Starting phenix.real_space_refine
on Wed Jun 11 12:54:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vg0_43196/06_2025/8vg0_43196.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vg0_43196/06_2025/8vg0_43196.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vg0_43196/06_2025/8vg0_43196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vg0_43196/06_2025/8vg0_43196.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vg0_43196/06_2025/8vg0_43196.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vg0_43196/06_2025/8vg0_43196.cif"
  }
  resolution = 3.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.108
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     318      5.49       5
     S      20      5.16       5
     C    7214      2.51       5
     N    2436      2.21       5
     O    3053      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13042
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "I"
      Number of atoms: 3258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 3258
          Classifications: {'DNA': 159}
          Link IDs: {'rna3p': 158}
    Chain: "J"
      Number of atoms: 3261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 3261
          Classifications: {'DNA': 159}
          Link IDs: {'rna3p': 158}
    Chain: "A"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 856
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "T"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 414
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 3, 'TRANS': 49}
    Chain: "T"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12647  SG  CYS T 271      13.598 101.162  82.539  1.00310.47           S
  ATOM  12666  SG  CYS T 274      13.084 100.826  78.752  1.00313.28           S
  ATOM  12809  SG  CYS T 292      16.436  99.804  80.350  1.00287.96           S
  ATOM  12828  SG  CYS T 295      15.448 103.401  80.082  1.00302.98           S

  Time building chain proxies: 7.55, per 1000 atoms: 0.58
  Number of scatterers: 13042
  At special positions: 0
  Unit cell: (81.312, 121.44, 147.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      20     16.00
     P     318     15.00
     O    3053      8.00
     N    2436      7.00
     C    7214      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.45
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN T 501 "
        pdb="ZN    ZN T 501 " - pdb=" SG  CYS T 295 "
        pdb="ZN    ZN T 501 " - pdb=" SG  CYS T 292 "
        pdb="ZN    ZN T 501 " - pdb=" SG  CYS T 274 "
        pdb="ZN    ZN T 501 " - pdb=" SG  CYS T 271 "
      Number of angles added : 6


  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1534

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 11 sheets defined
      69.5% alpha, 2.7% beta
      159 base pairs and 284 stacking pairs defined.
    Time for finding SS restraints: 6.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.821A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.534A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.700A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.316A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
      removed outlier: 3.600A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.930A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.699A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.306A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
    Processing helix  chain 'T' and resid 292 through 303
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.831A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.264A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.636A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.218A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.472A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'T' and resid 283 through 284

    423 hydrogen bonds defined for protein.
    1239 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      387 hydrogen bonds
      774 hydrogen bond angles
      0 basepair planarities
      159 basepair parallelities
      284 stacking parallelities
  Total time for adding SS restraints: 5.26

  Time building geometry restraints manager: 4.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2921
        1.34 -     1.45: 4077
        1.45 -     1.57: 6256
        1.57 -     1.69: 634
        1.69 -     1.81: 32
  Bond restraints: 13920
  Sorted by residual:
  bond pdb=" C1'  DT J  55 "
       pdb=" N1   DT J  55 "
    ideal  model  delta    sigma   weight residual
    1.490  1.544 -0.054 3.00e-02 1.11e+03 3.29e+00
  bond pdb=" N   ALA C  10 "
       pdb=" CA  ALA C  10 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  bond pdb=" C3'  DC J  93 "
       pdb=" O3'  DC J  93 "
    ideal  model  delta    sigma   weight residual
    1.422  1.475 -0.053 3.00e-02 1.11e+03 3.10e+00
  bond pdb=" CA  ASP F  24 "
       pdb=" CB  ASP F  24 "
    ideal  model  delta    sigma   weight residual
    1.528  1.553 -0.024 1.39e-02 5.18e+03 3.04e+00
  bond pdb=" N   LEU T 269 "
       pdb=" CA  LEU T 269 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  ... (remaining 13915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 19589
        2.15 -     4.30: 542
        4.30 -     6.45: 23
        6.45 -     8.60: 1
        8.60 -    10.75: 1
  Bond angle restraints: 20156
  Sorted by residual:
  angle pdb=" CB  MET T 299 "
        pdb=" CG  MET T 299 "
        pdb=" SD  MET T 299 "
      ideal   model   delta    sigma   weight residual
     112.70  123.45  -10.75 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" CA  MET T 299 "
        pdb=" CB  MET T 299 "
        pdb=" CG  MET T 299 "
      ideal   model   delta    sigma   weight residual
     114.10  120.52   -6.42 2.00e+00 2.50e-01 1.03e+01
  angle pdb=" C2'  DT I 161 "
        pdb=" C1'  DT I 161 "
        pdb=" N1   DT I 161 "
      ideal   model   delta    sigma   weight residual
     113.50  118.10   -4.60 1.50e+00 4.44e-01 9.41e+00
  angle pdb=" C2'  DT I  69 "
        pdb=" C1'  DT I  69 "
        pdb=" N1   DT I  69 "
      ideal   model   delta    sigma   weight residual
     113.50  117.69   -4.19 1.50e+00 4.44e-01 7.81e+00
  angle pdb=" C3'  DC J  93 "
        pdb=" O3'  DC J  93 "
        pdb=" P    DC J  94 "
      ideal   model   delta    sigma   weight residual
     120.20  124.38   -4.18 1.50e+00 4.44e-01 7.75e+00
  ... (remaining 20151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.38: 6117
       33.38 -    66.76: 1488
       66.76 -   100.14: 40
      100.14 -   133.53: 0
      133.53 -   166.91: 2
  Dihedral angle restraints: 7647
    sinusoidal: 5268
      harmonic: 2379
  Sorted by residual:
  dihedral pdb=" C4'  DG J 127 "
           pdb=" C3'  DG J 127 "
           pdb=" O3'  DG J 127 "
           pdb=" P    DG J 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   53.09  166.91     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'  DC J  93 "
           pdb=" C3'  DC J  93 "
           pdb=" O3'  DC J  93 "
           pdb=" P    DC J  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   65.81  154.19     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CG  ARG A 131 "
           pdb=" CD  ARG A 131 "
           pdb=" NE  ARG A 131 "
           pdb=" CZ  ARG A 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.09   44.91     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 7644 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1463
       0.029 -    0.058: 465
       0.058 -    0.087: 291
       0.087 -    0.116: 59
       0.116 -    0.145: 12
  Chirality restraints: 2290
  Sorted by residual:
  chirality pdb=" P    DC J  94 "
            pdb=" OP1  DC J  94 "
            pdb=" OP2  DC J  94 "
            pdb=" O5'  DC J  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.49   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  VAL T 304 "
            pdb=" N   VAL T 304 "
            pdb=" C   VAL T 304 "
            pdb=" CB  VAL T 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  ... (remaining 2287 not shown)

  Planarity restraints: 1448
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  83 "    0.001 2.00e-02 2.50e+03   1.50e-02 4.49e+00
        pdb=" CG  TYR D  83 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  83 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  83 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  83 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  83 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  83 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D  83 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 131 "    0.026 2.00e-02 2.50e+03   1.13e-02 3.84e+00
        pdb=" N9   DG I 131 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8   DG I 131 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I 131 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5   DG I 131 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DG I 131 "    0.006 2.00e-02 2.50e+03
        pdb=" O6   DG I 131 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I 131 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I 131 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I 131 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DG I 131 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I 131 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I 161 "    0.022 2.00e-02 2.50e+03   1.15e-02 3.31e+00
        pdb=" N1   DT I 161 "   -0.026 2.00e-02 2.50e+03
        pdb=" C2   DT I 161 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2   DT I 161 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I 161 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DT I 161 "    0.004 2.00e-02 2.50e+03
        pdb=" O4   DT I 161 "    0.008 2.00e-02 2.50e+03
        pdb=" C5   DT I 161 "    0.002 2.00e-02 2.50e+03
        pdb=" C7   DT I 161 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DT I 161 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1445 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 149
        2.65 -     3.21: 10629
        3.21 -     3.77: 24270
        3.77 -     4.34: 31659
        4.34 -     4.90: 44714
  Nonbonded interactions: 111421
  Sorted by model distance:
  nonbonded pdb=" OP1  DG J 103 "
            pdb=" OG  SER D  32 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   PHE G  25 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" OP1  DA I 144 "
            pdb=" OG  SER H  32 "
     model   vdw
     2.141 3.040
  nonbonded pdb=" OP1  DC I  53 "
            pdb=" NH1 ARG T 284 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" N   GLU B  52 "
            pdb=" OE1 GLU B  52 "
     model   vdw
     2.230 3.120
  ... (remaining 111416 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 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 10 through 118)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.960
  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:             0.020
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     38.720
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
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      :  0.005   0.054  13924  Z= 0.205
  Angle     :  0.710  10.746  20162  Z= 0.433
  Chirality :  0.038   0.145   2290
  Planarity :  0.004   0.037   1448
  Dihedral  : 27.185 166.908   6113
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 1.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.29), residues: 805
  helix:  2.64 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop :  0.05 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T 282 
 HIS   0.003   0.001   HIS D  82 
 PHE   0.005   0.001   PHE A  67 
 TYR   0.028   0.002   TYR D  83 
 ARG   0.003   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10245 (  810)
  hydrogen bonds       : angle       3.48845 ( 2013)
  metal coordination   : bond        0.00312 (    4)
  metal coordination   : angle       1.82904 (    6)
  covalent geometry    : bond        0.00478 (13920)
  covalent geometry    : angle       0.70906 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7893 (pm20) cc_final: 0.7370 (pm20)
REVERT: A   76 GLN cc_start: 0.8480 (tp40) cc_final: 0.8238 (tp40)
REVERT: A  115 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8773 (mtmm)
REVERT: B   88 TYR cc_start: 0.7682 (m-10) cc_final: 0.7441 (m-10)
REVERT: D   59 MET cc_start: 0.8795 (tpp) cc_final: 0.8586 (mmm)
REVERT: D   83 TYR cc_start: 0.8038 (m-80) cc_final: 0.7518 (m-80)
REVERT: H   86 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.7162 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.4174
  time to fit residues: 76.3999
Evaluate side-chains
  123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  27 GLN
F  75 HIS
T 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.122013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.072021 restraints weight = 22093.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.32
r_work: 0.2750 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13924  Z= 0.188
  Angle     :  0.585   7.380  20162  Z= 0.354
  Chirality :  0.035   0.136   2290
  Planarity :  0.004   0.039   1448
  Dihedral  : 30.177 179.734   4473
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  8.47 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.94 (0.29), residues: 805
  helix:  2.74 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.06 (0.36), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T 282 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.037   0.002   TYR D  83 
 ARG   0.004   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04167 (  810)
  hydrogen bonds       : angle       2.81215 ( 2013)
  metal coordination   : bond        0.00435 (    4)
  metal coordination   : angle       2.46848 (    6)
  covalent geometry    : bond        0.00425 (13920)
  covalent geometry    : angle       0.58317 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
REVERT: B   95 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8231 (mtp85)
REVERT: D  101 LEU cc_start: 0.8478 (mt) cc_final: 0.8192 (mt)
REVERT: E   59 GLU cc_start: 0.8115 (pm20) cc_final: 0.7851 (pm20)
REVERT: F   25 ASN cc_start: 0.8407 (m110) cc_final: 0.8199 (m110)
REVERT: H   86 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.7122 (mtm180)
  outliers start: 12
  outliers final: 6
  residues processed: 137
  average time/residue: 0.4292
  time to fit residues: 75.7918
Evaluate side-chains
  122 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
F  93 GLN
H  47 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.122157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.072196 restraints weight = 22348.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 2.32
r_work: 0.2755 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13924  Z= 0.171
  Angle     :  0.565   5.560  20162  Z= 0.344
  Chirality :  0.034   0.140   2290
  Planarity :  0.004   0.034   1448
  Dihedral  : 30.173 177.509   4473
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.95 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.03 (0.29), residues: 805
  helix:  2.80 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.11 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T 282 
 HIS   0.002   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.013   0.001   TYR D  40 
 ARG   0.004   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  810)
  hydrogen bonds       : angle       2.70936 ( 2013)
  metal coordination   : bond        0.00367 (    4)
  metal coordination   : angle       2.19758 (    6)
  covalent geometry    : bond        0.00383 (13920)
  covalent geometry    : angle       0.56350 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8029 (mmm) cc_final: 0.7725 (mmm)
REVERT: C   74 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8610 (mtpp)
REVERT: D   35 GLU cc_start: 0.8522 (pt0) cc_final: 0.8194 (pt0)
REVERT: D   93 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7728 (mp0)
REVERT: E   59 GLU cc_start: 0.8127 (pm20) cc_final: 0.7776 (pm20)
REVERT: F   25 ASN cc_start: 0.8446 (m110) cc_final: 0.8174 (m110)
REVERT: H   86 ARG cc_start: 0.8347 (mmt-90) cc_final: 0.7120 (mtm180)
REVERT: T  299 MET cc_start: 0.6439 (tmm) cc_final: 0.5604 (pmm)
  outliers start: 11
  outliers final: 9
  residues processed: 127
  average time/residue: 0.3920
  time to fit residues: 64.2935
Evaluate side-chains
  125 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   47 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.125500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.076277 restraints weight = 22070.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.90
r_work: 0.2852 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13924  Z= 0.173
  Angle     :  0.558   6.117  20162  Z= 0.341
  Chirality :  0.034   0.134   2290
  Planarity :  0.003   0.033   1448
  Dihedral  : 30.251 176.897   4473
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.24 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.10 (0.29), residues: 805
  helix:  2.87 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.10 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T 282 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.015   0.001   TYR D  83 
 ARG   0.003   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  810)
  hydrogen bonds       : angle       2.65532 ( 2013)
  metal coordination   : bond        0.00352 (    4)
  metal coordination   : angle       2.02455 (    6)
  covalent geometry    : bond        0.00388 (13920)
  covalent geometry    : angle       0.55653 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8300 (m-10) cc_final: 0.7911 (m-10)
REVERT: D   35 GLU cc_start: 0.8474 (pt0) cc_final: 0.8147 (pt0)
REVERT: D   83 TYR cc_start: 0.8446 (m-10) cc_final: 0.8008 (m-10)
REVERT: D   93 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8049 (mp0)
REVERT: E   59 GLU cc_start: 0.8342 (pm20) cc_final: 0.8017 (pm20)
REVERT: F   25 ASN cc_start: 0.8542 (m110) cc_final: 0.8283 (m110)
REVERT: H   86 ARG cc_start: 0.8632 (mmt-90) cc_final: 0.7518 (mtm180)
  outliers start: 12
  outliers final: 11
  residues processed: 133
  average time/residue: 0.3787
  time to fit residues: 65.5426
Evaluate side-chains
  129 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.123719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.073946 restraints weight = 22240.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.97
r_work: 0.2814 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13924  Z= 0.205
  Angle     :  0.582   9.118  20162  Z= 0.349
  Chirality :  0.035   0.135   2290
  Planarity :  0.004   0.034   1448
  Dihedral  : 30.490 177.112   4473
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.68 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (0.29), residues: 805
  helix:  2.78 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.01 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP T 282 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.014   0.002   TYR D  40 
 ARG   0.005   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04085 (  810)
  hydrogen bonds       : angle       2.74254 ( 2013)
  metal coordination   : bond        0.00362 (    4)
  metal coordination   : angle       2.13848 (    6)
  covalent geometry    : bond        0.00470 (13920)
  covalent geometry    : angle       0.58058 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
REVERT: D   35 GLU cc_start: 0.8465 (pt0) cc_final: 0.8108 (pt0)
REVERT: E   59 GLU cc_start: 0.8391 (pm20) cc_final: 0.7982 (pm20)
REVERT: E  120 MET cc_start: 0.8441 (mtt) cc_final: 0.8224 (mtt)
REVERT: F   25 ASN cc_start: 0.8589 (m110) cc_final: 0.8297 (m110)
REVERT: H   68 ASP cc_start: 0.9021 (t0) cc_final: 0.8712 (t0)
REVERT: H   86 ARG cc_start: 0.8595 (mmt-90) cc_final: 0.7515 (mtm180)
REVERT: T  299 MET cc_start: 0.7067 (tmm) cc_final: 0.6048 (pmm)
  outliers start: 13
  outliers final: 9
  residues processed: 135
  average time/residue: 0.3833
  time to fit residues: 67.1086
Evaluate side-chains
  129 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   47 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 102 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 64 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.124802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.075762 restraints weight = 22494.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.10
r_work: 0.2831 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13924  Z= 0.152
  Angle     :  0.551   8.224  20162  Z= 0.335
  Chirality :  0.033   0.132   2290
  Planarity :  0.003   0.034   1448
  Dihedral  : 30.146 173.997   4473
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.12 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.23 (0.29), residues: 805
  helix:  2.98 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.11 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP T 282 
 HIS   0.004   0.001   HIS H  49 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.022   0.001   TYR D  83 
 ARG   0.003   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  810)
  hydrogen bonds       : angle       2.53519 ( 2013)
  metal coordination   : bond        0.00269 (    4)
  metal coordination   : angle       1.50318 (    6)
  covalent geometry    : bond        0.00333 (13920)
  covalent geometry    : angle       0.55097 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: C   13 LYS cc_start: 0.8993 (tptt) cc_final: 0.8716 (tppp)
REVERT: D   35 GLU cc_start: 0.8445 (pt0) cc_final: 0.8076 (pt0)
REVERT: D   83 TYR cc_start: 0.8093 (m-10) cc_final: 0.7815 (m-10)
REVERT: D   93 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7715 (mp0)
REVERT: E   59 GLU cc_start: 0.7984 (pm20) cc_final: 0.7323 (pm20)
REVERT: F   25 ASN cc_start: 0.8487 (m110) cc_final: 0.8111 (m110)
REVERT: H   86 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.7130 (mtm180)
REVERT: T  299 MET cc_start: 0.7044 (tmm) cc_final: 0.6079 (pmm)
  outliers start: 11
  outliers final: 7
  residues processed: 132
  average time/residue: 0.3758
  time to fit residues: 64.4095
Evaluate side-chains
  126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 104 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 50 optimal weight:    0.3980
   chunk 62 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
A 125 GLN
B  27 GLN
F  93 GLN
G 104 GLN
H  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.124455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.075534 restraints weight = 22367.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.07
r_work: 0.2834 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13924  Z= 0.159
  Angle     :  0.550   7.633  20162  Z= 0.336
  Chirality :  0.033   0.135   2290
  Planarity :  0.003   0.034   1448
  Dihedral  : 30.174 173.768   4473
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.70 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.25 (0.29), residues: 805
  helix:  2.99 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.13 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP T 282 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.032   0.002   TYR B  88 
 ARG   0.004   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  810)
  hydrogen bonds       : angle       2.56745 ( 2013)
  metal coordination   : bond        0.00300 (    4)
  metal coordination   : angle       1.63764 (    6)
  covalent geometry    : bond        0.00354 (13920)
  covalent geometry    : angle       0.54971 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8158 (mmm) cc_final: 0.7927 (mmm)
REVERT: C   13 LYS cc_start: 0.9018 (tptt) cc_final: 0.8732 (tppp)
REVERT: D   35 GLU cc_start: 0.8436 (pt0) cc_final: 0.8063 (pt0)
REVERT: D   59 MET cc_start: 0.8810 (tpp) cc_final: 0.8533 (mmm)
REVERT: D   93 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7790 (mp0)
REVERT: E   59 GLU cc_start: 0.8024 (pm20) cc_final: 0.7538 (pm20)
REVERT: F   25 ASN cc_start: 0.8526 (m110) cc_final: 0.8156 (m110)
REVERT: G  104 GLN cc_start: 0.9048 (mm110) cc_final: 0.8732 (mm110)
REVERT: H   86 ARG cc_start: 0.8356 (mmt-90) cc_final: 0.7223 (mtm180)
REVERT: T  299 MET cc_start: 0.7111 (tmm) cc_final: 0.6145 (pmm)
  outliers start: 11
  outliers final: 8
  residues processed: 129
  average time/residue: 0.3659
  time to fit residues: 61.7518
Evaluate side-chains
  129 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   47 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 106 optimal weight:    0.1980
   chunk 79 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0870
   chunk 82 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
H  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.125095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.076215 restraints weight = 22411.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 2.10
r_work: 0.2837 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13924  Z= 0.149
  Angle     :  0.547   8.047  20162  Z= 0.334
  Chirality :  0.033   0.154   2290
  Planarity :  0.003   0.034   1448
  Dihedral  : 30.135 173.231   4473
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 12.85 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.26 (0.29), residues: 805
  helix:  3.00 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.14 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP T 282 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.035   0.002   TYR B  88 
 ARG   0.004   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03557 (  810)
  hydrogen bonds       : angle       2.54777 ( 2013)
  metal coordination   : bond        0.00267 (    4)
  metal coordination   : angle       1.56692 (    6)
  covalent geometry    : bond        0.00324 (13920)
  covalent geometry    : angle       0.54689 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
REVERT: C   13 LYS cc_start: 0.9011 (tptt) cc_final: 0.8721 (tppp)
REVERT: D   35 GLU cc_start: 0.8397 (pt0) cc_final: 0.8015 (pt0)
REVERT: D   59 MET cc_start: 0.8761 (tpp) cc_final: 0.8475 (mmm)
REVERT: D   93 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7773 (mp0)
REVERT: E   59 GLU cc_start: 0.7858 (pm20) cc_final: 0.7345 (pm20)
REVERT: E  120 MET cc_start: 0.7843 (mtt) cc_final: 0.7548 (mtt)
REVERT: F   25 ASN cc_start: 0.8475 (m110) cc_final: 0.8088 (m110)
REVERT: F   95 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7791 (ttm-80)
REVERT: H   86 ARG cc_start: 0.8316 (mmt-90) cc_final: 0.7167 (mtm180)
REVERT: T  299 MET cc_start: 0.7066 (tmm) cc_final: 0.6117 (pmm)
  outliers start: 7
  outliers final: 5
  residues processed: 125
  average time/residue: 0.3698
  time to fit residues: 60.2314
Evaluate side-chains
  123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain F residue   50 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
G 104 GLN
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.123553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.074471 restraints weight = 22205.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.86
r_work: 0.2825 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13924  Z= 0.219
  Angle     :  0.589   7.416  20162  Z= 0.354
  Chirality :  0.035   0.176   2290
  Planarity :  0.004   0.033   1448
  Dihedral  : 30.492 174.469   4473
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.70 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.30), residues: 805
  helix:  2.79 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.07 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP T 282 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.053   0.002   TYR B  88 
 ARG   0.005   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  810)
  hydrogen bonds       : angle       2.76690 ( 2013)
  metal coordination   : bond        0.00387 (    4)
  metal coordination   : angle       1.95548 (    6)
  covalent geometry    : bond        0.00504 (13920)
  covalent geometry    : angle       0.58783 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8925 (pm20) cc_final: 0.8716 (pm20)
REVERT: D   35 GLU cc_start: 0.8414 (pt0) cc_final: 0.8051 (pt0)
REVERT: E   59 GLU cc_start: 0.8210 (pm20) cc_final: 0.7731 (pm20)
REVERT: E  120 MET cc_start: 0.8491 (mtt) cc_final: 0.8255 (mtt)
REVERT: F   25 ASN cc_start: 0.8636 (m110) cc_final: 0.8353 (m110)
REVERT: F   95 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8243 (ttm-80)
REVERT: G  104 GLN cc_start: 0.9263 (mm110) cc_final: 0.8962 (mm110)
REVERT: H   68 ASP cc_start: 0.9057 (t0) cc_final: 0.8762 (t0)
REVERT: H   86 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.7610 (mtm180)
REVERT: T  299 MET cc_start: 0.7162 (tmm) cc_final: 0.6181 (pmm)
  outliers start: 10
  outliers final: 10
  residues processed: 134
  average time/residue: 0.3934
  time to fit residues: 68.4339
Evaluate side-chains
  133 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   47 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 105 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   chunk 54 optimal weight:    0.1980
   chunk 44 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.125080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.076372 restraints weight = 22327.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.09
r_work: 0.2847 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13924  Z= 0.150
  Angle     :  0.557   8.960  20162  Z= 0.338
  Chirality :  0.033   0.166   2290
  Planarity :  0.003   0.035   1448
  Dihedral  : 30.093 172.301   4473
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 13.14 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.12 (0.29), residues: 805
  helix:  2.88 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.11 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP T 282 
 HIS   0.014   0.001   HIS H  49 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.035   0.002   TYR B  88 
 ARG   0.004   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  810)
  hydrogen bonds       : angle       2.57439 ( 2013)
  metal coordination   : bond        0.00272 (    4)
  metal coordination   : angle       1.48176 (    6)
  covalent geometry    : bond        0.00325 (13920)
  covalent geometry    : angle       0.55644 (20156)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8737 (pm20) cc_final: 0.8408 (pm20)
REVERT: C   13 LYS cc_start: 0.9034 (tptt) cc_final: 0.8728 (tppp)
REVERT: D   35 GLU cc_start: 0.8414 (pt0) cc_final: 0.8043 (pt0)
REVERT: D   59 MET cc_start: 0.8815 (tpp) cc_final: 0.8582 (mmm)
REVERT: E   59 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7336 (pm20)
REVERT: E  120 MET cc_start: 0.7962 (mtt) cc_final: 0.7641 (mtt)
REVERT: F   25 ASN cc_start: 0.8510 (m110) cc_final: 0.8153 (m110)
REVERT: F   95 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7884 (ttm-80)
REVERT: G  104 GLN cc_start: 0.9051 (mm110) cc_final: 0.8780 (mm-40)
REVERT: H   86 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.7250 (mtm180)
REVERT: T  299 MET cc_start: 0.7096 (tmm) cc_final: 0.6153 (pmm)
  outliers start: 9
  outliers final: 6
  residues processed: 129
  average time/residue: 0.3686
  time to fit residues: 62.4209
Evaluate side-chains
  127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain H residue   47 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    0.1980
   chunk 8 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0470
   chunk 47 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8080

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.124543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.075745 restraints weight = 22474.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.09
r_work: 0.2829 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13924  Z= 0.165
  Angle     :  0.566   8.821  20162  Z= 0.342
  Chirality :  0.033   0.169   2290
  Planarity :  0.003   0.034   1448
  Dihedral  : 30.133 172.354   4473
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 13.72 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.13 (0.29), residues: 805
  helix:  2.88 (0.21), residues: 560
  sheet:  None (None), residues: 0
  loop :  0.13 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T 282 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.050   0.002   TYR B  88 
 ARG   0.005   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03674 (  810)
  hydrogen bonds       : angle       2.64056 ( 2013)
  metal coordination   : bond        0.00318 (    4)
  metal coordination   : angle       1.64265 (    6)
  covalent geometry    : bond        0.00368 (13920)
  covalent geometry    : angle       0.56543 (20156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6497.01 seconds
wall clock time: 111 minutes 48.71 seconds (6708.71 seconds total)