Starting phenix.real_space_refine
on Fri Aug 22 15:13:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqs_45821/08_2025/9cqs_45821.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqs_45821/08_2025/9cqs_45821.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqs_45821/08_2025/9cqs_45821.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqs_45821/08_2025/9cqs_45821.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqs_45821/08_2025/9cqs_45821.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqs_45821/08_2025/9cqs_45821.map"
  }
  resolution = 2.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      12      5.16       5
     C    2914      2.51       5
     N     764      2.21       5
     O    1096      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4790
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1050
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
    Chain: "B"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1110
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 1050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1050
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1110
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 78
          Classifications: {'water': 78}
          Link IDs: {None: 77}
    Chain: "B"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 59
          Classifications: {'water': 59}
          Link IDs: {None: 58}
    Chain: "C"
      Number of atoms: 92
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 92
          Classifications: {'water': 92}
          Link IDs: {None: 91}
    Chain: "D"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 61
          Classifications: {'water': 61}
          Link IDs: {None: 60}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   HOH B 331 " occ=0.78
  Time building chain proxies: 1.58, per 1000 atoms: 0.33
  Number of scatterers: 4790
  At special positions: 0
  Unit cell: (77.175, 72.03, 65.415, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      12     16.00
     O    1096      8.00
     N     764      7.00
     C    2914      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 190.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      87.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
      removed outlier: 3.683A  pdb=" N   THR A  41 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR A  42 " --> pdb=" O   THR A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 4.105A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 137
    Processing helix  chain 'B' and resid 4 through 18
      removed outlier: 3.985A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.370A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 77
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 94
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.027A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'B' and resid 143 through 146
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
      removed outlier: 3.597A  pdb=" N   THR C  41 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR C  42 " --> pdb=" O   THR C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 89
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 4.100A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS C  99 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.977A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 36 through 46
      removed outlier: 4.092A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   SER D  44 " --> pdb=" O   PHE D  41 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
      removed outlier: 3.550A  pdb=" N   LYS D  95 " --> pdb=" O   LEU D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 119
      removed outlier: 3.739A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 142
    Processing helix  chain 'D' and resid 143 through 146

    333 hydrogen bonds defined for protein.
    951 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: 0.76

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.20 -     1.38: 1627
        1.38 -     1.55: 2966
        1.55 -     1.72: 11
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4638
  Sorted by residual:
  bond pdb=" N   VAL B  18 "
       pdb=" CA  VAL B  18 "
    ideal  model  delta    sigma   weight residual
    1.458  1.497 -0.040 1.27e-02 6.20e+03 9.75e+00
  bond pdb=" N   VAL B  23 "
       pdb=" CA  VAL B  23 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.17e-02 7.31e+03 9.74e+00
  bond pdb=" N   ASN B  19 "
       pdb=" CA  ASN B  19 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.22e-02 6.72e+03 7.07e+00
  bond pdb=" N   TRP B  15 "
       pdb=" CA  TRP B  15 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 6.92e+00
  bond pdb=" N   LYS B  17 "
       pdb=" CA  LYS B  17 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 6.86e+00
  ... (remaining 4633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 6139
        1.78 -     3.56: 181
        3.56 -     5.34: 32
        5.34 -     7.12: 5
        7.12 -     8.90: 1
  Bond angle restraints: 6358
  Sorted by residual:
  angle pdb=" CA  LYS A  16 "
        pdb=" CB  LYS A  16 "
        pdb=" CG  LYS A  16 "
      ideal   model   delta    sigma   weight residual
     114.10  123.00   -8.90 2.00e+00 2.50e-01 1.98e+01
  angle pdb=" CA  LYS B  17 "
        pdb=" C   LYS B  17 "
        pdb=" O   LYS B  17 "
      ideal   model   delta    sigma   weight residual
     120.55  116.92    3.63 1.06e+00 8.90e-01 1.17e+01
  angle pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
        pdb=" O   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     121.17  117.63    3.54 1.06e+00 8.90e-01 1.12e+01
  angle pdb=" CA  SER C 133 "
        pdb=" C   SER C 133 "
        pdb=" O   SER C 133 "
      ideal   model   delta    sigma   weight residual
     120.55  117.05    3.50 1.06e+00 8.90e-01 1.09e+01
  angle pdb=" CA  GLY B  24 "
        pdb=" C   GLY B  24 "
        pdb=" O   GLY B  24 "
      ideal   model   delta    sigma   weight residual
     120.75  117.57    3.18 1.03e+00 9.43e-01 9.53e+00
  ... (remaining 6353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 2247
       17.14 -    34.28: 262
       34.28 -    51.43: 90
       51.43 -    68.57: 19
       68.57 -    85.71: 8
  Dihedral angle restraints: 2626
    sinusoidal: 998
      harmonic: 1628
  Sorted by residual:
  dihedral pdb=" CA  LYS C  16 "
           pdb=" C   LYS C  16 "
           pdb=" N   VAL C  17 "
           pdb=" CA  VAL C  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.68   17.32     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" C1A HEM C 201 "
           pdb=" C2A HEM C 201 "
           pdb=" CAA HEM C 201 "
           pdb=" CBA HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.71  -85.71     2      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" C2D HEM D 201 "
           pdb=" C3D HEM D 201 "
           pdb=" CAD HEM D 201 "
           pdb=" CBD HEM D 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  100.77   79.23     2      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 2623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 616
       0.070 -    0.141: 64
       0.141 -    0.211: 6
       0.211 -    0.281: 1
       0.281 -    0.352: 1
  Chirality restraints: 688
  Sorted by residual:
  chirality pdb=" CB  VAL B  18 "
            pdb=" CA  VAL B  18 "
            pdb=" CG1 VAL B  18 "
            pdb=" CG2 VAL B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CA  VAL B  18 "
            pdb=" N   VAL B  18 "
            pdb=" C   VAL B  18 "
            pdb=" CB  VAL B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  VAL C 132 "
            pdb=" N   VAL C 132 "
            pdb=" C   VAL C 132 "
            pdb=" CB  VAL C 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.33e-01
  ... (remaining 685 not shown)

  Planarity restraints: 794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  94 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO C  95 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  94 "    0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A  95 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  19 "    0.008 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   ASN B  19 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASN B  19 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL B  20 "    0.010 2.00e-02 2.50e+03
  ... (remaining 791 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 149
        2.66 -     3.22: 4300
        3.22 -     3.78: 8370
        3.78 -     4.34: 11759
        4.34 -     4.90: 18228
  Nonbonded interactions: 42806
  Sorted by model distance:
  nonbonded pdb=" O   VAL C  93 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" NE2 HIS D  92 "
            pdb="FE   HEM D 201 "
     model   vdw
     2.139 3.080
  nonbonded pdb=" NE2 HIS B  92 "
            pdb="FE   HEM B 201 "
     model   vdw
     2.145 3.080
  nonbonded pdb=" NE2 HIS A  87 "
            pdb="FE   HEM A 201 "
     model   vdw
     2.157 3.080
  nonbonded pdb=" O   HOH A 323 "
            pdb=" O   HOH A 366 "
     model   vdw
     2.161 3.040
  ... (remaining 42801 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 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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=0.78 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.250
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.040
  Find NCS groups from input model:        0.080
  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:6.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
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      :  0.013   0.580   4642  Z= 0.257
  Angle     :  0.710   8.899   6358  Z= 0.414
  Chirality :  0.048   0.352    688
  Planarity :  0.006   0.051    794
  Dihedral  : 17.313  85.710   1574
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 17.84 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.54 (0.37), residues: 560
  helix:  2.54 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.83 (0.68), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 104 
 TYR   0.010   0.002   TYR D  35 
 PHE   0.018   0.002   PHE D  45 
 TRP   0.016   0.002   TRP B  15 
 HIS   0.006   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 4638)
  covalent geometry    : angle       0.71011 ( 6358)
  hydrogen bonds       : bond        0.09791 (  333)
  hydrogen bonds       : angle       4.05617 (  951)
  Misc. bond           : bond        0.42848 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7647 (mttt) cc_final: 0.6870 (mptt)
REVERT: A   76 MET cc_start: 0.7901 (mtt) cc_final: 0.7531 (mtt)
REVERT: B   61 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7126 (tttm)
REVERT: C   90 LYS cc_start: 0.8264 (mptt) cc_final: 0.7726 (tttt)
REVERT: D  120 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7610 (ptmm)
  outliers start: 4
  outliers final: 1
  residues processed: 78
  average time/residue: 0.7909
  time to fit residues: 63.4102
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   83 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A  68 ASN
** A  97 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 = 0.3618 r_free = 0.3618 target = 0.145913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.119120 restraints weight = 4568.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.67
r_work: 0.3176 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.0789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.015   0.565   4642  Z= 0.144
  Angle     :  0.738  16.469   6358  Z= 0.267
  Chirality :  0.039   0.158    688
  Planarity :  0.005   0.050    794
  Dihedral  :  9.889  86.753    622
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.32 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.75 (0.37), residues: 560
  helix:  2.67 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop :  2.01 (0.67), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 104 
 TYR   0.014   0.002   TYR C  24 
 PHE   0.010   0.001   PHE D  45 
 TRP   0.006   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4638)
  covalent geometry    : angle       0.73836 ( 6358)
  hydrogen bonds       : bond        0.03717 (  333)
  hydrogen bonds       : angle       3.70366 (  951)
  Misc. bond           : bond        0.51376 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7477 (mttt) cc_final: 0.6637 (mptt)
REVERT: A   92 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7338 (mtp180)
REVERT: B   61 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6834 (tttm)
REVERT: B  120 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7933 (tttp)
REVERT: C   85 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7683 (m-30)
REVERT: C   90 LYS cc_start: 0.8293 (mptt) cc_final: 0.7564 (tttt)
REVERT: C  116 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7370 (mp0)
REVERT: D   90 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7037 (tp30)
REVERT: D  120 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7391 (ptmm)
  outliers start: 11
  outliers final: 1
  residues processed: 82
  average time/residue: 0.7905
  time to fit residues: 66.6025
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   61 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A  58 HIS
A  72 HIS
** A  97 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 = 0.3622 r_free = 0.3622 target = 0.144204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.122476 restraints weight = 4815.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.32
r_work: 0.3292 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3179
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3179 r_free = 0.3179    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.253   4642  Z= 0.127
  Angle     :  0.735  15.658   6358  Z= 0.260
  Chirality :  0.039   0.165    688
  Planarity :  0.005   0.049    794
  Dihedral  :  9.720  86.354    620
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.20 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.74 (0.37), residues: 560
  helix:  2.66 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  2.04 (0.67), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.014   0.001   TYR C  24 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.009   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4638)
  covalent geometry    : angle       0.73457 ( 6358)
  hydrogen bonds       : bond        0.03553 (  333)
  hydrogen bonds       : angle       3.63127 (  951)
  Misc. bond           : bond        0.16997 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7717 (mttt) cc_final: 0.7147 (mptt)
REVERT: A   76 MET cc_start: 0.7919 (mtt) cc_final: 0.7606 (mtt)
REVERT: A   92 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7549 (mtp180)
REVERT: B   61 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7178 (tttm)
REVERT: B  120 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7533 (tttm)
REVERT: C   85 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7771 (m-30)
REVERT: C   90 LYS cc_start: 0.8295 (mptt) cc_final: 0.7733 (tttt)
REVERT: C  116 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7672 (mp0)
REVERT: D   90 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7330 (tp30)
REVERT: D  120 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7680 (ptmm)
  outliers start: 12
  outliers final: 1
  residues processed: 77
  average time/residue: 0.7951
  time to fit residues: 63.0340
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   61 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3626 r_free = 0.3626 target = 0.144435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.122594 restraints weight = 4800.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.32
r_work: 0.3297 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109   4642  Z= 0.118
  Angle     :  0.729  16.095   6358  Z= 0.253
  Chirality :  0.039   0.167    688
  Planarity :  0.005   0.048    794
  Dihedral  :  9.626  86.099    620
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.30 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.82 (0.36), residues: 560
  helix:  2.72 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  2.01 (0.66), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 104 
 TYR   0.011   0.001   TYR C  24 
 PHE   0.008   0.001   PHE D 118 
 TRP   0.008   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4638)
  covalent geometry    : angle       0.72923 ( 6358)
  hydrogen bonds       : bond        0.03336 (  333)
  hydrogen bonds       : angle       3.57131 (  951)
  Misc. bond           : bond        0.07709 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7712 (mttt) cc_final: 0.7133 (mptt)
REVERT: A   92 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7562 (mtp180)
REVERT: B  120 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7511 (tttm)
REVERT: C   85 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7765 (m-30)
REVERT: C   90 LYS cc_start: 0.8298 (mptt) cc_final: 0.7750 (tttt)
REVERT: D   90 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7306 (tp30)
REVERT: D  120 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7678 (ptmm)
  outliers start: 15
  outliers final: 1
  residues processed: 79
  average time/residue: 0.7807
  time to fit residues: 63.4528
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.146362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.124097 restraints weight = 4764.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.35
r_work: 0.3319 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.134   4642  Z= 0.148
  Angle     :  0.767  16.267   6358  Z= 0.272
  Chirality :  0.041   0.178    688
  Planarity :  0.006   0.047    794
  Dihedral  :  9.757  85.161    620
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.08 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.57 (0.36), residues: 560
  helix:  2.54 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.91 (0.66), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 104 
 TYR   0.012   0.002   TYR C  24 
 PHE   0.010   0.002   PHE D 118 
 TRP   0.010   0.002   TRP C  14 
 HIS   0.006   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4638)
  covalent geometry    : angle       0.76691 ( 6358)
  hydrogen bonds       : bond        0.03928 (  333)
  hydrogen bonds       : angle       3.69530 (  951)
  Misc. bond           : bond        0.09857 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7779 (mttt) cc_final: 0.7218 (mptt)
REVERT: A   76 MET cc_start: 0.7941 (mtt) cc_final: 0.7648 (mtt)
REVERT: A   92 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7622 (mtp180)
REVERT: B  120 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7588 (tttm)
REVERT: C   85 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7840 (m-30)
REVERT: C   90 LYS cc_start: 0.8312 (mptt) cc_final: 0.7836 (tttt)
REVERT: D   55 MET cc_start: 0.8721 (mmm) cc_final: 0.8408 (mmm)
REVERT: D   90 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7366 (tp30)
REVERT: D  120 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7709 (ptmm)
  outliers start: 13
  outliers final: 4
  residues processed: 75
  average time/residue: 0.7807
  time to fit residues: 60.2636
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0270
   chunk 51 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6642

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.149234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127678 restraints weight = 4888.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.33
r_work: 0.3346 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.127   4642  Z= 0.121
  Angle     :  0.747  16.321   6358  Z= 0.257
  Chirality :  0.039   0.169    688
  Planarity :  0.005   0.046    794
  Dihedral  :  9.623  85.976    620
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.18 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.73 (0.36), residues: 560
  helix:  2.69 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.83 (0.65), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 104 
 TYR   0.008   0.001   TYR C  24 
 PHE   0.008   0.001   PHE D 118 
 TRP   0.008   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4638)
  covalent geometry    : angle       0.74716 ( 6358)
  hydrogen bonds       : bond        0.03384 (  333)
  hydrogen bonds       : angle       3.59569 (  951)
  Misc. bond           : bond        0.09453 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7749 (mttt) cc_final: 0.7201 (mptt)
REVERT: A   92 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7646 (mtp180)
REVERT: B   43 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7115 (mp0)
REVERT: B  120 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7772 (mttt)
REVERT: C   85 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7813 (m-30)
REVERT: C   90 LYS cc_start: 0.8305 (mptt) cc_final: 0.7837 (tttt)
REVERT: D   90 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7372 (tp30)
REVERT: D  120 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7718 (ptmm)
  outliers start: 11
  outliers final: 2
  residues processed: 70
  average time/residue: 0.8134
  time to fit residues: 58.5970
Evaluate side-chains
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 52 optimal weight:    0.2980
   chunk 35 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3691 r_free = 0.3691 target = 0.149329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.127762 restraints weight = 4810.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.32
r_work: 0.3345 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.141   4642  Z= 0.120
  Angle     :  0.747  16.148   6358  Z= 0.257
  Chirality :  0.039   0.181    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.550  85.258    620
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.62 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.84 (0.36), residues: 560
  helix:  2.76 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.92 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.008   0.001   TYR C  24 
 PHE   0.008   0.001   PHE D 118 
 TRP   0.009   0.002   TRP C  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4638)
  covalent geometry    : angle       0.74745 ( 6358)
  hydrogen bonds       : bond        0.03390 (  333)
  hydrogen bonds       : angle       3.58368 (  951)
  Misc. bond           : bond        0.09473 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7736 (mttt) cc_final: 0.7190 (mptt)
REVERT: A   76 MET cc_start: 0.7924 (mtt) cc_final: 0.7665 (mtt)
REVERT: A   92 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7626 (mtp180)
REVERT: B   43 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7105 (mp0)
REVERT: B  120 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7791 (mttt)
REVERT: C   85 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7823 (m-30)
REVERT: C   90 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7828 (tttt)
REVERT: D   90 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7342 (tp30)
REVERT: D  120 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7724 (ptmm)
  outliers start: 12
  outliers final: 4
  residues processed: 68
  average time/residue: 0.7795
  time to fit residues: 54.5361
Evaluate side-chains
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3684 r_free = 0.3684 target = 0.148127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.125754 restraints weight = 4787.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.36
r_work: 0.3341 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.139   4642  Z= 0.118
  Angle     :  0.743  16.106   6358  Z= 0.255
  Chirality :  0.039   0.184    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.510  85.212    620
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.28 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.87 (0.36), residues: 560
  helix:  2.78 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.95 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 104 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.008   0.001   PHE D 118 
 TRP   0.008   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4638)
  covalent geometry    : angle       0.74316 ( 6358)
  hydrogen bonds       : bond        0.03303 (  333)
  hydrogen bonds       : angle       3.56970 (  951)
  Misc. bond           : bond        0.09055 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7737 (mttt) cc_final: 0.7189 (mptt)
REVERT: A   76 MET cc_start: 0.7955 (mtt) cc_final: 0.7545 (mtt)
REVERT: A   92 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7650 (mtp180)
REVERT: B  120 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7824 (mttt)
REVERT: C   85 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7823 (m-30)
REVERT: C   90 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7834 (tttt)
REVERT: D   90 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7366 (tp30)
REVERT: D  120 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7726 (ptmm)
  outliers start: 10
  outliers final: 4
  residues processed: 68
  average time/residue: 0.8018
  time to fit residues: 56.1587
Evaluate side-chains
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 9 optimal weight:    0.0770
   chunk 50 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.5740

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3637 r_free = 0.3637 target = 0.147208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.122703 restraints weight = 4642.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.47
r_work: 0.3219 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.124   4642  Z= 0.114
  Angle     :  0.738  15.881   6358  Z= 0.253
  Chirality :  0.039   0.184    688
  Planarity :  0.005   0.044    794
  Dihedral  :  9.464  84.947    620
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.72 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.89 (0.36), residues: 560
  helix:  2.81 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.92 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.007   0.001   PHE D 118 
 TRP   0.008   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4638)
  covalent geometry    : angle       0.73819 ( 6358)
  hydrogen bonds       : bond        0.03237 (  333)
  hydrogen bonds       : angle       3.54560 (  951)
  Misc. bond           : bond        0.08180 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7562 (mttt) cc_final: 0.6750 (mptt)
REVERT: A   92 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7502 (mtp180)
REVERT: B  120 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7602 (mttt)
REVERT: C   85 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7665 (m-30)
REVERT: C   90 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7730 (tttt)
REVERT: D   90 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7129 (tp30)
REVERT: D   95 LYS cc_start: 0.7903 (tttm) cc_final: 0.7325 (mmtp)
REVERT: D  120 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7538 (ptmm)
  outliers start: 9
  outliers final: 2
  residues processed: 68
  average time/residue: 0.7288
  time to fit residues: 51.1170
Evaluate side-chains
  66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue   14 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0370
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 53 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3641 r_free = 0.3641 target = 0.147541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.123043 restraints weight = 4645.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.47
r_work: 0.3225 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120   4642  Z= 0.113
  Angle     :  0.737  15.906   6358  Z= 0.253
  Chirality :  0.039   0.186    688
  Planarity :  0.005   0.044    794
  Dihedral  :  9.455  85.112    620
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 18.94 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.94 (0.36), residues: 560
  helix:  2.84 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.95 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.007   0.001   PHE D 118 
 TRP   0.008   0.001   TRP C  14 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4638)
  covalent geometry    : angle       0.73659 ( 6358)
  hydrogen bonds       : bond        0.03188 (  333)
  hydrogen bonds       : angle       3.53489 (  951)
  Misc. bond           : bond        0.07930 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7556 (mttt) cc_final: 0.6744 (mptt)
REVERT: A   76 MET cc_start: 0.7710 (mtt) cc_final: 0.7454 (mtt)
REVERT: A   92 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7505 (mtp180)
REVERT: B  120 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7584 (mttt)
REVERT: C   85 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7658 (m-30)
REVERT: C   90 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7723 (tttt)
REVERT: D   90 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7137 (tp30)
REVERT: D   95 LYS cc_start: 0.7908 (tttm) cc_final: 0.7327 (mmtp)
REVERT: D  120 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7535 (ptmm)
  outliers start: 7
  outliers final: 3
  residues processed: 66
  average time/residue: 0.8030
  time to fit residues: 54.5974
Evaluate side-chains
  67 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue   14 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3622 r_free = 0.3622 target = 0.145785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.121169 restraints weight = 4643.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.48
r_work: 0.3201 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.188   4642  Z= 0.134
  Angle     :  0.766  16.206   6358  Z= 0.266
  Chirality :  0.040   0.188    688
  Planarity :  0.006   0.044    794
  Dihedral  :  9.610  84.738    620
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.06 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.68 (0.36), residues: 560
  helix:  2.66 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.83 (0.65), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 104 
 TYR   0.008   0.001   TYR D  35 
 PHE   0.009   0.001   PHE D 118 
 TRP   0.010   0.002   TRP C  14 
 HIS   0.005   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4638)
  covalent geometry    : angle       0.76639 ( 6358)
  hydrogen bonds       : bond        0.03646 (  333)
  hydrogen bonds       : angle       3.62127 (  951)
  Misc. bond           : bond        0.11911 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1919.20 seconds
wall clock time: 33 minutes 26.74 seconds (2006.74 seconds total)