Starting phenix.real_space_refine
on Wed Jun  4 15:56:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5d_37286/06_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_37286/06_2025/8w5d_37286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5d_37286/06_2025/8w5d_37286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5d_37286/06_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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 396.8 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: 0.44
  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: 0.75

  Time building geometry restraints manager: 0.91 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:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.860
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.930
-------------------------------------------------------------------------------
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  : 0.360 
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: 0.2008
  time to fit residues: 36.1025
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 = 31)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.059261 restraints weight = 14770.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.061017 restraints weight = 8499.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.062251 restraints weight = 5674.154|
|-----------------------------------------------------------------------------|
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  : 0.385 
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: 0.8772 (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: 0.9112 (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: 0.1634
  time to fit residues: 22.5764
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  : 0.385 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3089 r_free = 0.3089 target = 0.069070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.058899 restraints weight = 14466.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.060594 restraints weight = 8502.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.061729 restraints weight = 5699.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.4378

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= 0.233
  Angle     :  0.791   9.956   4748  Z= 0.412
  Chirality :  0.046   0.145    544
  Planarity :  0.005   0.045    620
  Dihedral  :  6.976  37.403    479
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.87 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  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: -3.91 (0.35), residues: 437
  helix: -1.63 (0.66), residues: 48
  sheet: -1.56 (0.47), residues: 126
  loop : -3.51 (0.31), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP H  55 
 HIS   0.008   0.002   HIS H  38 
 PHE   0.026   0.002   PHE L  78 
 TYR   0.014   0.002   TYR H 105 
 ARG   0.004   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04074 (   95)
  hydrogen bonds       : angle       5.80079 (  231)
  covalent geometry    : bond        0.00505 ( 3494)
  covalent geometry    : angle       0.79121 ( 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  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8764 (mt0) cc_final: 0.8475 (mt0)
REVERT: H   73 ARG cc_start: 0.8873 (ttp-110) cc_final: 0.8204 (ttp-110)
REVERT: H   75 ASP cc_start: 0.9051 (m-30) cc_final: 0.8819 (m-30)
REVERT: H  105 TYR cc_start: 0.9179 (m-80) cc_final: 0.8476 (m-10)
REVERT: c   37 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: c   65 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8031 (tm-30)
REVERT: c   67 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8643 (ttmm)
REVERT: c  122 ILE cc_start: 0.8973 (pt) cc_final: 0.8679 (pt)
REVERT: c  127 GLN cc_start: 0.8973 (mp10) cc_final: 0.8324 (mp10)
REVERT: C   11 ILE cc_start: 0.9438 (pt) cc_final: 0.8985 (pt)
REVERT: C  111 GLU cc_start: 0.9119 (pt0) cc_final: 0.8816 (pt0)
REVERT: L   27 ARG cc_start: 0.8489 (ptp-170) cc_final: 0.8232 (ptp-170)
REVERT: L   80 LEU cc_start: 0.8436 (tp) cc_final: 0.8113 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1686
  time to fit residues: 21.5997
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  : 0.342 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:   30.0000
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.8586

-------------------------------------------------------------------------------
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 ** 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 = 0.3145 r_free = 0.3145 target = 0.071146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.060797 restraints weight = 14349.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.062594 restraints weight = 8249.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.063858 restraints weight = 5494.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.4556

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= 0.125
  Angle     :  0.734   8.738   4748  Z= 0.376
  Chirality :  0.046   0.140    544
  Planarity :  0.004   0.043    620
  Dihedral  :  6.510  36.707    479
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.67 %
    Favored  : 88.33 %
  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 (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: -3.58 (0.37), residues: 437
  helix: -1.32 (0.71), residues: 48
  sheet: -1.41 (0.45), residues: 135
  loop : -3.31 (0.33), residues: 254

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   0.016   0.002   PHE L  78 
 TYR   0.010   0.001   TYR L 103 
 ARG   0.003   0.000   ARG c 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (   95)
  hydrogen bonds       : angle       5.50075 (  231)
  covalent geometry    : bond        0.00274 ( 3494)
  covalent geometry    : angle       0.73398 ( 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
  111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8565 (mt0) cc_final: 0.8297 (mt0)
REVERT: H   42 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8770 (tm-30)
REVERT: H   50 TRP cc_start: 0.7879 (p-90) cc_final: 0.7556 (p-90)
REVERT: H   71 SER cc_start: 0.9236 (m) cc_final: 0.8774 (p)
REVERT: H   73 ARG cc_start: 0.8773 (ttp-110) cc_final: 0.8163 (ttp-110)
REVERT: H   80 GLN cc_start: 0.9057 (mm110) cc_final: 0.8809 (mm-40)
REVERT: H   84 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8883 (tmtt)
REVERT: H  101 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: H  105 TYR cc_start: 0.9028 (m-80) cc_final: 0.8607 (m-10)
REVERT: H  108 ASN cc_start: 0.9259 (m-40) cc_final: 0.8831 (t0)
REVERT: c   37 GLN cc_start: 0.8737 (tm-30) cc_final: 0.7994 (tm-30)
REVERT: c   65 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8030 (tm-30)
REVERT: c   67 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8684 (ttmm)
REVERT: c  102 ASP cc_start: 0.9249 (p0) cc_final: 0.8977 (p0)
REVERT: c  122 ILE cc_start: 0.8923 (pt) cc_final: 0.8617 (pt)
REVERT: c  127 GLN cc_start: 0.8915 (mp10) cc_final: 0.8340 (mp10)
REVERT: C   11 ILE cc_start: 0.9377 (pt) cc_final: 0.9027 (pt)
REVERT: C   69 GLN cc_start: 0.9031 (pt0) cc_final: 0.8785 (mt0)
REVERT: C  111 GLU cc_start: 0.9180 (pt0) cc_final: 0.8844 (pt0)
REVERT: L   49 GLN cc_start: 0.8341 (pm20) cc_final: 0.8136 (pm20)
REVERT: L   80 LEU cc_start: 0.8247 (tp) cc_final: 0.7949 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1519
  time to fit residues: 20.4206
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  : 0.396 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 17 optimal weight:   40.0000
   chunk 14 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0570
   chunk 24 optimal weight:    8.9990
   chunk 8 optimal weight:   20.0000
   chunk 41 optimal weight:    0.0970
   chunk 32 optimal weight:    5.9990
   overall best weight:    3.8302

-------------------------------------------------------------------------------
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 = 0.3125 r_free = 0.3125 target = 0.070309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.060075 restraints weight = 14689.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.061817 restraints weight = 8298.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.063027 restraints weight = 5491.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.4847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3494  Z= 0.183
  Angle     :  0.759   9.374   4748  Z= 0.390
  Chirality :  0.046   0.145    544
  Planarity :  0.004   0.041    620
  Dihedral  :  6.496  36.235    479
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.87 %
    Favored  : 85.13 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.65 %
    Favored  : 97.09 %
  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: -3.33 (0.38), residues: 437
  helix: -1.44 (0.69), residues: 48
  sheet: -1.32 (0.45), residues: 145
  loop : -3.07 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  55 
 HIS   0.001   0.001   HIS H  38 
 PHE   0.017   0.002   PHE L  78 
 TYR   0.018   0.001   TYR L 103 
 ARG   0.002   0.000   ARG H  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (   95)
  hydrogen bonds       : angle       5.65652 (  231)
  covalent geometry    : bond        0.00397 ( 3494)
  covalent geometry    : angle       0.75865 ( 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
  104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8656 (mt0) cc_final: 0.8277 (mt0)
REVERT: H   42 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8935 (tm-30)
REVERT: H   50 TRP cc_start: 0.8051 (p-90) cc_final: 0.7686 (p-90)
REVERT: H   71 SER cc_start: 0.9356 (m) cc_final: 0.8768 (p)
REVERT: H   75 ASP cc_start: 0.8924 (m-30) cc_final: 0.8704 (m-30)
REVERT: H   80 GLN cc_start: 0.8848 (mm110) cc_final: 0.8362 (mm-40)
REVERT: H   84 LYS cc_start: 0.9235 (ttpp) cc_final: 0.8773 (tmtt)
REVERT: H   89 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8198 (tm-30)
REVERT: H  101 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: H  105 TYR cc_start: 0.9115 (m-80) cc_final: 0.8673 (m-10)
REVERT: c   37 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8142 (tm-30)
REVERT: c   46 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8096 (mmmt)
REVERT: c   65 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: c   67 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8649 (ttmm)
REVERT: C   11 ILE cc_start: 0.9312 (pt) cc_final: 0.9028 (pt)
REVERT: C   37 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8702 (tm-30)
REVERT: C   46 LYS cc_start: 0.8824 (mptt) cc_final: 0.8243 (mtmt)
REVERT: C   70 ASN cc_start: 0.9132 (m-40) cc_final: 0.8932 (m-40)
REVERT: C  111 GLU cc_start: 0.9217 (pt0) cc_final: 0.8816 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1573
  time to fit residues: 19.7688
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  : 0.400 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 34 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0570
   chunk 5 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    2.3102

-------------------------------------------------------------------------------
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  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 = 0.3145 r_free = 0.3145 target = 0.071589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.060937 restraints weight = 14345.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.062823 restraints weight = 7876.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.064137 restraints weight = 5102.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.5192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3494  Z= 0.140
  Angle     :  0.754   9.959   4748  Z= 0.390
  Chirality :  0.046   0.151    544
  Planarity :  0.005   0.051    620
  Dihedral  :  6.374  36.256    479
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  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 : 0.48 %

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: -3.12 (0.39), residues: 437
  helix: -1.35 (0.70), residues: 48
  sheet: -1.16 (0.46), residues: 145
  loop : -2.92 (0.36), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 110 
 HIS   0.004   0.001   HIS L  83 
 PHE   0.012   0.001   PHE L  78 
 TYR   0.008   0.001   TYR L 103 
 ARG   0.007   0.001   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03557 (   95)
  hydrogen bonds       : angle       5.46267 (  231)
  covalent geometry    : bond        0.00303 ( 3494)
  covalent geometry    : angle       0.75375 ( 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
  102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8635 (mt0) cc_final: 0.8222 (mt0)
REVERT: H   32 LEU cc_start: 0.9239 (tp) cc_final: 0.8909 (tp)
REVERT: H   35 TYR cc_start: 0.8443 (m-80) cc_final: 0.8207 (m-80)
REVERT: H   42 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8877 (tm-30)
REVERT: H   50 TRP cc_start: 0.7812 (p-90) cc_final: 0.7564 (p-90)
REVERT: H   54 ILE cc_start: 0.9002 (pt) cc_final: 0.7958 (mm)
REVERT: H   71 SER cc_start: 0.9320 (m) cc_final: 0.8814 (p)
REVERT: H   73 ARG cc_start: 0.8837 (ttp-110) cc_final: 0.8136 (ttp-110)
REVERT: H   80 GLN cc_start: 0.8818 (mm110) cc_final: 0.8392 (mm-40)
REVERT: H  101 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8041 (tm-30)
REVERT: H  105 TYR cc_start: 0.8999 (m-80) cc_final: 0.8474 (m-10)
REVERT: c   37 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: c   65 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8043 (tm-30)
REVERT: c   67 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8667 (ttmm)
REVERT: c  109 ARG cc_start: 0.9369 (ttp80) cc_final: 0.8842 (tmm-80)
REVERT: C   37 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8643 (tm-30)
REVERT: C   46 LYS cc_start: 0.8895 (mptt) cc_final: 0.8430 (mtmt)
REVERT: C   69 GLN cc_start: 0.8975 (mt0) cc_final: 0.8566 (mt0)
REVERT: C  111 GLU cc_start: 0.9185 (pt0) cc_final: 0.8889 (pt0)
REVERT: L   99 LYS cc_start: 0.8420 (mmmm) cc_final: 0.7993 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1620
  time to fit residues: 20.0920
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  : 0.393 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 11 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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**
C  10 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 = 0.3102 r_free = 0.3102 target = 0.069572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.059246 restraints weight = 14389.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.061021 restraints weight = 8028.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.062229 restraints weight = 5272.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.5418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   3494  Z= 0.229
  Angle     :  0.820  10.016   4748  Z= 0.422
  Chirality :  0.048   0.152    544
  Planarity :  0.004   0.027    620
  Dihedral  :  6.647  38.168    479
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.56 %
    Favored  : 84.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  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: -3.25 (0.38), residues: 437
  helix: -1.50 (0.67), residues: 48
  sheet: -1.37 (0.46), residues: 139
  loop : -2.88 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  55 
 HIS   0.011   0.003   HIS L  83 
 PHE   0.022   0.002   PHE H 113 
 TYR   0.014   0.002   TYR H 112 
 ARG   0.006   0.001   ARG L  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (   95)
  hydrogen bonds       : angle       5.49825 (  231)
  covalent geometry    : bond        0.00497 ( 3494)
  covalent geometry    : angle       0.82025 ( 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
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8780 (mt0) cc_final: 0.8301 (mt0)
REVERT: H   35 TYR cc_start: 0.8545 (m-80) cc_final: 0.8128 (m-80)
REVERT: H   71 SER cc_start: 0.9394 (m) cc_final: 0.8747 (p)
REVERT: H   75 ASP cc_start: 0.9067 (m-30) cc_final: 0.8862 (m-30)
REVERT: H   80 GLN cc_start: 0.8923 (mm110) cc_final: 0.8515 (mm-40)
REVERT: H  101 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8189 (tm-30)
REVERT: H  105 TYR cc_start: 0.9007 (m-80) cc_final: 0.8545 (m-10)
REVERT: c   65 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: c   67 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8602 (ttmm)
REVERT: C   46 LYS cc_start: 0.9130 (mptt) cc_final: 0.8803 (mttm)
REVERT: C   47 ARG cc_start: 0.9147 (mtm110) cc_final: 0.8765 (mtp85)
REVERT: C   69 GLN cc_start: 0.8959 (mt0) cc_final: 0.8379 (mt0)
REVERT: C   70 ASN cc_start: 0.9119 (m-40) cc_final: 0.8723 (m-40)
REVERT: C  111 GLU cc_start: 0.9188 (pt0) cc_final: 0.8791 (pt0)
REVERT: L   40 MET cc_start: 0.9317 (tpt) cc_final: 0.8906 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1545
  time to fit residues: 17.0054
Evaluate side-chains
  70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 40 optimal weight:   20.0000
   chunk 33 optimal weight:    4.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 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 = 0.3094 r_free = 0.3094 target = 0.068859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.058676 restraints weight = 14513.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.060487 restraints weight = 7952.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.061727 restraints weight = 5138.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.5654

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= 0.224
  Angle     :  0.825   9.679   4748  Z= 0.423
  Chirality :  0.047   0.145    544
  Planarity :  0.005   0.053    620
  Dihedral  :  6.775  37.450    479
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.19 %
    Favored  : 85.81 %
  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 (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: -3.18 (0.39), residues: 437
  helix: -1.34 (0.69), residues: 48
  sheet: -1.54 (0.43), residues: 152
  loop : -2.74 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP H  50 
 HIS   0.004   0.002   HIS L  83 
 PHE   0.026   0.002   PHE H 113 
 TYR   0.031   0.002   TYR H 112 
 ARG   0.009   0.001   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (   95)
  hydrogen bonds       : angle       5.58567 (  231)
  covalent geometry    : bond        0.00493 ( 3494)
  covalent geometry    : angle       0.82526 ( 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
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 GLN cc_start: 0.8758 (mt0) cc_final: 0.8303 (mt0)
REVERT: H   35 TYR cc_start: 0.8613 (m-80) cc_final: 0.8158 (m-80)
REVERT: H   71 SER cc_start: 0.9412 (m) cc_final: 0.8799 (p)
REVERT: H   80 GLN cc_start: 0.8999 (mm110) cc_final: 0.8557 (mm-40)
REVERT: H  101 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: H  105 TYR cc_start: 0.9028 (m-80) cc_final: 0.8489 (m-10)
REVERT: c   65 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: c   67 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8605 (ttmm)
REVERT: C   46 LYS cc_start: 0.9007 (mptt) cc_final: 0.8543 (mttt)
REVERT: C   69 GLN cc_start: 0.8960 (mt0) cc_final: 0.8498 (mt0)
REVERT: C   70 ASN cc_start: 0.9132 (m-40) cc_final: 0.8782 (m-40)
REVERT: C  111 GLU cc_start: 0.9202 (pt0) cc_final: 0.8793 (pt0)
REVERT: C  121 LEU cc_start: 0.9592 (mm) cc_final: 0.9333 (mt)
REVERT: L   99 LYS cc_start: 0.8597 (tptm) cc_final: 0.8275 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1523
  time to fit residues: 17.2525
Evaluate side-chains
  72 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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  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 = 0.3152 r_free = 0.3152 target = 0.071871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.061638 restraints weight = 14169.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.063489 restraints weight = 7808.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.064739 restraints weight = 5078.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.5734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3494  Z= 0.142
  Angle     :  0.781   8.963   4748  Z= 0.396
  Chirality :  0.047   0.140    544
  Planarity :  0.004   0.020    620
  Dihedral  :  6.330  35.509    479
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.04 %
    Favored  : 86.96 %
  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 (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: -2.87 (0.40), residues: 437
  helix: -1.15 (0.72), residues: 48
  sheet: -1.07 (0.45), residues: 149
  loop : -2.71 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H 110 
 HIS   0.004   0.001   HIS L  83 
 PHE   0.020   0.002   PHE H 113 
 TYR   0.016   0.001   TYR H 112 
 ARG   0.006   0.001   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03372 (   95)
  hydrogen bonds       : angle       5.43218 (  231)
  covalent geometry    : bond        0.00314 ( 3494)
  covalent geometry    : angle       0.78101 ( 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
  104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.8718 (m-80) cc_final: 0.8377 (m-80)
REVERT: H   42 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8966 (tm-30)
REVERT: H   54 ILE cc_start: 0.8906 (pt) cc_final: 0.8104 (mm)
REVERT: H   71 SER cc_start: 0.9411 (m) cc_final: 0.8785 (p)
REVERT: H   80 GLN cc_start: 0.9071 (mm110) cc_final: 0.8697 (mm-40)
REVERT: H  101 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: H  105 TYR cc_start: 0.8935 (m-80) cc_final: 0.8462 (m-10)
REVERT: c   14 ASP cc_start: 0.8543 (p0) cc_final: 0.8238 (p0)
REVERT: c   65 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8084 (tm-30)
REVERT: c   67 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8624 (ttmm)
REVERT: C   46 LYS cc_start: 0.9225 (mptt) cc_final: 0.8901 (mttm)
REVERT: C   47 ARG cc_start: 0.9219 (mtm-85) cc_final: 0.8399 (ttm-80)
REVERT: C   69 GLN cc_start: 0.8897 (mt0) cc_final: 0.8455 (mt0)
REVERT: C   70 ASN cc_start: 0.9115 (m-40) cc_final: 0.8750 (m-40)
REVERT: C  111 GLU cc_start: 0.9190 (pt0) cc_final: 0.8754 (pt0)
REVERT: C  121 LEU cc_start: 0.9553 (mm) cc_final: 0.9293 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1599
  time to fit residues: 20.1259
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  : 0.434 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0870
   chunk 18 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 34 optimal weight:   20.0000
   overall best weight:    3.2164

-------------------------------------------------------------------------------
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  41 ASN
L  81 ASN
L  97 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.071591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.061356 restraints weight = 14638.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.063110 restraints weight = 8356.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.064354 restraints weight = 5533.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.5999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3494  Z= 0.167
  Angle     :  0.807   9.340   4748  Z= 0.412
  Chirality :  0.047   0.140    544
  Planarity :  0.004   0.038    620
  Dihedral  :  6.282  32.705    479
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.27 %
    Favored  : 86.73 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  0.26 %
    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: -2.94 (0.39), residues: 437
  helix: -1.14 (0.71), residues: 48
  sheet: -1.34 (0.43), residues: 152
  loop : -2.60 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP H  50 
 HIS   0.003   0.001   HIS L  83 
 PHE   0.021   0.002   PHE H 113 
 TYR   0.016   0.002   TYR L 103 
 ARG   0.009   0.001   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03485 (   95)
  hydrogen bonds       : angle       5.39085 (  231)
  covalent geometry    : bond        0.00375 ( 3494)
  covalent geometry    : angle       0.80651 ( 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
  101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.8718 (m-80) cc_final: 0.8393 (m-80)
REVERT: H   42 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8984 (tm-30)
REVERT: H   71 SER cc_start: 0.9422 (m) cc_final: 0.8823 (p)
REVERT: H   78 LYS cc_start: 0.9007 (pttm) cc_final: 0.8631 (pttp)
REVERT: H   80 GLN cc_start: 0.8879 (mm110) cc_final: 0.8407 (mm-40)
REVERT: H  101 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8115 (tm-30)
REVERT: H  105 TYR cc_start: 0.8375 (m-80) cc_final: 0.8026 (m-10)
REVERT: c   14 ASP cc_start: 0.8481 (p0) cc_final: 0.8197 (p0)
REVERT: c   65 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8243 (tm-30)
REVERT: C   46 LYS cc_start: 0.9249 (mptt) cc_final: 0.8933 (mttm)
REVERT: C   47 ARG cc_start: 0.9129 (mtm-85) cc_final: 0.8415 (ttm-80)
REVERT: C   69 GLN cc_start: 0.8882 (mt0) cc_final: 0.8642 (mt0)
REVERT: C   70 ASN cc_start: 0.9074 (m-40) cc_final: 0.8682 (m-40)
REVERT: C  111 GLU cc_start: 0.9157 (pt0) cc_final: 0.8730 (pt0)
REVERT: C  115 LEU cc_start: 0.9752 (tp) cc_final: 0.9515 (tt)
REVERT: C  121 LEU cc_start: 0.9568 (mm) cc_final: 0.9129 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 100
  average time/residue: 0.2038
  time to fit residues: 24.2978
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  : 0.441 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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**
** 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 = 0.3096 r_free = 0.3096 target = 0.069949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.059639 restraints weight = 14946.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.061413 restraints weight = 8261.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.062654 restraints weight = 5409.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.6089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3494  Z= 0.227
  Angle     :  0.854   9.917   4748  Z= 0.435
  Chirality :  0.047   0.144    544
  Planarity :  0.005   0.037    620
  Dihedral  :  6.462  34.001    479
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.79 %
    Favored  : 84.21 %
  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 (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: -3.05 (0.38), residues: 437
  helix: -1.23 (0.70), residues: 48
  sheet: -1.50 (0.42), residues: 152
  loop : -2.61 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.004   TRP H  55 
 HIS   0.005   0.002   HIS L  83 
 PHE   0.014   0.002   PHE L  78 
 TYR   0.019   0.002   TYR H 112 
 ARG   0.009   0.001   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (   95)
  hydrogen bonds       : angle       5.50692 (  231)
  covalent geometry    : bond        0.00495 ( 3494)
  covalent geometry    : angle       0.85378 ( 4748)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1408.90 seconds
wall clock time: 25 minutes 20.19 seconds (1520.19 seconds total)