Starting phenix.real_space_refine
on Sat May 10 09:15:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p0a_17331/05_2025/8p0a_17331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p0a_17331/05_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_17331/05_2025/8p0a_17331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p0a_17331/05_2025/8p0a_17331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p0a_17331/05_2025/8p0a_17331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p0a_17331/05_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.68, per 1000 atoms: 0.81
  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: 1.32
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.58
  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: 1.35

  Time building geometry restraints manager: 1.57 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:             1.620
  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:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.030
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.010
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.870
-------------------------------------------------------------------------------
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= 0.142
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17653 (  215)
  hydrogen bonds       : angle       7.44300 (  591)
  covalent geometry    : bond        0.00316 ( 5866)
  covalent geometry    : angle       0.65468 ( 7904)

*********************** 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  : 0.600 
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: 0.1777
  time to fit residues: 28.3567
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  : 0.699 
-------------------------------------------------------------------------------
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 = 48)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.159418 restraints weight = 20500.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.166937 restraints weight = 9454.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.172251 restraints weight = 5682.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4145 r_free = 0.4145    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 = 0.4146 r_free = 0.4146    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
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= 0.179
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04696 (  215)
  hydrogen bonds       : angle       5.93156 (  591)
  covalent geometry    : bond        0.00417 ( 5866)
  covalent geometry    : angle       0.68178 ( 7904)

*********************** 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  : 0.694 
Fit side-chains
   revert: symmetry clash
REVERT: B  141 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7615 (tt0)
REVERT: B 1115 LEU cc_start: 0.8157 (mm) cc_final: 0.7895 (mm)
REVERT: B 1211 GLU cc_start: 0.7893 (tp30) cc_final: 0.7589 (tp30)
REVERT: C  596 LYS cc_start: 0.8377 (ptpp) cc_final: 0.7994 (ptpp)
REVERT: C  607 GLN cc_start: 0.7191 (pp30) cc_final: 0.6725 (pp30)
  outliers start: 8
  outliers final: 6
  residues processed: 110
  average time/residue: 0.1633
  time to fit residues: 24.0176
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  : 0.654 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
A1080 ASN
B1119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.201327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.166443 restraints weight = 16563.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.174203 restraints weight = 9028.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.177830 restraints weight = 4625.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4195 r_free = 0.4195    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4195 r_free = 0.4195    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.1687

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= 0.141
  Angle     :  0.646  10.839   7904  Z= 0.329
  Chirality :  0.048   0.182    872
  Planarity :  0.004   0.048   1015
  Dihedral  : 11.269  89.128    841
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.86 %
    Favored  : 82.85 %
  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: -0.99 (0.31), residues: 246
  sheet: -0.67 (0.46), residues: 143
  loop : -1.08 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 115 
 PHE   0.022   0.002   PHE B  47 
 TYR   0.017   0.002   TYR A1194 
 ARG   0.004   0.000   ARG A1066 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04106 (  215)
  hydrogen bonds       : angle       5.61835 (  591)
  covalent geometry    : bond        0.00323 ( 5866)
  covalent geometry    : angle       0.64560 ( 7904)

*********************** 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
  123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7307 (ptm) cc_final: 0.6966 (ptm)
REVERT: B  141 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7505 (tt0)
REVERT: B 1115 LEU cc_start: 0.8122 (mm) cc_final: 0.7783 (mm)
REVERT: B 1119 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7057 (mm-40)
REVERT: B 1211 GLU cc_start: 0.8189 (tp30) cc_final: 0.7786 (tp30)
REVERT: C  607 GLN cc_start: 0.7277 (pp30) cc_final: 0.6759 (pp30)
  outliers start: 8
  outliers final: 5
  residues processed: 121
  average time/residue: 0.1875
  time to fit residues: 29.9117
Evaluate side-chains
  107 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ASP
Chi-restraints excluded: chain A residue 1176 GLU
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:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.200282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.163904 restraints weight = 23922.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.172548 restraints weight = 11396.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.179246 restraints weight = 5673.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4199 r_free = 0.4199    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4199 r_free = 0.4199    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.1959

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= 0.139
  Angle     :  0.640   9.972   7904  Z= 0.327
  Chirality :  0.048   0.194    872
  Planarity :  0.004   0.052   1015
  Dihedral  : 10.942  88.061    841
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.31 %
    Favored  : 80.10 %
  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: -1.53 (0.31), residues: 709
  helix: -0.89 (0.32), residues: 240
  sheet: -0.65 (0.46), residues: 145
  loop : -1.15 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 115 
 PHE   0.022   0.001   PHE B  47 
 TYR   0.017   0.002   TYR A1173 
 ARG   0.004   0.000   ARG A1066 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  215)
  hydrogen bonds       : angle       5.51201 (  591)
  covalent geometry    : bond        0.00318 ( 5866)
  covalent geometry    : angle       0.63972 ( 7904)

*********************** 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
  120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7272 (ptm) cc_final: 0.6928 (ptm)
REVERT: A  160 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7737 (mmm160)
REVERT: B  141 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7279 (tt0)
REVERT: B 1115 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7840 (mt)
REVERT: B 1211 GLU cc_start: 0.8335 (tp30) cc_final: 0.7875 (tp30)
REVERT: C  607 GLN cc_start: 0.7283 (pp30) cc_final: 0.6756 (pp30)
  outliers start: 16
  outliers final: 10
  residues processed: 115
  average time/residue: 0.1715
  time to fit residues: 26.3308
Evaluate side-chains
  112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
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 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 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 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:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0020
   chunk 26 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.6188

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.201529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.165330 restraints weight = 14037.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.171837 restraints weight = 7429.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.176502 restraints weight = 4838.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4182 r_free = 0.4182    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4182 r_free = 0.4182    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5866  Z= 0.134
  Angle     :  0.647  10.186   7904  Z= 0.329
  Chirality :  0.048   0.198    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.768  88.251    841
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.74 %
    Favored  : 77.83 %
  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: -1.48 (0.32), residues: 709
  helix: -0.79 (0.32), residues: 240
  sheet: -0.71 (0.46), residues: 142
  loop : -1.13 (0.35), residues: 327

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   0.018   0.002   TYR A1194 
 ARG   0.003   0.000   ARG A1066 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  215)
  hydrogen bonds       : angle       5.47666 (  591)
  covalent geometry    : bond        0.00307 ( 5866)
  covalent geometry    : angle       0.64678 ( 7904)

*********************** 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
  121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7343 (ptm) cc_final: 0.6951 (ptm)
REVERT: B  141 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7472 (tt0)
REVERT: B 1115 LEU cc_start: 0.8095 (mm) cc_final: 0.7799 (mt)
REVERT: B 1178 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7260 (mm-30)
REVERT: B 1211 GLU cc_start: 0.8316 (tp30) cc_final: 0.7860 (tp30)
REVERT: C  607 GLN cc_start: 0.7284 (pp30) cc_final: 0.6763 (pp30)
  outliers start: 15
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1674
  time to fit residues: 26.3771
Evaluate side-chains
  106 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
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 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  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 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:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4425 r_free = 0.4425 target = 0.198285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.162828 restraints weight = 16376.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.171161 restraints weight = 8905.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.174975 restraints weight = 4521.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4161 r_free = 0.4161    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4161 r_free = 0.4161    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.2297

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= 0.163
  Angle     :  0.683  11.062   7904  Z= 0.350
  Chirality :  0.049   0.214    872
  Planarity :  0.004   0.052   1015
  Dihedral  : 10.764  88.735    841
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.09 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.51 (0.31), residues: 709
  helix: -0.62 (0.33), residues: 233
  sheet: -0.88 (0.47), residues: 139
  loop : -1.23 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.025   0.002   PHE B  47 
 TYR   0.016   0.002   TYR A1194 
 ARG   0.003   0.000   ARG A1066 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04107 (  215)
  hydrogen bonds       : angle       5.43482 (  591)
  covalent geometry    : bond        0.00379 ( 5866)
  covalent geometry    : angle       0.68289 ( 7904)

*********************** 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
  119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  141 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7427 (tt0)
REVERT: B 1115 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7838 (mt)
REVERT: B 1178 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7327 (mm-30)
REVERT: B 1211 GLU cc_start: 0.8296 (tp30) cc_final: 0.7871 (tp30)
REVERT: C  607 GLN cc_start: 0.7273 (pp30) cc_final: 0.6742 (pp30)
  outliers start: 23
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1541
  time to fit residues: 24.0039
Evaluate side-chains
  108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
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   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  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 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:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 40 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 8 optimal weight:    5.9990
   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  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.199056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.162153 restraints weight = 29126.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.171360 restraints weight = 13348.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.176565 restraints weight = 5892.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.4160
-------------------------------------------------------------------------------
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 = 0.43   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 = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5866  Z= 0.156
  Angle     :  0.691  11.222   7904  Z= 0.351
  Chirality :  0.049   0.209    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.686  88.889    841
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 19.90 %
    Favored  : 76.54 %
  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 (0.32), residues: 709
  helix: -0.70 (0.33), residues: 233
  sheet: -0.82 (0.45), residues: 146
  loop : -1.21 (0.35), residues: 330

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   0.003   0.000   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04052 (  215)
  hydrogen bonds       : angle       5.50929 (  591)
  covalent geometry    : bond        0.00363 ( 5866)
  covalent geometry    : angle       0.69077 ( 7904)

*********************** 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
  124 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  141 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7309 (tt0)
REVERT: B 1115 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7770 (mt)
REVERT: B 1211 GLU cc_start: 0.8524 (tp30) cc_final: 0.7988 (tp30)
REVERT: C  607 GLN cc_start: 0.7277 (pp30) cc_final: 0.6770 (pp30)
  outliers start: 22
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1677
  time to fit residues: 26.8175
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  : 0.606 
-------------------------------------------------------------------------------
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   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 1115 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:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   chunk 3 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6360

-------------------------------------------------------------------------------
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 = 0.4456 r_free = 0.4456 target = 0.201249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.161694 restraints weight = 20909.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.169578 restraints weight = 9299.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.174971 restraints weight = 5451.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6820
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5866  Z= 0.138
  Angle     :  0.684  13.532   7904  Z= 0.346
  Chirality :  0.049   0.225    872
  Planarity :  0.004   0.054   1015
  Dihedral  : 10.344  85.296    841
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.39 %
    Favored  : 76.21 %
  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: -1.40 (0.32), residues: 709
  helix: -0.55 (0.33), residues: 233
  sheet: -0.82 (0.47), residues: 137
  loop : -1.15 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.029   0.002   PHE B  47 
 TYR   0.019   0.002   TYR A1194 
 ARG   0.003   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  215)
  hydrogen bonds       : angle       5.38765 (  591)
  covalent geometry    : bond        0.00317 ( 5866)
  covalent geometry    : angle       0.68415 ( 7904)

*********************** 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
  120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 PHE cc_start: 0.7863 (m-10) cc_final: 0.7650 (m-10)
REVERT: B  141 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7319 (tt0)
REVERT: B 1205 MET cc_start: 0.7456 (mtp) cc_final: 0.7118 (ttp)
REVERT: B 1211 GLU cc_start: 0.8450 (tp30) cc_final: 0.7994 (tp30)
REVERT: C  607 GLN cc_start: 0.7285 (pp30) cc_final: 0.6815 (pp30)
  outliers start: 21
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1738
  time to fit residues: 26.3962
Evaluate side-chains
  114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4427 r_free = 0.4427 target = 0.198266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.163258 restraints weight = 26969.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.172333 restraints weight = 13182.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.176279 restraints weight = 6130.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4163 r_free = 0.4163    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5866  Z= 0.164
  Angle     :  0.718  13.219   7904  Z= 0.361
  Chirality :  0.050   0.233    872
  Planarity :  0.004   0.053   1015
  Dihedral  : 10.550  88.494    841
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.84 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.57 (0.32), residues: 709
  helix: -0.71 (0.33), residues: 238
  sheet: -0.93 (0.46), residues: 139
  loop : -1.22 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.042   0.002   PHE C 600 
 TYR   0.017   0.002   TYR A1194 
 ARG   0.004   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  215)
  hydrogen bonds       : angle       5.47751 (  591)
  covalent geometry    : bond        0.00383 ( 5866)
  covalent geometry    : angle       0.71826 ( 7904)

*********************** 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
  114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7691 (t0)
REVERT: B  141 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7271 (tt0)
REVERT: B 1115 LEU cc_start: 0.8149 (mt) cc_final: 0.7778 (mm)
REVERT: B 1178 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7356 (mm-30)
REVERT: B 1205 MET cc_start: 0.7639 (mtp) cc_final: 0.7339 (ttp)
REVERT: B 1211 GLU cc_start: 0.8520 (tp30) cc_final: 0.8044 (tp30)
REVERT: C  607 GLN cc_start: 0.7315 (pp30) cc_final: 0.6877 (pp30)
  outliers start: 17
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1768
  time to fit residues: 25.8183
Evaluate side-chains
  110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
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   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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:   10.0000
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4441 r_free = 0.4441 target = 0.199782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.164983 restraints weight = 13967.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.172329 restraints weight = 7620.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.175469 restraints weight = 4428.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5866  Z= 0.145
  Angle     :  0.715  14.076   7904  Z= 0.358
  Chirality :  0.049   0.235    872
  Planarity :  0.004   0.054   1015
  Dihedral  : 10.385  87.126    841
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 22.17 %
    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: -1.44 (0.32), residues: 709
  helix: -0.65 (0.33), residues: 239
  sheet: -0.89 (0.47), residues: 137
  loop : -1.09 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.044   0.002   PHE C 600 
 TYR   0.019   0.002   TYR A1194 
 ARG   0.009   0.001   ARG B1176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03900 (  215)
  hydrogen bonds       : angle       5.42016 (  591)
  covalent geometry    : bond        0.00340 ( 5866)
  covalent geometry    : angle       0.71542 ( 7904)

********************** 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
  114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.6983 (mtm180) cc_final: 0.6531 (mtm180)
REVERT: A   63 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7652 (t0)
REVERT: B   42 PHE cc_start: 0.7862 (m-10) cc_final: 0.7642 (m-10)
REVERT: B  141 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7368 (tt0)
REVERT: B 1115 LEU cc_start: 0.8150 (mt) cc_final: 0.7752 (mm)
REVERT: B 1178 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7233 (mm-30)
REVERT: B 1205 MET cc_start: 0.7402 (mtp) cc_final: 0.7060 (ttp)
REVERT: B 1211 GLU cc_start: 0.8455 (tp30) cc_final: 0.7978 (tp30)
REVERT: C  607 GLN cc_start: 0.7277 (pp30) cc_final: 0.6814 (pp30)
  outliers start: 17
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1595
  time to fit residues: 23.6279
Evaluate side-chains
  111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
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   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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 54 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0570
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.4566 r_free = 0.4566 target = 0.208131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.170947 restraints weight = 25656.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.181089 restraints weight = 10434.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.188103 restraints weight = 4960.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4351 r_free = 0.4351    target_work(ls_wunit_k1) = 0.186         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4352 r_free = 0.4352    target_work(ls_wunit_k1) = 0.186         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.2767

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= 0.141
  Angle     :  0.712  13.593   7904  Z= 0.356
  Chirality :  0.049   0.236    872
  Planarity :  0.004   0.054   1015
  Dihedral  : 10.329  87.062    841
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 22.82 %
    Favored  : 74.60 %
  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: -1.41 (0.32), residues: 709
  helix: -0.55 (0.34), residues: 235
  sheet: -0.88 (0.47), residues: 137
  loop : -1.13 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 115 
 PHE   0.025   0.002   PHE B  47 
 TYR   0.020   0.002   TYR A1194 
 ARG   0.009   0.001   ARG B1176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03840 (  215)
  hydrogen bonds       : angle       5.36456 (  591)
  covalent geometry    : bond        0.00328 ( 5866)
  covalent geometry    : angle       0.71249 ( 7904)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2277.85 seconds
wall clock time: 40 minutes 44.58 seconds (2444.58 seconds total)