Starting phenix.real_space_refine
on Thu Mar  6 07:30:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eh5_28135/03_2025/8eh5_28135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eh5_28135/03_2025/8eh5_28135.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eh5_28135/03_2025/8eh5_28135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eh5_28135/03_2025/8eh5_28135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eh5_28135/03_2025/8eh5_28135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eh5_28135/03_2025/8eh5_28135.cif"
  }
  resolution = 3.36
  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=   0.003 sd=   0.064
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      24      5.16       5
     C    3481      2.51       5
     N     939      2.21       5
     O    1059      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5503
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "G"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 187
          Classifications: {'peptide': 26}
          Link IDs: {'PTRANS': 6, 'TRANS': 19}
    Chain: "H"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 940
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "M"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 940
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "N"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "O"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 940
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "P"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 832
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
  Time building chain proxies: 3.90, per 1000 atoms: 0.71
  Number of scatterers: 5503
  At special positions: 0
  Unit cell: (60.61, 98.23, 109.725, 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      24     16.00
     O    1059      8.00
     N     939      7.00
     C    3481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  22 " - pdb=" SG  CYS O  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  23 " - pdb=" SG  CYS P  88 " distance=2.05

  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: 1.22
  Conformation dependent library (CDL) restraints added in 635.1 milliseconds
  

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1276

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 18 sheets defined
      6.5% alpha, 42.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'H' and resid 52 through 55
      removed outlier: 3.964A  pdb=" N   SER H  55 " --> pdb=" O   PHE H  52A" (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'M' and resid 53 through 55
      No H-bonds generated for 'chain 'M' and resid 53 through 55'
    Processing helix  chain 'M' and resid 61 through 64
    Processing helix  chain 'M' and resid 83 through 87
    Processing helix  chain 'N' and resid 79 through 83
    Processing helix  chain 'O' and resid 83 through 87
    Processing helix  chain 'P' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.103A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 110 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 97
      removed outlier: 3.589A  pdb=" N   PHE H  96 " --> pdb=" O   PHE H 100C" (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.514A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'M' and resid 10 through 11
      removed outlier: 6.114A  pdb=" N   GLY M  10 " --> pdb=" O   THR M 110 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   MET M  34 " --> pdb=" O   VAL M  50 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL M  50 " --> pdb=" O   MET M  34 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   TRP M  36 " --> pdb=" O   VAL M  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'M' and resid 96 through 97
    Processing sheet with id=AB1, first strand: chain 'N' and resid 4 through 5
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 13
      removed outlier: 5.307A  pdb=" N   LEU N  33 " --> pdb=" O   TYR N  49 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   TYR N  49 " --> pdb=" O   LEU N  33 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LYS N  50 " --> pdb=" O   SER N  53 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 13
    Processing sheet with id=AB4, first strand: chain 'O' and resid 3 through 7
    Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 12
      removed outlier: 6.682A  pdb=" N   MET O  34 " --> pdb=" O   VAL O  50 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL O  50 " --> pdb=" O   MET O  34 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   TRP O  36 " --> pdb=" O   VAL O  48 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   TRP O  52 " --> pdb=" O   ASN O  56 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   ASN O  56 " --> pdb=" O   TRP O  52 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'O' and resid 96 through 98
    Processing sheet with id=AB7, first strand: chain 'P' and resid 4 through 6
    Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 13
      removed outlier: 4.584A  pdb=" N   LEU P  33 " --> pdb=" O   TYR P  49 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   TYR P  49 " --> pdb=" O   LEU P  33 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   TRP P  35 " --> pdb=" O   LEU P  47 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   SER P  53 " --> pdb=" O   TYR P  49 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'P' and resid 10 through 13

    233 hydrogen bonds defined for protein.
    516 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: 1.56

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 950
        1.31 -     1.44: 1715
        1.44 -     1.57: 2910
        1.57 -     1.70: 33
        1.70 -     1.83: 35
  Bond restraints: 5643
  Sorted by residual:
  bond pdb=" CB  HIS O  35 "
       pdb=" CG  HIS O  35 "
    ideal  model  delta    sigma   weight residual
    1.497  1.403  0.094 1.40e-02 5.10e+03 4.52e+01
  bond pdb=" CB  ARG O  38 "
       pdb=" CG  ARG O  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.353  0.167 3.00e-02 1.11e+03 3.10e+01
  bond pdb=" CB  ARG H  38 "
       pdb=" CG  ARG H  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.357  0.163 3.00e-02 1.11e+03 2.95e+01
  bond pdb=" CB  PHE O  52A"
       pdb=" CG  PHE O  52A"
    ideal  model  delta    sigma   weight residual
    1.502  1.379  0.123 2.30e-02 1.89e+03 2.86e+01
  bond pdb=" CB  HIS M  93 "
       pdb=" CG  HIS M  93 "
    ideal  model  delta    sigma   weight residual
    1.497  1.423  0.074 1.40e-02 5.10e+03 2.79e+01
  ... (remaining 5638 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 6661
        2.60 -     5.21: 857
        5.21 -     7.81: 128
        7.81 -    10.41: 6
       10.41 -    13.01: 1
  Bond angle restraints: 7653
  Sorted by residual:
  angle pdb=" C   GLY M 100A"
        pdb=" N   PRO M 100B"
        pdb=" CA  PRO M 100B"
      ideal   model   delta    sigma   weight residual
     120.31  127.92   -7.61 9.80e-01 1.04e+00 6.03e+01
  angle pdb=" CA  ASP O  98 "
        pdb=" CB  ASP O  98 "
        pdb=" CG  ASP O  98 "
      ideal   model   delta    sigma   weight residual
     112.60  120.06   -7.46 1.00e+00 1.00e+00 5.57e+01
  angle pdb=" C   TYR H  32 "
        pdb=" CA  TYR H  32 "
        pdb=" CB  TYR H  32 "
      ideal   model   delta    sigma   weight residual
     109.54  122.55  -13.01 1.84e+00 2.95e-01 5.00e+01
  angle pdb=" N   ILE N  29 "
        pdb=" CA  ILE N  29 "
        pdb=" C   ILE N  29 "
      ideal   model   delta    sigma   weight residual
     111.81  106.23    5.58 8.60e-01 1.35e+00 4.22e+01
  angle pdb=" C   GLY O 100A"
        pdb=" N   PRO O 100B"
        pdb=" CA  PRO O 100B"
      ideal   model   delta    sigma   weight residual
     120.14  126.48   -6.34 1.06e+00 8.90e-01 3.58e+01
  ... (remaining 7648 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 3168
       17.98 -    35.96: 85
       35.96 -    53.95: 27
       53.95 -    71.93: 14
       71.93 -    89.91: 4
  Dihedral angle restraints: 3298
    sinusoidal: 1286
      harmonic: 2012
  Sorted by residual:
  dihedral pdb=" CB  CYS N  23 "
           pdb=" SG  CYS N  23 "
           pdb=" SG  CYS N  88 "
           pdb=" CB  CYS N  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.66  -73.66     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" C   TYR H  32 "
           pdb=" N   TYR H  32 "
           pdb=" CA  TYR H  32 "
           pdb=" CB  TYR H  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.96   18.36     0      2.50e+00 1.60e-01 5.40e+01
  dihedral pdb=" N   TYR H  32 "
           pdb=" C   TYR H  32 "
           pdb=" CA  TYR H  32 "
           pdb=" CB  TYR H  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.69  -12.89     0      2.50e+00 1.60e-01 2.66e+01
  ... (remaining 3295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 670
       0.120 -    0.239: 130
       0.239 -    0.359: 10
       0.359 -    0.478: 1
       0.478 -    0.598: 1
  Chirality restraints: 812
  Sorted by residual:
  chirality pdb=" CA  TYR H  32 "
            pdb=" N   TYR H  32 "
            pdb=" C   TYR H  32 "
            pdb=" CB  TYR H  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.93e+00
  chirality pdb=" CA  ILE H  28 "
            pdb=" N   ILE H  28 "
            pdb=" C   ILE H  28 "
            pdb=" CB  ILE H  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.82   -0.38 2.00e-01 2.50e+01 3.65e+00
  chirality pdb=" CA  ARG H  94 "
            pdb=" N   ARG H  94 "
            pdb=" C   ARG H  94 "
            pdb=" CB  ARG H  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.17e+00
  ... (remaining 809 not shown)

  Planarity restraints: 983
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP N  35 "   -0.049 2.00e-02 2.50e+03   2.61e-02 1.71e+01
        pdb=" CG  TRP N  35 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TRP N  35 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP N  35 "    0.029 2.00e-02 2.50e+03
        pdb=" NE1 TRP N  35 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP N  35 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP N  35 "    0.039 2.00e-02 2.50e+03
        pdb=" CZ2 TRP N  35 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP N  35 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP N  35 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY O 100A"    0.019 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   GLY O 100A"   -0.065 2.00e-02 2.50e+03
        pdb=" O   GLY O 100A"    0.025 2.00e-02 2.50e+03
        pdb=" N   PRO O 100B"    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO H 100B"    0.019 2.00e-02 2.50e+03   3.75e-02 1.40e+01
        pdb=" C   PRO H 100B"   -0.065 2.00e-02 2.50e+03
        pdb=" O   PRO H 100B"    0.024 2.00e-02 2.50e+03
        pdb=" N   PHE H 100C"    0.022 2.00e-02 2.50e+03
  ... (remaining 980 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1134
        2.77 -     3.30: 4662
        3.30 -     3.83: 9543
        3.83 -     4.37: 11595
        4.37 -     4.90: 19224
  Nonbonded interactions: 46158
  Sorted by model distance:
  nonbonded pdb=" OH  TYR H 102 "
            pdb=" OG  SER P  67 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" N   ASP H 101 "
            pdb=" OD1 ASP H 101 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" OD2 ASP O  72 "
            pdb=" NZ  LYS O  75 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" OD2 ASP H  72 "
            pdb=" NZ  LYS H  75 "
     model   vdw
     2.429 3.120
  nonbonded pdb=" O   TYR H  32 "
            pdb=" NH1 ARG H  94 "
     model   vdw
     2.432 3.120
  ... (remaining 46153 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 'H'
  selection = chain 'M'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.650
  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:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.090
  Find NCS groups from input model:        0.180
  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:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
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      :  0.023   0.167   5643  Z= 1.446
  Angle     :  1.807  13.013   7653  Z= 1.206
  Chirality :  0.094   0.598    812
  Planarity :  0.008   0.043    983
  Dihedral  : 10.683  89.909   2004
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  3.91 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  0.84 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.43 (0.32), residues: 690
  helix:  None (None), residues: 0
  sheet: -0.35 (0.29), residues: 282
  loop :  0.98 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.009   TRP N  35 
 HIS   0.011   0.003   HIS H  93 
 PHE   0.033   0.006   PHE N  98 
 TYR   0.043   0.006   TYR N  49 
 ARG   0.007   0.001   ARG O  38 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 187
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   93 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6346 (t70)
REVERT: H   95 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6998 (t0)
REVERT: L    4 MET cc_start: 0.8205 (mmm) cc_final: 0.7943 (mmm)
REVERT: M   68 THR cc_start: 0.7417 (m) cc_final: 0.7096 (p)
REVERT: M   77 THR cc_start: 0.6485 (m) cc_final: 0.6100 (m)
REVERT: N   24 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7473 (ttt90)
REVERT: O   46 GLU cc_start: 0.7849 (tt0) cc_final: 0.7438 (mt-10)
REVERT: P   72 THR cc_start: 0.8330 (m) cc_final: 0.8003 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 189
  average time/residue: 0.2169
  time to fit residues: 50.4411
Evaluate side-chains
  128 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain H residue   95 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M   1 GLN
M  76 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.165778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.137406 restraints weight = 7425.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 2.56
r_work: 0.3736 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   5643  Z= 0.217
  Angle     :  0.687   8.950   7653  Z= 0.371
  Chirality :  0.048   0.205    812
  Planarity :  0.005   0.026    983
  Dihedral  :  5.655  45.457    776
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.33 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  9.20 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.32 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.09 (0.29), residues: 291
  loop :  0.47 (0.35), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP M  52 
 HIS   0.007   0.002   HIS H  93 
 PHE   0.020   0.002   PHE O 100C
 TYR   0.026   0.002   TYR M  32 
 ARG   0.006   0.001   ARG M  19 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   43 LYS cc_start: 0.7921 (mttp) cc_final: 0.7630 (mtmm)
REVERT: H   83 ARG cc_start: 0.7601 (tpt170) cc_final: 0.7047 (mmt-90)
REVERT: H   93 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6301 (t70)
REVERT: H  101 ASP cc_start: 0.7735 (p0) cc_final: 0.7307 (p0)
REVERT: L   61 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7873 (mtm180)
REVERT: M   34 MET cc_start: 0.7908 (tpp) cc_final: 0.7692 (mtt)
REVERT: N   24 ARG cc_start: 0.7334 (mtt-85) cc_final: 0.6374 (ttt90)
REVERT: O  102 TYR cc_start: 0.6881 (m-80) cc_final: 0.6665 (m-10)
REVERT: P    3 GLN cc_start: 0.7371 (mp10) cc_final: 0.7040 (mp10)
REVERT: P    4 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7829 (mtp)
REVERT: P   24 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7008 (tpt170)
REVERT: P   72 THR cc_start: 0.8111 (m) cc_final: 0.7583 (p)
  outliers start: 11
  outliers final: 5
  residues processed: 145
  average time/residue: 0.2383
  time to fit residues: 43.0793
Evaluate side-chains
  127 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain P residue    4 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 44 optimal weight:    0.2980
   chunk 45 optimal weight:    0.5980
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  76 ASN ** 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 = 0.4107 r_free = 0.4107 target = 0.161493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133274 restraints weight = 7758.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 2.51
r_work: 0.3664 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   5643  Z= 0.218
  Angle     :  0.634   8.330   7653  Z= 0.346
  Chirality :  0.047   0.170    812
  Planarity :  0.004   0.030    983
  Dihedral  :  5.347  46.717    774
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.93 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 11.71 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.17 (0.33), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.29 (0.29), residues: 285
  loop :  0.09 (0.35), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP O  52 
 HIS   0.007   0.002   HIS H  93 
 PHE   0.020   0.002   PHE O  52A
 TYR   0.018   0.002   TYR M  32 
 ARG   0.004   0.001   ARG M  66 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7491 (tt)
REVERT: H   43 LYS cc_start: 0.7979 (mttp) cc_final: 0.7747 (mtmm)
REVERT: H   83 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7321 (mmt180)
REVERT: H   93 HIS cc_start: 0.7170 (OUTLIER) cc_final: 0.6637 (t70)
REVERT: H  101 ASP cc_start: 0.7625 (p0) cc_final: 0.7271 (p0)
REVERT: L   82 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7744 (t0)
REVERT: M   85 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7450 (tm-30)
REVERT: N   24 ARG cc_start: 0.7244 (mtt-85) cc_final: 0.6394 (ttt90)
REVERT: N   89 GLN cc_start: 0.6697 (tt0) cc_final: 0.6354 (tp40)
REVERT: O   83 ARG cc_start: 0.8125 (mmm160) cc_final: 0.7583 (mmm160)
REVERT: P    4 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7709 (mtp)
REVERT: P   18 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8500 (mtp-110)
REVERT: P   24 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7239 (mtt-85)
REVERT: P   72 THR cc_start: 0.8015 (m) cc_final: 0.7535 (p)
  outliers start: 22
  outliers final: 11
  residues processed: 133
  average time/residue: 0.2204
  time to fit residues: 36.0219
Evaluate side-chains
  129 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 ASN
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   22 THR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   66 ARG
Chi-restraints excluded: chain O residue   82 MET
Chi-restraints excluded: chain P residue    4 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 40 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
G 129 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  76 ASN ** 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 = 0.4066 r_free = 0.4066 target = 0.159930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.131651 restraints weight = 7597.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.53
r_work: 0.3629 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.4532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   5643  Z= 0.314
  Angle     :  0.669   8.006   7653  Z= 0.360
  Chirality :  0.047   0.179    812
  Planarity :  0.005   0.047    983
  Dihedral  :  5.562  49.443    774
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.80 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 11.54 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.17 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.11 (0.30), residues: 291
  loop : -0.20 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP O  52 
 HIS   0.009   0.002   HIS H  93 
 PHE   0.019   0.002   PHE O  52A
 TYR   0.026   0.002   TYR N  49 
 ARG   0.003   0.001   ARG H  71 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
REVERT: H   43 LYS cc_start: 0.7928 (mttp) cc_final: 0.7681 (mtmm)
REVERT: H   93 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.6413 (t70)
REVERT: H  101 ASP cc_start: 0.7684 (p0) cc_final: 0.7248 (p0)
REVERT: M   85 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: N   89 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6740 (tp40)
REVERT: N  102 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7431 (p)
REVERT: O   85 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6303 (pm20)
REVERT: P    3 GLN cc_start: 0.7242 (mp10) cc_final: 0.7041 (mp10)
REVERT: P    4 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7837 (mtp)
REVERT: P   24 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7341 (mtt-85)
REVERT: P   72 THR cc_start: 0.8205 (m) cc_final: 0.7668 (p)
  outliers start: 27
  outliers final: 16
  residues processed: 125
  average time/residue: 0.2224
  time to fit residues: 34.2703
Evaluate side-chains
  128 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 ASN
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   49 TYR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue    2 ILE
Chi-restraints excluded: chain N residue   22 THR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain O residue   66 ARG
Chi-restraints excluded: chain O residue   85 GLU
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    0.3980
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 40 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0000
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 105 GLN
O  76 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.165779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.138255 restraints weight = 7442.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 2.48
r_work: 0.3713 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3559 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5643  Z= 0.161
  Angle     :  0.585   7.713   7653  Z= 0.312
  Chirality :  0.045   0.146    812
  Planarity :  0.004   0.039    983
  Dihedral  :  5.296  52.211    774
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.78 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 13.38 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.03 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.48 (0.29), residues: 318
  loop : -0.41 (0.36), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP O  52 
 HIS   0.007   0.001   HIS H  93 
 PHE   0.015   0.001   PHE O  52A
 TYR   0.018   0.001   TYR M  32 
 ARG   0.003   0.000   ARG N  31 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: H   43 LYS cc_start: 0.8058 (mttp) cc_final: 0.7783 (mtmm)
REVERT: H   83 ARG cc_start: 0.8134 (tpt170) cc_final: 0.7424 (mmt180)
REVERT: H   93 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6138 (t70)
REVERT: H  101 ASP cc_start: 0.7742 (p0) cc_final: 0.7151 (p0)
REVERT: M   77 THR cc_start: 0.6950 (p) cc_final: 0.6726 (p)
REVERT: M   85 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7375 (tm-30)
REVERT: N   89 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6974 (tp40)
REVERT: N  102 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7326 (p)
REVERT: O   83 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7555 (mmm160)
REVERT: O  100 PHE cc_start: 0.6899 (m-80) cc_final: 0.6606 (m-80)
REVERT: P    3 GLN cc_start: 0.7176 (mp10) cc_final: 0.6461 (mp10)
REVERT: P    4 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7942 (mtp)
REVERT: P   72 THR cc_start: 0.8126 (m) cc_final: 0.7647 (p)
  outliers start: 17
  outliers final: 11
  residues processed: 123
  average time/residue: 0.2300
  time to fit residues: 34.8256
Evaluate side-chains
  115 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain N residue    2 ILE
Chi-restraints excluded: chain N residue   22 THR
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0070
   chunk 47 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   chunk 52 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    1.4000

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

Flipped N/Q/H residues before XYZ refinement:
G 113 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  70 HIS
M  95 ASN
** O  76 ASN ** 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 = 0.4088 r_free = 0.4088 target = 0.159207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.131211 restraints weight = 7741.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 2.43
r_work: 0.3638 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.5030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5643  Z= 0.234
  Angle     :  0.624   7.590   7653  Z= 0.334
  Chirality :  0.046   0.151    812
  Planarity :  0.005   0.035    983
  Dihedral  :  5.456  58.400    774
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.52 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 12.54 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.09 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.44 (0.29), residues: 324
  loop : -0.47 (0.37), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP O  36 
 HIS   0.008   0.002   HIS H  93 
 PHE   0.017   0.002   PHE M 100C
 TYR   0.017   0.002   TYR N  49 
 ARG   0.005   0.001   ARG L  31 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7550 (tt)
REVERT: H   43 LYS cc_start: 0.8167 (mttp) cc_final: 0.7923 (mtmm)
REVERT: M   32 TYR cc_start: 0.6986 (m-10) cc_final: 0.6772 (m-10)
REVERT: M   77 THR cc_start: 0.7073 (p) cc_final: 0.6832 (p)
REVERT: M   85 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7296 (tm-30)
REVERT: N   89 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6806 (tp40)
REVERT: N  102 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7420 (p)
REVERT: O   83 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7762 (mmm160)
REVERT: P    3 GLN cc_start: 0.7108 (mp10) cc_final: 0.6490 (mp10)
REVERT: P    4 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7779 (mtp)
REVERT: P   72 THR cc_start: 0.8051 (m) cc_final: 0.7580 (p)
  outliers start: 23
  outliers final: 14
  residues processed: 123
  average time/residue: 0.2271
  time to fit residues: 34.4480
Evaluate side-chains
  121 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  113 ASN
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
G 109 ASN
G 113 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M   1 GLN
M 105 GLN
O  76 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.161361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.132544 restraints weight = 7823.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 2.53
r_work: 0.3652 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.5236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5643  Z= 0.201
  Angle     :  0.594   8.274   7653  Z= 0.317
  Chirality :  0.046   0.138    812
  Planarity :  0.004   0.039    983
  Dihedral  :  5.386  53.780    774
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.94 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 13.88 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.06 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.63 (0.29), residues: 318
  loop : -0.63 (0.37), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP O  36 
 HIS   0.007   0.001   HIS H  93 
 PHE   0.014   0.002   PHE M  52A
 TYR   0.014   0.001   TYR H  91 
 ARG   0.005   0.001   ARG L  31 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
REVERT: H   43 LYS cc_start: 0.8133 (mttp) cc_final: 0.7896 (mtmm)
REVERT: M   32 TYR cc_start: 0.6708 (m-10) cc_final: 0.6395 (m-10)
REVERT: M   77 THR cc_start: 0.7015 (p) cc_final: 0.6799 (p)
REVERT: M   85 GLU cc_start: 0.7713 (tm-30) cc_final: 0.6987 (tm-30)
REVERT: N   89 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6871 (tp40)
REVERT: N  102 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7417 (p)
REVERT: O   83 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7724 (mmm160)
REVERT: P    4 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7518 (mtm)
REVERT: P   72 THR cc_start: 0.8045 (m) cc_final: 0.7580 (p)
  outliers start: 22
  outliers final: 16
  residues processed: 120
  average time/residue: 0.2141
  time to fit residues: 32.1682
Evaluate side-chains
  121 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  109 ASN
Chi-restraints excluded: chain G residue  113 ASN
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   90 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 40 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 51 optimal weight:    9.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 113 ASN
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M   1 GLN
M 105 GLN
** O  76 ASN ** 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 = 0.4099 r_free = 0.4099 target = 0.160069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.131131 restraints weight = 7863.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.53
r_work: 0.3630 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   5643  Z= 0.246
  Angle     :  0.624   9.169   7653  Z= 0.333
  Chirality :  0.046   0.138    812
  Planarity :  0.005   0.037    983
  Dihedral  :  5.399  57.736    774
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.81 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 13.55 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.14 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.62 (0.29), residues: 318
  loop : -0.72 (0.37), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP O  36 
 HIS   0.007   0.002   HIS H  93 
 PHE   0.035   0.003   PHE M  52A
 TYR   0.017   0.002   TYR N  49 
 ARG   0.004   0.001   ARG L  31 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7602 (tt)
REVERT: H   43 LYS cc_start: 0.8130 (mttp) cc_final: 0.7896 (mtmm)
REVERT: M   85 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7089 (tm-30)
REVERT: N   89 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6837 (tp40)
REVERT: N  102 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7379 (p)
REVERT: P   24 ARG cc_start: 0.7765 (mtt-85) cc_final: 0.7310 (mtt-85)
REVERT: P   72 THR cc_start: 0.8115 (m) cc_final: 0.7633 (p)
  outliers start: 27
  outliers final: 17
  residues processed: 117
  average time/residue: 0.2054
  time to fit residues: 29.9536
Evaluate side-chains
  115 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   66 ARG
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue    7 SER
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   90 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    0.1980
   chunk 59 optimal weight:    0.6980
   chunk 61 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 113 ASN
H  93 HIS
L   6 GLN
M   1 GLN
M 105 GLN
** O  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.162497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.133688 restraints weight = 7874.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 2.55
r_work: 0.3663 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.5538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5643  Z= 0.197
  Angle     :  0.600   9.036   7653  Z= 0.320
  Chirality :  0.045   0.139    812
  Planarity :  0.004   0.042    983
  Dihedral  :  4.953  41.683    774
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.67 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 13.38 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.05 (0.35), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.69 (0.29), residues: 318
  loop : -0.66 (0.37), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP O  36 
 HIS   0.005   0.001   HIS H  93 
 PHE   0.036   0.003   PHE M  52A
 TYR   0.015   0.001   TYR H  91 
 ARG   0.004   0.000   ARG O  19 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
REVERT: H   18 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7656 (tt)
REVERT: H   43 LYS cc_start: 0.8113 (mttp) cc_final: 0.7869 (mtmm)
REVERT: N    4 MET cc_start: 0.7126 (mmm) cc_final: 0.6662 (mmm)
REVERT: N   89 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6798 (tp40)
REVERT: N  102 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7409 (p)
REVERT: P   72 THR cc_start: 0.8066 (m) cc_final: 0.7603 (p)
  outliers start: 25
  outliers final: 18
  residues processed: 115
  average time/residue: 0.2287
  time to fit residues: 32.3038
Evaluate side-chains
  110 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   66 ARG
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue    7 SER
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   69 THR
Chi-restraints excluded: chain P residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 59 optimal weight:    0.3980
   chunk 57 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 26 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M   1 GLN
M 105 GLN
** O  76 ASN ** 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 = 0.4077 r_free = 0.4077 target = 0.158435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.129394 restraints weight = 7989.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.54
r_work: 0.3604 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.5551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   5643  Z= 0.293
  Angle     :  0.644   8.797   7653  Z= 0.345
  Chirality :  0.047   0.144    812
  Planarity :  0.005   0.048    983
  Dihedral  :  5.243  51.312    774
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.97 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 13.38 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.24 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.55 (0.29), residues: 318
  loop : -0.79 (0.37), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP O  36 
 HIS   0.008   0.002   HIS H  93 
 PHE   0.036   0.003   PHE M  52A
 TYR   0.019   0.002   TYR P  91 
 ARG   0.005   0.001   ARG L  61 

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

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

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1380 Ramachandran restraints generated.
    690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.645 
Fit side-chains
REVERT: H   18 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7574 (tt)
REVERT: H   43 LYS cc_start: 0.8162 (mttp) cc_final: 0.7889 (mtmm)
REVERT: H   75 LYS cc_start: 0.6142 (tptp) cc_final: 0.5890 (tptt)
REVERT: M   85 GLU cc_start: 0.7608 (tm-30) cc_final: 0.6822 (tm-30)
REVERT: N    4 MET cc_start: 0.6947 (mmm) cc_final: 0.6453 (mmm)
REVERT: N   89 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6931 (tp40)
REVERT: N  102 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7568 (p)
REVERT: P    3 GLN cc_start: 0.7186 (mp10) cc_final: 0.6822 (mp10)
REVERT: P   72 THR cc_start: 0.8249 (m) cc_final: 0.7748 (p)
  outliers start: 22
  outliers final: 18
  residues processed: 110
  average time/residue: 0.2090
  time to fit residues: 28.7900
Evaluate side-chains
  112 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue   93 HIS
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain M residue   66 ARG
Chi-restraints excluded: chain M residue   69 ILE
Chi-restraints excluded: chain N residue   74 THR
Chi-restraints excluded: chain N residue   89 GLN
Chi-restraints excluded: chain N residue  102 THR
Chi-restraints excluded: chain O residue    7 SER
Chi-restraints excluded: chain O residue   12 VAL
Chi-restraints excluded: chain O residue   31 THR
Chi-restraints excluded: chain O residue   48 VAL
Chi-restraints excluded: chain P residue    4 MET
Chi-restraints excluded: chain P residue    7 SER
Chi-restraints excluded: chain P residue   19 VAL
Chi-restraints excluded: chain P residue   69 THR
Chi-restraints excluded: chain P residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 113 ASN
M   1 GLN
M 105 GLN
O  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.160399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.131401 restraints weight = 8029.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.56
r_work: 0.3638 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.5683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5643  Z= 0.227
  Angle     :  0.612   8.663   7653  Z= 0.326
  Chirality :  0.046   0.148    812
  Planarity :  0.004   0.036    983
  Dihedral  :  5.110  50.140    774
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.96 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 14.05 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.23 (0.34), residues: 690
  helix:  None (None), residues: 0
  sheet:  0.55 (0.28), residues: 318
  loop : -0.76 (0.37), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP O  36 
 HIS   0.007   0.002   HIS H  93 
 PHE   0.029   0.003   PHE M  52A
 TYR   0.017   0.002   TYR P  91 
 ARG   0.004   0.001   ARG O  83 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2805.31 seconds
wall clock time: 48 minutes 59.80 seconds (2939.80 seconds total)