Starting phenix.real_space_refine
on Fri Aug 22 15:13:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqt_45822/08_2025/9cqt_45822.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqt_45822/08_2025/9cqt_45822.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqt_45822/08_2025/9cqt_45822.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqt_45822/08_2025/9cqt_45822.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqt_45822/08_2025/9cqt_45822.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqt_45822/08_2025/9cqt_45822.map"
  }
  resolution = 2.37
  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=   0.027
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 21 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: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 79
          Classifications: {'water': 79}
          Link IDs: {None: 78}
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 61
          Classifications: {'water': 61}
          Link IDs: {None: 60}
    Chain: "C"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 87
          Classifications: {'water': 87}
          Link IDs: {None: 86}
    Chain: "D"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 63
          Classifications: {'water': 63}
          Link IDs: {None: 62}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   HOH B 318 " occ=0.59
  Time building chain proxies: 1.25, per 1000 atoms: 0.26
  Number of scatterers: 4790
  At special positions: 0
  Unit cell: (77.175, 72.765, 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: 0.30
  Conformation dependent library (CDL) restraints added in 163.3 milliseconds
  
  Enol-peptide restraints added in 476.8 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
      87.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  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
    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 95 through 113
      removed outlier: 3.789A  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 17
      removed outlier: 3.925A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.180A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 4.107A  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 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.040A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.664A  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: 3.506A  pdb=" N   THR C  41 " --> pdb=" O   THR C  38 " (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 90
    Processing helix  chain 'C' and resid 95 through 113
      removed outlier: 3.809A  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: 3.887A  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: 4.121A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   SER D  44 " --> pdb=" O   PHE D  41 " (cutoff:3.500A)
      removed outlier: 4.195A  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: 3.544A  pdb=" N   LYS D  95 " --> pdb=" O   LEU D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 119
      removed outlier: 3.749A  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

    338 hydrogen bonds defined for protein.
    957 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: 0.63

  Time building geometry restraints manager: 0.44 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: 1560
        1.38 -     1.55: 3034
        1.55 -     1.72: 10
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4638
  Sorted by residual:
  bond pdb=" N   THR C  39 "
       pdb=" CA  THR C  39 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.82e+00
  bond pdb=" N   VAL A  93 "
       pdb=" CA  VAL A  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.24e-02 6.50e+03 9.58e+00
  bond pdb=" N   LYS C  40 "
       pdb=" CA  LYS C  40 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.90e+00
  bond pdb=" N   LEU A  91 "
       pdb=" CA  LEU A  91 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.23e-02 6.61e+03 7.50e+00
  bond pdb=" N   THR C  41 "
       pdb=" CA  THR C  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 6.80e+00
  ... (remaining 4633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 6014
        1.20 -     2.40: 227
        2.40 -     3.60: 74
        3.60 -     4.80: 31
        4.80 -     6.00: 12
  Bond angle restraints: 6358
  Sorted by residual:
  angle pdb=" C   PHE C  36 "
        pdb=" N   PRO C  37 "
        pdb=" CA  PRO C  37 "
      ideal   model   delta    sigma   weight residual
     119.56  124.15   -4.59 1.02e+00 9.61e-01 2.02e+01
  angle pdb=" C   ALA A  88 "
        pdb=" N   HIS A  89 "
        pdb=" CA  HIS A  89 "
      ideal   model   delta    sigma   weight residual
     122.42  116.74    5.68 1.55e+00 4.16e-01 1.34e+01
  angle pdb=" CA  PHE C  43 "
        pdb=" CB  PHE C  43 "
        pdb=" CG  PHE C  43 "
      ideal   model   delta    sigma   weight residual
     113.80  117.40   -3.60 1.00e+00 1.00e+00 1.30e+01
  angle pdb=" CA  THR C  41 "
        pdb=" C   THR C  41 "
        pdb=" O   THR C  41 "
      ideal   model   delta    sigma   weight residual
     120.55  116.97    3.58 1.06e+00 8.90e-01 1.14e+01
  angle pdb=" CA  LEU A  91 "
        pdb=" C   LEU A  91 "
        pdb=" O   LEU A  91 "
      ideal   model   delta    sigma   weight residual
     120.42  116.89    3.53 1.06e+00 8.90e-01 1.11e+01
  ... (remaining 6353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 2259
       17.75 -    35.49: 251
       35.49 -    53.24: 82
       53.24 -    70.99: 25
       70.99 -    88.73: 9
  Dihedral angle restraints: 2626
    sinusoidal: 998
      harmonic: 1628
  Sorted by residual:
  dihedral pdb=" C1A HEM A 201 "
           pdb=" C2A HEM A 201 "
           pdb=" CAA HEM A 201 "
           pdb=" CBA HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   93.16   86.84     2      2.00e+01 2.50e-03 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
     180.00   94.37   85.63     2      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" C1A HEM B 201 "
           pdb=" C2A HEM B 201 "
           pdb=" CAA HEM B 201 "
           pdb=" CBA HEM B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.08  -80.08     2      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 2623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 505
       0.043 -    0.086: 141
       0.086 -    0.129: 34
       0.129 -    0.172: 5
       0.172 -    0.214: 3
  Chirality restraints: 688
  Sorted by residual:
  chirality pdb=" CA  PHE C  43 "
            pdb=" N   PHE C  43 "
            pdb=" C   PHE C  43 "
            pdb=" CB  PHE C  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CB  THR A 134 "
            pdb=" CA  THR A 134 "
            pdb=" OG1 THR A 134 "
            pdb=" CG2 THR A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 7.92e-01
  chirality pdb=" CB  THR C 134 "
            pdb=" CA  THR C 134 "
            pdb=" OG1 THR C 134 "
            pdb=" CG2 THR C 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.48e-01
  ... (remaining 685 not shown)

  Planarity restraints: 794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  50 "    0.044 5.00e-02 4.00e+02   6.62e-02 7.00e+00
        pdb=" N   PRO B  51 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B  51 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  51 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  94 "    0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO C  95 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A  87 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   HIS A  87 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   HIS A  87 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A  88 "    0.011 2.00e-02 2.50e+03
  ... (remaining 791 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 136
        2.65 -     3.21: 4258
        3.21 -     3.78: 8510
        3.78 -     4.34: 11898
        4.34 -     4.90: 18118
  Nonbonded interactions: 42920
  Sorted by model distance:
  nonbonded pdb=" O   VAL C  93 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" NE2 HIS D  92 "
            pdb="FE   HEM D 201 "
     model   vdw
     2.145 3.080
  nonbonded pdb=" NE2 HIS B  92 "
            pdb="FE   HEM B 201 "
     model   vdw
     2.146 3.080
  nonbonded pdb=" OD1 ASP C  85 "
            pdb=" O   HOH C 301 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O   HOH C 357 "
            pdb=" O   HOH D 346 "
     model   vdw
     2.189 3.040
  ... (remaining 42915 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=0.59 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:             4.070
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.340
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
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      :  0.014   0.588   4642  Z= 0.221
  Angle     :  0.684   6.005   6358  Z= 0.378
  Chirality :  0.043   0.214    688
  Planarity :  0.006   0.066    794
  Dihedral  : 18.270  88.735   1574
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 19.82 %
    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:  3.48 (0.37), residues: 560
  helix:  2.50 (0.24), residues: 428
  sheet:  None (None), residues: 0
  loop :  1.87 (0.67), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  92 
 TYR   0.011   0.002   TYR C  42 
 PHE   0.013   0.002   PHE C  43 
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 4638)
  covalent geometry    : angle       0.68415 ( 6358)
  hydrogen bonds       : bond        0.10178 (  338)
  hydrogen bonds       : angle       4.29880 (  957)
  Misc. bond           : bond        0.45647 (    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
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7955 (mmmm) cc_final: 0.7662 (tptm)
REVERT: A   90 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7543 (tttt)
REVERT: B   84 THR cc_start: 0.8113 (m) cc_final: 0.7894 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 81
  average time/residue: 0.7205
  time to fit residues: 60.2396
Evaluate side-chains
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.153679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.131059 restraints weight = 4274.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.11
r_work: 0.3317 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.0691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.018   0.697   4642  Z= 0.154
  Angle     :  0.727  14.798   6358  Z= 0.279
  Chirality :  0.041   0.167    688
  Planarity :  0.006   0.060    794
  Dihedral  : 10.344  86.258    624
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.54 %
    Favored  : 82.82 %
  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:  3.36 (0.36), residues: 560
  helix:  2.38 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.89 (0.66), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  92 
 TYR   0.010   0.002   TYR D  35 
 PHE   0.010   0.002   PHE B 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4638)
  covalent geometry    : angle       0.72680 ( 6358)
  hydrogen bonds       : bond        0.04112 (  338)
  hydrogen bonds       : angle       3.93766 (  957)
  Misc. bond           : bond        0.59762 (    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
  91 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8130 (mppt) cc_final: 0.7638 (tttt)
REVERT: B   84 THR cc_start: 0.8076 (m) cc_final: 0.7869 (m)
REVERT: C   38 THR cc_start: 0.8348 (p) cc_final: 0.8106 (t)
REVERT: C   60 LYS cc_start: 0.8435 (tttm) cc_final: 0.7840 (ttmp)
REVERT: C   85 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7827 (t70)
REVERT: C  126 ASP cc_start: 0.8072 (t70) cc_final: 0.7796 (t70)
  outliers start: 12
  outliers final: 1
  residues processed: 82
  average time/residue: 0.6709
  time to fit residues: 56.6704
Evaluate side-chains
  81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue  127 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0870
   chunk 41 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.155070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.132844 restraints weight = 4258.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.08
r_work: 0.3338 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.240   4642  Z= 0.118
  Angle     :  0.714  15.530   6358  Z= 0.257
  Chirality :  0.039   0.167    688
  Planarity :  0.006   0.058    794
  Dihedral  : 10.012  85.103    620
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.20 %
    Favored  : 82.82 %
  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:  3.69 (0.36), residues: 560
  helix:  2.62 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.03 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  92 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4638)
  covalent geometry    : angle       0.71407 ( 6358)
  hydrogen bonds       : bond        0.03508 (  338)
  hydrogen bonds       : angle       3.80322 (  957)
  Misc. bond           : bond        0.21759 (    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
  88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7879 (ttmp)
REVERT: A   90 LYS cc_start: 0.8131 (mppt) cc_final: 0.7649 (tttt)
REVERT: C   38 THR cc_start: 0.8339 (p) cc_final: 0.8109 (t)
REVERT: C   60 LYS cc_start: 0.8421 (tttm) cc_final: 0.7838 (ttmp)
REVERT: C  126 ASP cc_start: 0.8059 (t70) cc_final: 0.7779 (t70)
  outliers start: 9
  outliers final: 0
  residues processed: 82
  average time/residue: 0.6649
  time to fit residues: 56.1075
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 11 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.156416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.132351 restraints weight = 4257.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.19
r_work: 0.3336 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.0946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.097   4642  Z= 0.123
  Angle     :  0.743  16.197   6358  Z= 0.263
  Chirality :  0.039   0.177    688
  Planarity :  0.006   0.057    794
  Dihedral  : 10.033  85.974    620
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.64 %
    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 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:  2.62 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.98 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  92 
 TYR   0.008   0.001   TYR D  35 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4638)
  covalent geometry    : angle       0.74348 ( 6358)
  hydrogen bonds       : bond        0.03684 (  338)
  hydrogen bonds       : angle       3.79712 (  957)
  Misc. bond           : bond        0.08109 (    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
  89 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7816 (ttmp)
REVERT: A   85 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7694 (t70)
REVERT: A   90 LYS cc_start: 0.8118 (mppt) cc_final: 0.7589 (tttt)
REVERT: B  121 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7834 (mt-10)
REVERT: C   38 THR cc_start: 0.8333 (p) cc_final: 0.8131 (t)
REVERT: C   60 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7767 (ttmp)
REVERT: C  126 ASP cc_start: 0.8011 (t70) cc_final: 0.7730 (t70)
REVERT: D   95 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7236 (tmtt)
  outliers start: 11
  outliers final: 1
  residues processed: 81
  average time/residue: 0.6873
  time to fit residues: 57.3284
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain C residue   60 LYS
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   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  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.156028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.131940 restraints weight = 4259.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.19
r_work: 0.3333 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   4642  Z= 0.124
  Angle     :  0.756  16.901   6358  Z= 0.265
  Chirality :  0.040   0.180    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.035  85.783    620
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.86 %
    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 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:  3.62 (0.36), residues: 560
  helix:  2.58 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.93 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 104 
 TYR   0.008   0.001   TYR D  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4638)
  covalent geometry    : angle       0.75611 ( 6358)
  hydrogen bonds       : bond        0.03700 (  338)
  hydrogen bonds       : angle       3.80144 (  957)
  Misc. bond           : bond        0.07592 (    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
  88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7813 (ttmp)
REVERT: A   85 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7696 (t70)
REVERT: A   90 LYS cc_start: 0.8119 (mppt) cc_final: 0.7582 (tttt)
REVERT: B  120 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8068 (tttm)
REVERT: C   38 THR cc_start: 0.8359 (p) cc_final: 0.8151 (t)
REVERT: C   60 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7763 (ttmp)
REVERT: C  126 ASP cc_start: 0.8008 (t70) cc_final: 0.7668 (t70)
REVERT: D   95 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7254 (tmtt)
  outliers start: 10
  outliers final: 1
  residues processed: 82
  average time/residue: 0.6699
  time to fit residues: 56.5698
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   60 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   95 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:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 47 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.155786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.131631 restraints weight = 4331.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.20
r_work: 0.3330 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.123   4642  Z= 0.123
  Angle     :  0.756  16.949   6358  Z= 0.263
  Chirality :  0.039   0.183    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.022  85.777    620
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.74 %
    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:  3.69 (0.36), residues: 560
  helix:  2.63 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.00 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 104 
 TYR   0.008   0.001   TYR D  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4638)
  covalent geometry    : angle       0.75580 ( 6358)
  hydrogen bonds       : bond        0.03673 (  338)
  hydrogen bonds       : angle       3.77848 (  957)
  Misc. bond           : bond        0.08371 (    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
  87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7814 (ttmp)
REVERT: A   85 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7708 (t70)
REVERT: A   90 LYS cc_start: 0.8114 (mppt) cc_final: 0.7568 (tttt)
REVERT: B  120 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8103 (tttm)
REVERT: C   60 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7776 (ttmp)
REVERT: C  126 ASP cc_start: 0.8010 (t70) cc_final: 0.7673 (t70)
REVERT: D   95 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7225 (tmtt)
  outliers start: 9
  outliers final: 1
  residues processed: 81
  average time/residue: 0.6581
  time to fit residues: 54.8869
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   60 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 28 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.156026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.132034 restraints weight = 4253.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.18
r_work: 0.3333 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134   4642  Z= 0.122
  Angle     :  0.759  17.001   6358  Z= 0.263
  Chirality :  0.039   0.186    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.013  85.796    620
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.40 %
    Favored  : 80.84 %
  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 (0.36), residues: 560
  helix:  2.66 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.06 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  92 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4638)
  covalent geometry    : angle       0.75897 ( 6358)
  hydrogen bonds       : bond        0.03614 (  338)
  hydrogen bonds       : angle       3.75999 (  957)
  Misc. bond           : bond        0.09474 (    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
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7811 (ttmp)
REVERT: A   85 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7685 (t70)
REVERT: A   90 LYS cc_start: 0.8082 (mppt) cc_final: 0.7536 (tttt)
REVERT: C   60 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7774 (ttmp)
REVERT: C  126 ASP cc_start: 0.8011 (t70) cc_final: 0.7650 (t70)
REVERT: D   95 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7267 (tmtt)
  outliers start: 8
  outliers final: 1
  residues processed: 78
  average time/residue: 0.6648
  time to fit residues: 53.2958
Evaluate side-chains
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain C residue   60 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.155978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.131856 restraints weight = 4296.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.18
r_work: 0.3329 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134   4642  Z= 0.123
  Angle     :  0.763  17.079   6358  Z= 0.263
  Chirality :  0.039   0.187    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.009  85.801    620
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.18 %
    Favored  : 80.84 %
  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:  3.76 (0.36), residues: 560
  helix:  2.67 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.04 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 104 
 TYR   0.007   0.001   TYR D  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4638)
  covalent geometry    : angle       0.76323 ( 6358)
  hydrogen bonds       : bond        0.03626 (  338)
  hydrogen bonds       : angle       3.75109 (  957)
  Misc. bond           : bond        0.11709 (    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
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7810 (ttmp)
REVERT: A   85 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7697 (t70)
REVERT: C   60 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7816 (ttmp)
REVERT: C  126 ASP cc_start: 0.8014 (t70) cc_final: 0.7667 (t70)
REVERT: D   95 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7214 (tmtt)
  outliers start: 9
  outliers final: 3
  residues processed: 74
  average time/residue: 0.6435
  time to fit residues: 49.0638
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   60 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    0.1980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.155646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.131728 restraints weight = 4257.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.18
r_work: 0.3339 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.138   4642  Z= 0.124
  Angle     :  0.768  17.196   6358  Z= 0.265
  Chirality :  0.040   0.187    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.023  85.779    620
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.06 %
    Favored  : 80.18 %
  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 (0.36), residues: 560
  helix:  2.66 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.04 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 104 
 TYR   0.009   0.001   TYR C 140 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4638)
  covalent geometry    : angle       0.76795 ( 6358)
  hydrogen bonds       : bond        0.03662 (  338)
  hydrogen bonds       : angle       3.76189 (  957)
  Misc. bond           : bond        0.12914 (    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
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7811 (ttmp)
REVERT: A   85 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7688 (t70)
REVERT: C   60 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7772 (ttmp)
REVERT: C  126 ASP cc_start: 0.8008 (t70) cc_final: 0.7674 (t70)
REVERT: D   95 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7174 (tmtt)
  outliers start: 8
  outliers final: 2
  residues processed: 72
  average time/residue: 0.6993
  time to fit residues: 51.8499
Evaluate side-chains
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   60 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.155693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.131648 restraints weight = 4264.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.18
r_work: 0.3331 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.137   4642  Z= 0.124
  Angle     :  0.768  17.060   6358  Z= 0.266
  Chirality :  0.040   0.189    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.014  85.727    620
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 18.50 %
    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:  3.76 (0.36), residues: 560
  helix:  2.67 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.05 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 104 
 TYR   0.010   0.001   TYR C 140 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.006   0.001   TRP C  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4638)
  covalent geometry    : angle       0.76759 ( 6358)
  hydrogen bonds       : bond        0.03651 (  338)
  hydrogen bonds       : angle       3.75705 (  957)
  Misc. bond           : bond        0.13062 (    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
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7816 (ttmp)
REVERT: A   85 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7692 (t70)
REVERT: C   60 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7771 (ttmp)
REVERT: C  126 ASP cc_start: 0.8011 (t70) cc_final: 0.7677 (t70)
  outliers start: 5
  outliers final: 1
  residues processed: 70
  average time/residue: 0.7031
  time to fit residues: 50.6638
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain C residue   60 LYS
Chi-restraints excluded: chain C residue  127 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   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  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.156037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.132018 restraints weight = 4254.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.18
r_work: 0.3336 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1222

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= 0.120
  Angle     :  0.762  17.044   6358  Z= 0.263
  Chirality :  0.039   0.189    688
  Planarity :  0.006   0.056    794
  Dihedral  :  9.961  85.635    620
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 18.72 %
    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:  2.71 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.07 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 104 
 TYR   0.011   0.001   TYR C 140 
 PHE   0.008   0.001   PHE B 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4638)
  covalent geometry    : angle       0.76221 ( 6358)
  hydrogen bonds       : bond        0.03522 (  338)
  hydrogen bonds       : angle       3.73678 (  957)
  Misc. bond           : bond        0.12068 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1881.84 seconds
wall clock time: 32 minutes 46.28 seconds (1966.28 seconds total)