*********************** 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
  99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   71 SER cc_start: 0.9460 (m) cc_final: 0.8846 (p)
REVERT: H   75 ASP cc_start: 0.9122 (m-30) cc_final: 0.8911 (m-30)
REVERT: H   78 LYS cc_start: 0.9012 (pttm) cc_final: 0.8580 (tptt)
REVERT: H   79 ASN cc_start: 0.6996 (m-40) cc_final: 0.6789 (m110)
REVERT: H   80 GLN cc_start: 0.8892 (mm110) cc_final: 0.8372 (mm-40)
REVERT: H  105 TYR cc_start: 0.9069 (m-80) cc_final: 0.8514 (m-10)
REVERT: c   65 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8046 (tm-30)
REVERT: c   67 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8582 (ttmm)
REVERT: C   37 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8594 (tm-30)
REVERT: C   45 GLU cc_start: 0.8287 (pt0) cc_final: 0.8066 (pt0)
REVERT: C   46 LYS cc_start: 0.9037 (mptt) cc_final: 0.8069 (mtmm)
REVERT: C   47 ARG cc_start: 0.9140 (mtm110) cc_final: 0.8691 (mtp85)
REVERT: C   69 GLN cc_start: 0.8964 (mt0) cc_final: 0.8433 (mt0)
REVERT: C   70 ASN cc_start: 0.9142 (m-40) cc_final: 0.8776 (m-40)
REVERT: C  111 GLU cc_start: 0.9233 (pt0) cc_final: 0.8825 (pt0)
REVERT: L   99 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8129 (mmmm)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1666
  time to fit residues: 19.1646
Evaluate side-chains
  75 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   overall best weight:    4.1988

-------------------------------------------------------------------------------
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  10 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  81 ASN
** 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 = 0.3125 r_free = 0.3125 target = 0.070961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.060670 restraints weight = 14319.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.062414 restraints weight = 8119.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.063652 restraints weight = 5336.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.5956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3494  Z= 0.200
  Angle     :  0.832   9.487   4748  Z= 0.422
  Chirality :  0.050   0.245    544
  Planarity :  0.005   0.035    620
  Dihedral  :  6.572  34.460    479
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.96 %
    Favored  : 86.04 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.79 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.71 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.38), residues: 437
  helix: -1.13 (0.68), residues: 48
  sheet: -1.33 (0.43), residues: 149
  loop : -2.70 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP H  50 
 HIS   0.006   0.003   HIS L  83 
 PHE   0.023   0.002   PHE H 113 
 TYR   0.014   0.001   TYR H 106 
 ARG   0.010   0.001   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03823 (   95)
  hydrogen bonds       : angle       5.56123 (  231)
  covalent geometry    : bond        0.00444 ( 3494)
  covalent geometry    : angle       0.83159 ( 4748)

********************** 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
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.8671 (m-80) cc_final: 0.8304 (m-80)
REVERT: H   60 THR cc_start: 0.8825 (p) cc_final: 0.8533 (p)
REVERT: H   71 SER cc_start: 0.9415 (m) cc_final: 0.8783 (p)
REVERT: H   73 ARG cc_start: 0.8819 (ttp-110) cc_final: 0.8059 (ttp-110)
REVERT: H   78 LYS cc_start: 0.9070 (pttm) cc_final: 0.8543 (tptt)
REVERT: H   80 GLN cc_start: 0.8888 (mm110) cc_final: 0.8504 (mm-40)
REVERT: H  105 TYR cc_start: 0.8425 (m-80) cc_final: 0.7948 (m-10)
REVERT: c   14 ASP cc_start: 0.8587 (p0) cc_final: 0.8378 (p0)
REVERT: c   65 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8077 (tm-30)
REVERT: c   67 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8618 (ttmm)
REVERT: C   37 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: C   46 LYS cc_start: 0.8958 (mptt) cc_final: 0.8274 (mtmm)
REVERT: C   47 ARG cc_start: 0.9088 (mtm110) cc_final: 0.8787 (mtp85)
REVERT: C   69 GLN cc_start: 0.8898 (mt0) cc_final: 0.8483 (mt0)
REVERT: C   70 ASN cc_start: 0.9074 (m-40) cc_final: 0.8686 (m-40)
REVERT: C  111 GLU cc_start: 0.9148 (pt0) cc_final: 0.8758 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1920
  time to fit residues: 21.3946
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 14 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    2.4188

-------------------------------------------------------------------------------
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**
H 108 ASN
** c  10 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  81 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.072935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.062476 restraints weight = 14524.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.064267 restraints weight = 8166.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.065527 restraints weight = 5395.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.6082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3494  Z= 0.146
  Angle     :  0.809   9.197   4748  Z= 0.409
  Chirality :  0.049   0.222    544
  Planarity :  0.004   0.033    620
  Dihedral  :  6.359  33.281    479
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.13 %
    Favored  : 87.87 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.53 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.92 (0.39), residues: 437
  helix: -1.00 (0.71), residues: 48
  sheet: -1.16 (0.44), residues: 149
  loop : -2.74 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP H 110 
 HIS   0.005   0.002   HIS L  83 
 PHE   0.014   0.002   PHE L  78 
 TYR   0.012   0.001   TYR H 112 
 ARG   0.010   0.001   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (   95)
  hydrogen bonds       : angle       5.40462 (  231)
  covalent geometry    : bond        0.00331 ( 3494)
  covalent geometry    : angle       0.80850 ( 4748)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1366.01 seconds
wall clock time: 24 minutes 51.87 seconds (1491.87 seconds total)