Starting phenix.real_space_refine
on Thu Mar  6 10:09:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p0a_17331/03_2025/8p0a_17331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p0a_17331/03_2025/8p0a_17331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p0a_17331/03_2025/8p0a_17331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p0a_17331/03_2025/8p0a_17331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p0a_17331/03_2025/8p0a_17331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p0a_17331/03_2025/8p0a_17331.cif"
  }
  resolution = 3.67
  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=  -0.000 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      21      5.16       5
     C    3656      2.51       5
     N     989      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5764
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2805
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 355, 2796
          Classifications: {'peptide': 355}
          Link IDs: {'PTRANS': 14, 'TRANS': 340}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 355, 2796
          Classifications: {'peptide': 355}
          Link IDs: {'PTRANS': 14, 'TRANS': 340}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2836
    Chain: "B"
      Number of atoms: 2507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2507
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 10, 'TRANS': 303}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 388
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 3, 'TRANS': 45}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLN A 137 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 137 " occ=0.50
  Time building chain proxies: 5.04, per 1000 atoms: 0.87
  Number of scatterers: 5764
  At special positions: 0
  Unit cell: (75.684, 93.704, 99.11, 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)
     S      21     16.00
     P       6     15.00
     Mg      2     11.99
     O    1090      8.00
     N     989      7.00
     C    3656      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: 1.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1354

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      38.4% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 48
      removed outlier: 3.874A  pdb=" N   LEU A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   MET A  42 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 71
      removed outlier: 3.813A  pdb=" N   VAL A  70 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLY A  71 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 67 through 71'
    Processing helix  chain 'A' and resid 113 through 123
    Processing helix  chain 'A' and resid 138 through 144
      removed outlier: 3.717A  pdb=" N   ALA A 144 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 159
      removed outlier: 4.122A  pdb=" N   ALA A 153 " --> pdb=" O   LYS A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 167
      removed outlier: 5.059A  pdb=" N   GLN A 166 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 174
      removed outlier: 3.795A  pdb=" N   LYS A 172 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1057
    Processing helix  chain 'A' and resid 1059 through 1090
      removed outlier: 3.774A  pdb=" N   LYS A1063 " --> pdb=" O   PHE A1059 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER A1076 " --> pdb=" O   ALA A1072 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASP A1082 " --> pdb=" O   ALA A1078 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   GLU A1083 " --> pdb=" O   THR A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1124 through 1128
      removed outlier: 3.600A  pdb=" N   ASN A1127 " --> pdb=" O   PRO A1124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1142
      removed outlier: 3.750A  pdb=" N   THR A1134 " --> pdb=" O   GLY A1130 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL A1135 " --> pdb=" O   GLY A1131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1163 through 1178
      removed outlier: 4.043A  pdb=" N   GLY A1168 " --> pdb=" O   ASN A1164 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LYS A1169 " --> pdb=" O   THR A1165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1190 through 1196
      removed outlier: 3.661A  pdb=" N   TYR A1194 " --> pdb=" O   LYS A1190 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LYS A1196 " --> pdb=" O   GLU A1192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 46
    Processing helix  chain 'B' and resid 59 through 64
    Processing helix  chain 'B' and resid 117 through 120
    Processing helix  chain 'B' and resid 121 through 128
    Processing helix  chain 'B' and resid 151 through 162
      removed outlier: 3.544A  pdb=" N   ARG B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1033 through 1048
    Processing helix  chain 'B' and resid 1111 through 1115
    Processing helix  chain 'B' and resid 1118 through 1135
    Processing helix  chain 'B' and resid 1150 through 1163
      removed outlier: 4.090A  pdb=" N   MET B1160 " --> pdb=" O   ALA B1156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1178 through 1183
      removed outlier: 3.873A  pdb=" N   GLU B1181 " --> pdb=" O   GLU B1178 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER B1182 " --> pdb=" O   LEU B1179 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA B1183 " --> pdb=" O   LEU B1180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1178 through 1183'
    Processing helix  chain 'B' and resid 1202 through 1212
      removed outlier: 4.107A  pdb=" N   ASP B1212 " --> pdb=" O   ASP B1208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 581 through 585
    Processing helix  chain 'C' and resid 589 through 603
    Processing helix  chain 'C' and resid 604 through 607
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10
      removed outlier: 5.705A  pdb=" N   LEU A   4 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   SER A  85 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   LEU A   6 " --> pdb=" O   VAL A  83 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ALA A  78 " --> pdb=" O   ILE A  98 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   TYR A 105 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30
      removed outlier: 6.235A  pdb=" N   PHE A1153 " --> pdb=" O   ILE A1185 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   ILE A1187 " --> pdb=" O   PHE A1153 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   LEU A1155 " --> pdb=" O   ILE A1187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1095 through 1100
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1202 through 1206
    Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 9
      removed outlier: 3.698A  pdb=" N   GLN B   5 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL B  78 " --> pdb=" O   ARG B 100 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1139 through 1143
      removed outlier: 5.999A  pdb=" N   ASN B  28 " --> pdb=" O   THR B1172 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   TYR B1187 " --> pdb=" O   HIS B  27 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   VAL B  29 " --> pdb=" O   TYR B1187 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   VAL B1189 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL B  31 " --> pdb=" O   VAL B1189 " (cutoff:3.500A)
      removed outlier: 9.115A  pdb=" N   PHE B1191 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG B1192 " --> pdb=" O   VAL B1195 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1054 through 1057
    Processing sheet with id=AA8, first strand: chain 'C' and resid 609 through 610
      removed outlier: 3.635A  pdb=" N   THR C 623 " --> pdb=" O   GLU C 610 " (cutoff:3.500A)

    215 hydrogen bonds defined for protein.
    591 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 1.72 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: 1881
        1.34 -     1.46: 996
        1.46 -     1.58: 2944
        1.58 -     1.69: 9
        1.69 -     1.81: 36
  Bond restraints: 5866
  Sorted by residual:
  bond pdb=" CB  LYS B 105 "
       pdb=" CG  LYS B 105 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.11e+00
  bond pdb=" O3B ATP B2000 "
       pdb=" PB  ATP B2000 "
    ideal  model  delta    sigma   weight residual
    1.592  1.564  0.028 3.00e-02 1.11e+03 8.60e-01
  bond pdb=" C   ALA A  68 "
       pdb=" N   PRO A  69 "
    ideal  model  delta    sigma   weight residual
    1.339  1.370 -0.031 3.40e-02 8.65e+02 8.42e-01
  bond pdb=" CG  LYS B 105 "
       pdb=" CD  LYS B 105 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.88e-01
  bond pdb=" CB  ASN A1071 "
       pdb=" CG  ASN A1071 "
    ideal  model  delta    sigma   weight residual
    1.516  1.495  0.021 2.50e-02 1.60e+03 7.16e-01
  ... (remaining 5861 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 7701
        1.80 -     3.61: 176
        3.61 -     5.41: 18
        5.41 -     7.21: 4
        7.21 -     9.02: 5
  Bond angle restraints: 7904
  Sorted by residual:
  angle pdb=" C   LYS A1056 "
        pdb=" N   GLN A1057 "
        pdb=" CA  GLN A1057 "
      ideal   model   delta    sigma   weight residual
     121.94  115.15    6.79 2.00e+00 2.50e-01 1.15e+01
  angle pdb=" CB  LYS B 105 "
        pdb=" CG  LYS B 105 "
        pdb=" CD  LYS B 105 "
      ideal   model   delta    sigma   weight residual
     111.30  118.57   -7.27 2.30e+00 1.89e-01 9.98e+00
  angle pdb=" CB  MET A 145 "
        pdb=" CG  MET A 145 "
        pdb=" SD  MET A 145 "
      ideal   model   delta    sigma   weight residual
     112.70  121.72   -9.02 3.00e+00 1.11e-01 9.04e+00
  angle pdb=" N   PHE B  53 "
        pdb=" CA  PHE B  53 "
        pdb=" C   PHE B  53 "
      ideal   model   delta    sigma   weight residual
     114.04  110.40    3.64 1.24e+00 6.50e-01 8.60e+00
  angle pdb=" C   LYS A  59 "
        pdb=" N   THR A  60 "
        pdb=" CA  THR A  60 "
      ideal   model   delta    sigma   weight residual
     121.54  126.73   -5.19 1.91e+00 2.74e-01 7.37e+00
  ... (remaining 7899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 3179
       17.72 -    35.44: 346
       35.44 -    53.16: 66
       53.16 -    70.88: 27
       70.88 -    88.60: 8
  Dihedral angle restraints: 3626
    sinusoidal: 1535
      harmonic: 2091
  Sorted by residual:
  dihedral pdb=" CA  GLU A 174 "
           pdb=" C   GLU A 174 "
           pdb=" N   MET A 175 "
           pdb=" CA  MET A 175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.63   18.37     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  GLN A1157 "
           pdb=" C   GLN A1157 "
           pdb=" N   ILE A1158 "
           pdb=" CA  ILE A1158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.93   18.07     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  VAL A1186 "
           pdb=" C   VAL A1186 "
           pdb=" N   ILE A1187 "
           pdb=" CA  ILE A1187 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.13   17.87     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 3623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 578
       0.041 -    0.083: 199
       0.083 -    0.124: 84
       0.124 -    0.165: 9
       0.165 -    0.206: 2
  Chirality restraints: 872
  Sorted by residual:
  chirality pdb=" CB  ILE B 138 "
            pdb=" CA  ILE B 138 "
            pdb=" CG1 ILE B 138 "
            pdb=" CG2 ILE B 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  ILE A 126 "
            pdb=" CA  ILE A 126 "
            pdb=" CG1 ILE A 126 "
            pdb=" CG2 ILE A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.94e-01
  chirality pdb=" CA  ILE B 138 "
            pdb=" N   ILE B 138 "
            pdb=" C   ILE B 138 "
            pdb=" CB  ILE B 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.05e-01
  ... (remaining 869 not shown)

  Planarity restraints: 1015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  21 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO B  22 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B  22 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  22 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  57 "   -0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO B  58 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B  58 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  58 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 145 "   -0.007 2.00e-02 2.50e+03   1.42e-02 2.00e+00
        pdb=" C   MET A 145 "    0.024 2.00e-02 2.50e+03
        pdb=" O   MET A 145 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   LYS A 146 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1012 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 103
        2.61 -     3.18: 5329
        3.18 -     3.75: 9352
        3.75 -     4.33: 12558
        4.33 -     4.90: 20141
  Nonbonded interactions: 47483
  Sorted by model distance:
  nonbonded pdb=" O1G ATP B2000 "
            pdb="MG    MG B2001 "
     model   vdw
     2.036 2.170
  nonbonded pdb=" O1B ATP A2000 "
            pdb="MG    MG A2001 "
     model   vdw
     2.036 2.170
  nonbonded pdb=" O3B ATP B2000 "
            pdb="MG    MG B2001 "
     model   vdw
     2.078 2.170
  nonbonded pdb=" O2B ATP B2000 "
            pdb="MG    MG B2001 "
     model   vdw
     2.126 2.170
  nonbonded pdb=" OG1 THR A1217 "
            pdb=" O   PRO C 616 "
     model   vdw
     2.134 3.040
  ... (remaining 47478 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.750
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6824
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      :  0.003   0.032   5866  Z= 0.209
  Angle     :  0.655   9.018   7904  Z= 0.343
  Chirality :  0.048   0.206    872
  Planarity :  0.004   0.043   1015
  Dihedral  : 16.306  88.597   2272
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 19.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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: -1.96 (0.31), residues: 709
  helix: -1.39 (0.31), residues: 244
  sheet: -0.82 (0.46), residues: 144
  loop : -1.32 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  66 
 PHE   0.012   0.002   PHE A1067 
 TYR   0.016   0.002   TYR A1194 
 ARG   0.009   0.001   ARG A 160 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7279 (ptm) cc_final: 0.6985 (ptm)
REVERT: A 1217 THR cc_start: 0.8498 (p) cc_final: 0.8261 (p)
REVERT: B 1202 THR cc_start: 0.7696 (m) cc_final: 0.7446 (m)
REVERT: C  607 GLN cc_start: 0.7137 (pp30) cc_final: 0.6702 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1738
  time to fit residues: 27.8421
Evaluate side-chains
  99 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B1144 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.199197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.159395 restraints weight = 20500.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.166873 restraints weight = 9478.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.172117 restraints weight = 5696.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4144 r_free = 0.4144    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4145 r_free = 0.4145    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5866  Z= 0.274
  Angle     :  0.682  10.671   7904  Z= 0.353
  Chirality :  0.050   0.179    872
  Planarity :  0.004   0.041   1015
  Dihedral  : 12.014  89.988    841
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 18.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.14 %
    Favored  : 86.57 %
  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: -1.68 (0.31), residues: 709
  helix: -0.99 (0.32), residues: 238
  sheet: -0.80 (0.46), residues: 145
  loop : -1.23 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 115 
 PHE   0.023   0.002   PHE C 600 
 TYR   0.015   0.002   TYR B 137 
 ARG   0.006   0.001   ARG A 160 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
REVERT: B  141 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7614 (tt0)
REVERT: B 1115 LEU cc_start: 0.8160 (mm) cc_final: 0.7900 (mm)
REVERT: B 1211 GLU cc_start: 0.7903 (tp30) cc_final: 0.7595 (tp30)
REVERT: C  596 LYS cc_start: 0.8376 (ptpp) cc_final: 0.7994 (ptpp)
REVERT: C  607 GLN cc_start: 0.7193 (pp30) cc_final: 0.6731 (pp30)
  outliers start: 8
  outliers final: 6
  residues processed: 110
  average time/residue: 0.1627
  time to fit residues: 24.2249
Evaluate side-chains
  113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1203 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1055 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.0170
   chunk 68 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 34 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.2620

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

Flipped N/Q/H residues before XYZ refinement:
B1119 GLN
B1193 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.197210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.161030 restraints weight = 16429.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.168193 restraints weight = 9389.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.171839 restraints weight = 5041.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4129
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4129 r_free = 0.4129    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4129 r_free = 0.4129    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4129
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5866  Z= 0.288
  Angle     :  0.679  11.053   7904  Z= 0.349
  Chirality :  0.049   0.183    872
  Planarity :  0.004   0.048   1015
  Dihedral  : 11.513  88.922    841
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 18.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.34 %
    Favored  : 81.72 %
  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: -1.75 (0.31), residues: 709
  helix: -1.12 (0.31), residues: 246
  sheet: -0.87 (0.45), residues: 145
  loop : -1.18 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 115 
 PHE   0.021   0.002   PHE B  47 
 TYR   0.014   0.002   TYR A1194 
 ARG   0.005   0.000   ARG A1066 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLN cc_start: 0.6637 (mp10) cc_final: 0.6287 (mp10)
REVERT: B  141 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7558 (tt0)
REVERT: B 1119 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7174 (mm-40)
REVERT: B 1211 GLU cc_start: 0.8226 (tp30) cc_final: 0.7793 (tp30)
REVERT: C  607 GLN cc_start: 0.7253 (pp30) cc_final: 0.6796 (pp30)
  outliers start: 12
  outliers final: 8
  residues processed: 123
  average time/residue: 0.2309
  time to fit residues: 38.4868
Evaluate side-chains
  112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1055 LEU
Chi-restraints excluded: chain B residue 1119 GLN
Chi-restraints excluded: chain B residue 1149 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0770
   chunk 43 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 5 optimal weight:    0.1980
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A1080 ASN
A1112 ASN
B  17 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.200670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.160276 restraints weight = 21464.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.168093 restraints weight = 9797.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.173510 restraints weight = 5872.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4160 r_free = 0.4160    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4160 r_free = 0.4160    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5866  Z= 0.206
  Angle     :  0.650  12.064   7904  Z= 0.330
  Chirality :  0.048   0.177    872
  Planarity :  0.004   0.052   1015
  Dihedral  : 11.035  88.848    841
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.12 %
    Favored  : 79.45 %
  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: -1.55 (0.31), residues: 709
  helix: -0.92 (0.32), residues: 240
  sheet: -0.73 (0.46), residues: 143
  loop : -1.12 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  27 
 PHE   0.022   0.001   PHE B  47 
 TYR   0.019   0.002   TYR A1194 
 ARG   0.006   0.000   ARG A 160 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  141 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7426 (tt0)
REVERT: B 1115 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7912 (mt)
REVERT: B 1211 GLU cc_start: 0.8304 (tp30) cc_final: 0.7863 (tp30)
REVERT: C  607 GLN cc_start: 0.7256 (pp30) cc_final: 0.6730 (pp30)
  outliers start: 15
  outliers final: 9
  residues processed: 114
  average time/residue: 0.2126
  time to fit residues: 32.5094
Evaluate side-chains
  108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1203 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1048 VAL
Chi-restraints excluded: chain B residue 1055 LEU
Chi-restraints excluded: chain B residue 1115 LEU
Chi-restraints excluded: chain B residue 1149 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.199055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.163175 restraints weight = 13312.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.169374 restraints weight = 7254.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.173753 restraints weight = 4797.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4160 r_free = 0.4160    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4160 r_free = 0.4160    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5866  Z= 0.232
  Angle     :  0.666  12.170   7904  Z= 0.337
  Chirality :  0.048   0.203    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.895  88.712    841
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.23 %
    Favored  : 77.02 %
  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: -1.63 (0.31), residues: 709
  helix: -0.92 (0.32), residues: 240
  sheet: -0.84 (0.46), residues: 145
  loop : -1.18 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 115 
 PHE   0.024   0.002   PHE B  47 
 TYR   0.017   0.002   TYR A1194 
 ARG   0.005   0.000   ARG A 160 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 LYS cc_start: 0.7373 (tptp) cc_final: 0.7144 (tptt)
REVERT: B  141 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7444 (tt0)
REVERT: B 1115 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7878 (mt)
REVERT: B 1178 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7285 (mm-30)
REVERT: B 1211 GLU cc_start: 0.8313 (tp30) cc_final: 0.7842 (tp30)
REVERT: C  607 GLN cc_start: 0.7250 (pp30) cc_final: 0.6735 (pp30)
  outliers start: 17
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1713
  time to fit residues: 26.0155
Evaluate side-chains
  105 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1203 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1048 VAL
Chi-restraints excluded: chain B residue 1055 LEU
Chi-restraints excluded: chain B residue 1115 LEU
Chi-restraints excluded: chain B residue 1149 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0570
   chunk 3 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.7498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.199974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.164910 restraints weight = 15995.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.170712 restraints weight = 8502.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.177329 restraints weight = 4841.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.4188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4188 r_free = 0.4188    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4188 r_free = 0.4188    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5866  Z= 0.216
  Angle     :  0.658  11.154   7904  Z= 0.335
  Chirality :  0.048   0.208    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.691  87.529    841
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.71 %
    Favored  : 76.05 %
  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: -1.55 (0.32), residues: 709
  helix: -0.81 (0.32), residues: 240
  sheet: -0.84 (0.46), residues: 145
  loop : -1.16 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 115 
 PHE   0.025   0.002   PHE B  47 
 TYR   0.015   0.002   TYR A1194 
 ARG   0.005   0.000   ARG A 160 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1057 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8586 (pm20)
REVERT: B  141 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7333 (tt0)
REVERT: B 1033 PHE cc_start: 0.7639 (t80) cc_final: 0.7413 (t80)
REVERT: B 1115 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7891 (mt)
REVERT: B 1211 GLU cc_start: 0.8303 (tp30) cc_final: 0.7857 (tp30)
REVERT: C  607 GLN cc_start: 0.7268 (pp30) cc_final: 0.6746 (pp30)
  outliers start: 20
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1875
  time to fit residues: 28.0893
Evaluate side-chains
  107 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1203 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1048 VAL
Chi-restraints excluded: chain B residue 1055 LEU
Chi-restraints excluded: chain B residue 1115 LEU
Chi-restraints excluded: chain B residue 1149 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0770
   chunk 25 optimal weight:    0.0770
   chunk 63 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.7098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.199349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.163411 restraints weight = 29343.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.172223 restraints weight = 13924.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.175825 restraints weight = 6604.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4154 r_free = 0.4154    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4154 r_free = 0.4154    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5866  Z= 0.214
  Angle     :  0.663  12.739   7904  Z= 0.339
  Chirality :  0.048   0.221    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.536  87.909    841
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.04 %
    Favored  : 75.57 %
  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: -1.58 (0.32), residues: 709
  helix: -0.84 (0.32), residues: 238
  sheet: -0.85 (0.45), residues: 146
  loop : -1.18 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.021   0.001   PHE B  47 
 TYR   0.016   0.002   TYR A1194 
 ARG   0.004   0.000   ARG A 160 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 LYS cc_start: 0.7426 (tptp) cc_final: 0.7223 (tptt)
REVERT: B  141 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7281 (tt0)
REVERT: B 1115 LEU cc_start: 0.8146 (mm) cc_final: 0.7918 (mt)
REVERT: B 1211 GLU cc_start: 0.8451 (tp30) cc_final: 0.7950 (tp30)
REVERT: C  607 GLN cc_start: 0.7305 (pp30) cc_final: 0.6811 (pp30)
  outliers start: 21
  outliers final: 17
  residues processed: 120
  average time/residue: 0.2205
  time to fit residues: 35.3667
Evaluate side-chains
  117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1203 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1045 GLN
Chi-restraints excluded: chain B residue 1048 VAL
Chi-restraints excluded: chain B residue 1055 LEU
Chi-restraints excluded: chain B residue 1149 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    0.4980
   chunk 59 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.199437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.158215 restraints weight = 21663.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.166356 restraints weight = 9369.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.172042 restraints weight = 5530.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4143 r_free = 0.4143    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4143 r_free = 0.4143    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6853
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5866  Z= 0.221
  Angle     :  0.682  13.588   7904  Z= 0.345
  Chirality :  0.049   0.238    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.443  83.703    841
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.20 %
    Favored  : 74.92 %
  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: -1.49 (0.32), residues: 709
  helix: -0.69 (0.33), residues: 233
  sheet: -0.84 (0.45), residues: 144
  loop : -1.17 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.028   0.002   PHE A1067 
 TYR   0.016   0.002   TYR A1194 
 ARG   0.005   0.000   ARG A 160 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.7017 (mtm180) cc_final: 0.6594 (mtm180)
REVERT: A   82 MET cc_start: 0.7308 (ptm) cc_final: 0.6907 (ptm)
REVERT: B  141 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7434 (tt0)
REVERT: B 1115 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7844 (mt)
REVERT: B 1211 GLU cc_start: 0.8398 (tp30) cc_final: 0.7984 (tp30)
REVERT: C  607 GLN cc_start: 0.7299 (pp30) cc_final: 0.6779 (pp30)
  outliers start: 24
  outliers final: 18
  residues processed: 120
  average time/residue: 0.2041
  time to fit residues: 32.7419
Evaluate side-chains
  118 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1203 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1045 GLN
Chi-restraints excluded: chain B residue 1048 VAL
Chi-restraints excluded: chain B residue 1055 LEU
Chi-restraints excluded: chain B residue 1115 LEU
Chi-restraints excluded: chain B residue 1149 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 60 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A1112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.197667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.162907 restraints weight = 27042.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.171547 restraints weight = 12808.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.174802 restraints weight = 6188.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4146 r_free = 0.4146    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4146 r_free = 0.4146    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5866  Z= 0.262
  Angle     :  0.709  13.269   7904  Z= 0.360
  Chirality :  0.049   0.243    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.644  86.940    841
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.36 %
    Favored  : 75.24 %
  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: -1.65 (0.32), residues: 709
  helix: -0.85 (0.32), residues: 238
  sheet: -0.92 (0.44), residues: 146
  loop : -1.23 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 115 
 PHE   0.018   0.002   PHE B  47 
 TYR   0.016   0.002   TYR A1173 
 ARG   0.014   0.001   ARG A 171 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.7117 (mtm180) cc_final: 0.6710 (mtm180)
REVERT: A   63 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7633 (t0)
REVERT: B  141 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7307 (tt0)
REVERT: B 1115 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7858 (mt)
REVERT: B 1211 GLU cc_start: 0.8528 (tp30) cc_final: 0.8019 (tp30)
REVERT: C  607 GLN cc_start: 0.7333 (pp30) cc_final: 0.6802 (pp30)
  outliers start: 21
  outliers final: 17
  residues processed: 117
  average time/residue: 0.1868
  time to fit residues: 30.9236
Evaluate side-chains
  121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1203 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1045 GLN
Chi-restraints excluded: chain B residue 1048 VAL
Chi-restraints excluded: chain B residue 1055 LEU
Chi-restraints excluded: chain B residue 1115 LEU
Chi-restraints excluded: chain B residue 1149 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 69 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.198862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.163500 restraints weight = 15067.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.170623 restraints weight = 8201.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.173733 restraints weight = 5010.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4144 r_free = 0.4144    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4144 r_free = 0.4144    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5866  Z= 0.241
  Angle     :  0.736  14.199   7904  Z= 0.370
  Chirality :  0.050   0.239    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.618  89.543    841
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.68 %
    Favored  : 74.92 %
  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: -1.64 (0.31), residues: 709
  helix: -0.87 (0.33), residues: 233
  sheet: -0.93 (0.44), residues: 146
  loop : -1.20 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.019   0.001   PHE B  47 
 TYR   0.016   0.002   TYR A1194 
 ARG   0.013   0.001   ARG A 171 

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.7079 (mtm180) cc_final: 0.6696 (mtm180)
REVERT: A   63 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7594 (t0)
REVERT: B   93 LYS cc_start: 0.7472 (tptp) cc_final: 0.7209 (tptt)
REVERT: B  141 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7396 (tt0)
REVERT: B 1115 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7874 (mt)
REVERT: B 1211 GLU cc_start: 0.8480 (tp30) cc_final: 0.7997 (tp30)
REVERT: C  596 LYS cc_start: 0.8310 (ptpp) cc_final: 0.8013 (ptpp)
REVERT: C  607 GLN cc_start: 0.7284 (pp30) cc_final: 0.6765 (pp30)
  outliers start: 21
  outliers final: 17
  residues processed: 117
  average time/residue: 0.1530
  time to fit residues: 24.0782
Evaluate side-chains
  117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue 1057 GLN
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1165 THR
Chi-restraints excluded: chain A residue 1176 GLU
Chi-restraints excluded: chain A residue 1203 VAL
Chi-restraints excluded: chain B residue   25 SER
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue 1036 VAL
Chi-restraints excluded: chain B residue 1045 GLN
Chi-restraints excluded: chain B residue 1048 VAL
Chi-restraints excluded: chain B residue 1055 LEU
Chi-restraints excluded: chain B residue 1115 LEU
Chi-restraints excluded: chain B residue 1149 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0980
   chunk 27 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.210347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.169859 restraints weight = 28406.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.178741 restraints weight = 11268.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.184596 restraints weight = 6339.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4324 r_free = 0.4324    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4324 r_free = 0.4324    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5866  Z= 0.207
  Angle     :  0.724  13.526   7904  Z= 0.364
  Chirality :  0.049   0.237    872
  Planarity :  0.004   0.054   1015
  Dihedral  : 10.429  88.143    841
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.01 %
    Favored  : 75.08 %
  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: -1.52 (0.31), residues: 709
  helix: -0.76 (0.33), residues: 233
  sheet: -0.82 (0.45), residues: 144
  loop : -1.16 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.021   0.001   PHE B  47 
 TYR   0.018   0.002   TYR A1194 
 ARG   0.012   0.001   ARG A 171 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2454.41 seconds
wall clock time: 45 minutes 30.49 seconds (2730.49 seconds total)