Starting phenix.real_space_refine
on Fri Apr  5 20:09:08 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/04_2024/8p79_17522_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/04_2024/8p79_17522.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/04_2024/8p79_17522.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/04_2024/8p79_17522.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/04_2024/8p79_17522_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/04_2024/8p79_17522_updated.pdb"
  }
  resolution = 1.7
  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=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    3269      2.51       5
     N     864      2.21       5
     O    1092      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "H GLU  264": "OE1" <-> "OE2"
    Residue "H TYR  287": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP  299": "OD1" <-> "OD2"
    Residue "I PHE   13": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I GLU  137": "OE1" <-> "OE2"
    Residue "I GLU  141": "OE1" <-> "OE2"
    Residue "I GLU  182": "OE1" <-> "OE2"
    Residue "I GLU  263": "OE1" <-> "OE2"
    Residue "I GLU  278": "OE1" <-> "OE2"
    Residue "J PHE   23": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ASP   79": "OD1" <-> "OD2"
    Residue "J PHE   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J PHE  252": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 5256
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2281
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 279, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2283
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 24
          Classifications: {'water': 24}
          Link IDs: {None: 23}
    Chain: "I"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 71
          Classifications: {'water': 71}
          Link IDs: {None: 70}
    Chain: "J"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 85
          Classifications: {'water': 85}
          Link IDs: {None: 84}
  Time building chain proxies: 3.60, per 1000 atoms: 0.68
  Number of scatterers: 5256
  At special positions: 0
  Unit cell: (85.5, 93.3375, 68.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1092      8.00
     N     864      7.00
     C    3269      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  - 3.50
        Amino acid           : False - 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: 2.17
  Conformation dependent library (CDL) restraints added in 986.0 milliseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1196

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      54.1% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'H' and resid 263 through 269
      removed outlier: 4.517A  pdb=" N   GLY H 267 " --> pdb=" O   GLU H 264 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU H 269 " --> pdb=" O   LEU H 266 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 271 through 274
    Processing helix  chain 'H' and resid 280 through 285
    Processing helix  chain 'H' and resid 289 through 301
    Processing helix  chain 'I' and resid 2 through 4
      No H-bonds generated for 'chain 'I' and resid 2 through 4'
    Processing helix  chain 'I' and resid 6 through 10
    Processing helix  chain 'I' and resid 16 through 37
    Processing helix  chain 'I' and resid 50 through 70
    Processing helix  chain 'I' and resid 77 through 92
    Processing helix  chain 'I' and resid 101 through 115
      removed outlier: 3.817A  pdb=" N   LEU I 106 " --> pdb=" O   ARG I 102 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS I 114 " --> pdb=" O   PHE I 110 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 122 through 128
      removed outlier: 3.679A  pdb=" N   ASN I 128 " --> pdb=" O   GLN I 124 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 133 through 153
      removed outlier: 4.690A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 177
    Processing helix  chain 'I' and resid 184 through 200
      removed outlier: 4.875A  pdb=" N   LYS I 189 " --> pdb=" O   ILE I 186 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR I 190 " --> pdb=" O   LEU I 187 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 203 through 206
      No H-bonds generated for 'chain 'I' and resid 203 through 206'
    Processing helix  chain 'I' and resid 209 through 224
    Processing helix  chain 'I' and resid 229 through 233
    Processing helix  chain 'I' and resid 242 through 260
    Processing helix  chain 'I' and resid 267 through 283
      removed outlier: 3.736A  pdb=" N   ALA I 283 " --> pdb=" O   ARG I 279 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 57 through 68
      removed outlier: 3.942A  pdb=" N   GLU J  68 " --> pdb=" O   LYS J  64 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 98 through 103
    Processing helix  chain 'J' and resid 111 through 131
    Processing helix  chain 'J' and resid 140 through 142
      No H-bonds generated for 'chain 'J' and resid 140 through 142'
    Processing helix  chain 'J' and resid 176 through 178
      No H-bonds generated for 'chain 'J' and resid 176 through 178'
    Processing helix  chain 'J' and resid 181 through 184
      No H-bonds generated for 'chain 'J' and resid 181 through 184'
    Processing helix  chain 'J' and resid 192 through 208
      removed outlier: 4.040A  pdb=" N   TRP J 197 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU J 208 " --> pdb=" O   GLU J 205 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 218 through 229
    Processing helix  chain 'J' and resid 240 through 242
      No H-bonds generated for 'chain 'J' and resid 240 through 242'
    Processing helix  chain 'J' and resid 257 through 260
      No H-bonds generated for 'chain 'J' and resid 257 through 260'
    Processing helix  chain 'J' and resid 266 through 275
    Processing helix  chain 'J' and resid 286 through 291
    Processing helix  chain 'J' and resid 293 through 296
      No H-bonds generated for 'chain 'J' and resid 293 through 296'
    Processing helix  chain 'J' and resid 304 through 306
      No H-bonds generated for 'chain 'J' and resid 304 through 306'
    Processing sheet with id=  A, first strand: chain 'J' and resid 77 through 83
      removed outlier: 6.909A  pdb=" N   VAL J  90 " --> pdb=" O   LEU J  78 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ALA J  80 " --> pdb=" O   SER J  88 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   SER J  88 " --> pdb=" O   ALA J  80 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   GLY J  82 " --> pdb=" O   ASN J  86 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ASN J  86 " --> pdb=" O   GLY J  82 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   LYS J  28 " --> pdb=" O   PHE J  17 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   PHE J  17 " --> pdb=" O   LYS J  28 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'J' and resid 143 through 145

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

  Time building geometry restraints manager: 2.33 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 824
        1.31 -     1.44: 1380
        1.44 -     1.57: 2944
        1.57 -     1.71: 0
        1.71 -     1.84: 49
  Bond restraints: 5197
  Sorted by residual:
  bond pdb=" CA  SER I 210 "
       pdb=" CB  SER I 210 "
    ideal  model  delta    sigma   weight residual
    1.529  1.452  0.077 1.55e-02 4.16e+03 2.44e+01
  bond pdb=" C   PRO I 209 "
       pdb=" O   PRO I 209 "
    ideal  model  delta    sigma   weight residual
    1.237  1.177  0.061 1.26e-02 6.30e+03 2.31e+01
  bond pdb=" C   MET J 120 "
       pdb=" O   MET J 120 "
    ideal  model  delta    sigma   weight residual
    1.236  1.284 -0.048 1.15e-02 7.56e+03 1.73e+01
  bond pdb=" C   LEU J 143 "
       pdb=" O   LEU J 143 "
    ideal  model  delta    sigma   weight residual
    1.232  1.281 -0.049 1.20e-02 6.94e+03 1.66e+01
  bond pdb=" CA  SER I   5 "
       pdb=" CB  SER I   5 "
    ideal  model  delta    sigma   weight residual
    1.529  1.462  0.067 1.66e-02 3.63e+03 1.64e+01
  ... (remaining 5192 not shown)

  Histogram of bond angle deviations from ideal:
       99.53 -   106.47: 189
      106.47 -   113.40: 2679
      113.40 -   120.34: 2315
      120.34 -   127.27: 1811
      127.27 -   134.20: 39
  Bond angle restraints: 7033
  Sorted by residual:
  angle pdb=" C   GLU I 168 "
        pdb=" N   GLY I 169 "
        pdb=" CA  GLY I 169 "
      ideal   model   delta    sigma   weight residual
     119.98  126.46   -6.48 1.11e+00 8.12e-01 3.41e+01
  angle pdb=" CA  ILE I 104 "
        pdb=" C   ILE I 104 "
        pdb=" O   ILE I 104 "
      ideal   model   delta    sigma   weight residual
     120.95  115.86    5.09 1.04e+00 9.25e-01 2.40e+01
  angle pdb=" C   GLN J 221 "
        pdb=" N   LEU J 222 "
        pdb=" CA  LEU J 222 "
      ideal   model   delta    sigma   weight residual
     120.28  126.80   -6.52 1.34e+00 5.57e-01 2.37e+01
  angle pdb=" CA  TYR I 164 "
        pdb=" C   TYR I 164 "
        pdb=" O   TYR I 164 "
      ideal   model   delta    sigma   weight residual
     120.70  115.75    4.95 1.03e+00 9.43e-01 2.31e+01
  angle pdb=" C   LYS J 115 "
        pdb=" N   ALA J 116 "
        pdb=" CA  ALA J 116 "
      ideal   model   delta    sigma   weight residual
     120.44  126.62   -6.18 1.30e+00 5.92e-01 2.26e+01
  ... (remaining 7028 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.68: 2759
       14.68 -    29.36: 271
       29.36 -    44.03: 79
       44.03 -    58.71: 29
       58.71 -    73.39: 9
  Dihedral angle restraints: 3147
    sinusoidal: 1300
      harmonic: 1847
  Sorted by residual:
  dihedral pdb=" CA  LEU J 243 "
           pdb=" C   LEU J 243 "
           pdb=" N   PRO J 244 "
           pdb=" CA  PRO J 244 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.81  -20.19     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  ARG I   9 "
           pdb=" C   ARG I   9 "
           pdb=" N   HIS I  10 "
           pdb=" CA  HIS I  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.83  -20.17     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  THR J 175 "
           pdb=" C   THR J 175 "
           pdb=" N   ARG J 176 "
           pdb=" CA  ARG J 176 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.81  -19.19     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 3144 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 308
       0.048 -    0.095: 270
       0.095 -    0.143: 141
       0.143 -    0.191: 46
       0.191 -    0.238: 10
  Chirality restraints: 775
  Sorted by residual:
  chirality pdb=" CA  VAL H 260 "
            pdb=" N   VAL H 260 "
            pdb=" C   VAL H 260 "
            pdb=" CB  VAL H 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  ILE J  75 "
            pdb=" CA  ILE J  75 "
            pdb=" CG1 ILE J  75 "
            pdb=" CG2 ILE J  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  LEU J 134 "
            pdb=" N   LEU J 134 "
            pdb=" C   LEU J 134 "
            pdb=" CB  LEU J 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 772 not shown)

  Planarity restraints: 901
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR I   2 "    0.033 2.00e-02 2.50e+03   2.39e-02 1.14e+01
        pdb=" CG  TYR I   2 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TYR I   2 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR I   2 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR I   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR I   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR I   2 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR I   2 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR I  86 "    0.029 2.00e-02 2.50e+03   2.23e-02 9.92e+00
        pdb=" CG  TYR I  86 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR I  86 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR I  86 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 TYR I  86 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR I  86 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR I  86 "   -0.022 2.00e-02 2.50e+03
        pdb=" OH  TYR I  86 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET I  85 "    0.014 2.00e-02 2.50e+03   2.91e-02 8.44e+00
        pdb=" C   MET I  85 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   MET I  85 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TYR I  86 "    0.017 2.00e-02 2.50e+03
  ... (remaining 898 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 739
        2.78 -     3.31: 5631
        3.31 -     3.84: 9455
        3.84 -     4.37: 12247
        4.37 -     4.90: 19042
  Nonbonded interactions: 47114
  Sorted by model distance:
  nonbonded pdb=" O   GLN J 236 "
            pdb=" O   HOH J 401 "
     model   vdw
     2.251 2.440
  nonbonded pdb=" O   GLU I 145 "
            pdb=" O   HOH I 401 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" OH  TYR J 178 "
            pdb=" OE1 GLU J 205 "
     model   vdw
     2.335 2.440
  nonbonded pdb=" NH1 ARG J  57 "
            pdb=" O   HOH J 402 "
     model   vdw
     2.345 2.520
  nonbonded pdb=" O   ILE I 198 "
            pdb=" OG1 THR I 201 "
     model   vdw
     2.380 2.440
  ... (remaining 47109 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.770
  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:          12.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.040
  Process input model:                     19.960
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.077   5197  Z= 0.887
  Angle     :  1.732   7.369   7033  Z= 1.301
  Chirality :  0.083   0.238    775
  Planarity :  0.007   0.029    901
  Dihedral  : 14.303  73.391   1951
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  6.32 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 (0.29), residues: 618
  helix: -1.14 (0.22), residues: 348
  sheet:  0.87 (1.26), residues: 14
  loop : -0.61 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.007   TRP I  11 
 HIS   0.016   0.004   HIS I   3 
 PHE   0.030   0.006   PHE J 295 
 TYR   0.057   0.007   TYR I   2 
 ARG   0.017   0.001   ARG I  89 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.617 
Fit side-chains
REVERT: H  268 ARG cc_start: 0.7166 (mtm110) cc_final: 0.6782 (mtp180)
REVERT: H  281 GLN cc_start: 0.7302 (pt0) cc_final: 0.7026 (tt0)
REVERT: H  306 TRP cc_start: 0.7636 (t60) cc_final: 0.7436 (t60)
REVERT: I   17 GLU cc_start: 0.6530 (mp0) cc_final: 0.6105 (mp0)
REVERT: I   18 GLN cc_start: 0.7347 (tt0) cc_final: 0.7095 (tt0)
REVERT: I   29 LYS cc_start: 0.6977 (mtpt) cc_final: 0.6001 (pttp)
REVERT: I   61 GLU cc_start: 0.7353 (tt0) cc_final: 0.7145 (tt0)
REVERT: I   62 LYS cc_start: 0.7722 (mtpp) cc_final: 0.7422 (mmtt)
REVERT: I   77 ARG cc_start: 0.6737 (mmp80) cc_final: 0.6197 (ptt180)
REVERT: I  138 LYS cc_start: 0.7095 (tttp) cc_final: 0.6850 (ttpp)
REVERT: I  189 LYS cc_start: 0.7530 (tttm) cc_final: 0.7294 (tttp)
REVERT: I  197 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6702 (mtt90)
REVERT: I  223 ARG cc_start: 0.6570 (ttt-90) cc_final: 0.6225 (mmt90)
REVERT: I  234 GLU cc_start: 0.6582 (pt0) cc_final: 0.6299 (mm-30)
REVERT: I  247 GLN cc_start: 0.6646 (mt0) cc_final: 0.6444 (mt0)
REVERT: I  279 ARG cc_start: 0.6179 (mtm-85) cc_final: 0.5881 (ttp-110)
REVERT: J   41 LYS cc_start: 0.7610 (ttpt) cc_final: 0.7398 (ttmm)
REVERT: J  219 LEU cc_start: 0.6090 (mm) cc_final: 0.5837 (tp)
REVERT: J  298 ARG cc_start: 0.6836 (mpp-170) cc_final: 0.6481 (mtt90)
  outliers start: 5
  outliers final: 1
  residues processed: 133
  average time/residue: 1.6583
  time to fit residues: 227.3327
Evaluate side-chains
  108 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  247 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.3980
   chunk 46 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
H 294 HIS
H 298 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5197  Z= 0.187
  Angle     :  0.560   5.496   7033  Z= 0.295
  Chirality :  0.040   0.140    775
  Planarity :  0.005   0.039    901
  Dihedral  :  4.963  55.969    690
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.84 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.29 (0.33), residues: 618
  helix:  1.49 (0.27), residues: 336
  sheet:  0.10 (1.11), residues: 19
  loop :  0.21 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J 132 
 HIS   0.006   0.001   HIS J 131 
 PHE   0.018   0.002   PHE J 295 
 TYR   0.021   0.002   TYR I 207 
 ARG   0.005   0.001   ARG J  57 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.656 
Fit side-chains
REVERT: H  262 GLU cc_start: 0.6619 (tt0) cc_final: 0.6364 (tt0)
REVERT: I   29 LYS cc_start: 0.6724 (mtpt) cc_final: 0.5813 (pttp)
REVERT: I   62 LYS cc_start: 0.7582 (mtpp) cc_final: 0.7296 (mmtt)
REVERT: I   77 ARG cc_start: 0.6798 (mmp80) cc_final: 0.6262 (ptt180)
REVERT: I  189 LYS cc_start: 0.7258 (tttm) cc_final: 0.7017 (tptt)
REVERT: I  197 ARG cc_start: 0.7290 (mtp85) cc_final: 0.6667 (mtt90)
REVERT: I  223 ARG cc_start: 0.6621 (ttt-90) cc_final: 0.6166 (mmt90)
REVERT: J   25 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.7060 (m)
REVERT: J  120 MET cc_start: 0.8081 (mtm) cc_final: 0.7791 (mtm)
REVERT: J  188 ARG cc_start: 0.6077 (mpp-170) cc_final: 0.5450 (mmp-170)
REVERT: J  219 LEU cc_start: 0.6023 (mm) cc_final: 0.5764 (tp)
  outliers start: 5
  outliers final: 1
  residues processed: 117
  average time/residue: 1.6976
  time to fit residues: 205.1657
Evaluate side-chains
  114 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue  247 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 31 optimal weight:    0.0980
   chunk 17 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN
I  18 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5197  Z= 0.198
  Angle     :  0.559   5.157   7033  Z= 0.292
  Chirality :  0.040   0.140    775
  Planarity :  0.005   0.038    901
  Dihedral  :  4.896  56.536    690
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.83 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.69 (0.33), residues: 618
  helix:  1.81 (0.28), residues: 336
  sheet:  0.02 (1.09), residues: 19
  loop :  0.42 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP J 132 
 HIS   0.006   0.002   HIS J 131 
 PHE   0.018   0.002   PHE J 295 
 TYR   0.016   0.002   TYR I 207 
 ARG   0.007   0.001   ARG J  57 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.691 
Fit side-chains
REVERT: I   29 LYS cc_start: 0.6822 (mtpt) cc_final: 0.5892 (pttp)
REVERT: I   62 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7280 (mmtt)
REVERT: I   77 ARG cc_start: 0.6862 (mmp80) cc_final: 0.6303 (ptt180)
REVERT: I  189 LYS cc_start: 0.7143 (tttm) cc_final: 0.6916 (tptt)
REVERT: I  197 ARG cc_start: 0.7299 (mtp85) cc_final: 0.6658 (mtt90)
REVERT: I  223 ARG cc_start: 0.6675 (ttt-90) cc_final: 0.6181 (mmt90)
REVERT: J  120 MET cc_start: 0.8109 (mtm) cc_final: 0.7769 (mtm)
REVERT: J  188 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5560 (mmt90)
REVERT: J  219 LEU cc_start: 0.5980 (mm) cc_final: 0.5726 (tp)
REVERT: J  224 ARG cc_start: 0.6624 (mtt-85) cc_final: 0.6402 (mtt90)
  outliers start: 6
  outliers final: 1
  residues processed: 112
  average time/residue: 1.6075
  time to fit residues: 186.2611
Evaluate side-chains
  106 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue  188 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 59 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN
I  18 GLN
J 129 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5197  Z= 0.310
  Angle     :  0.658   5.634   7033  Z= 0.347
  Chirality :  0.043   0.155    775
  Planarity :  0.005   0.039    901
  Dihedral  :  5.062  54.991    689
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.65 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.22 (0.33), residues: 618
  helix:  1.31 (0.27), residues: 345
  sheet: -0.14 (1.11), residues: 19
  loop :  0.35 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP J 132 
 HIS   0.010   0.002   HIS J 131 
 PHE   0.023   0.003   PHE I  30 
 TYR   0.019   0.003   TYR I  91 
 ARG   0.007   0.001   ARG J  57 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.639 
Fit side-chains
REVERT: I    1 MET cc_start: 0.7420 (mmm) cc_final: 0.7124 (mmm)
REVERT: I   29 LYS cc_start: 0.6899 (mtpt) cc_final: 0.6027 (pttp)
REVERT: I   62 LYS cc_start: 0.7621 (mtpp) cc_final: 0.7305 (mmtt)
REVERT: I   77 ARG cc_start: 0.6961 (mmp80) cc_final: 0.6412 (ptt180)
REVERT: I  189 LYS cc_start: 0.7154 (tttm) cc_final: 0.6925 (tptt)
REVERT: I  197 ARG cc_start: 0.7299 (mtp85) cc_final: 0.6630 (mtt90)
REVERT: J   41 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7458 (ttmm)
REVERT: J  120 MET cc_start: 0.8179 (mtm) cc_final: 0.7904 (mtm)
REVERT: J  188 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5623 (mmt90)
REVERT: J  219 LEU cc_start: 0.6014 (mm) cc_final: 0.5765 (tp)
  outliers start: 6
  outliers final: 0
  residues processed: 108
  average time/residue: 1.5727
  time to fit residues: 175.5694
Evaluate side-chains
  104 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  188 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 34 optimal weight:    0.0010
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN
I  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5197  Z= 0.183
  Angle     :  0.541   5.718   7033  Z= 0.280
  Chirality :  0.040   0.139    775
  Planarity :  0.004   0.038    901
  Dihedral  :  4.826  55.813    689
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 10.47 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.82 (0.34), residues: 618
  helix:  1.87 (0.28), residues: 336
  sheet:  0.10 (1.13), residues: 19
  loop :  0.56 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP J 132 
 HIS   0.006   0.001   HIS J 131 
 PHE   0.015   0.002   PHE I  30 
 TYR   0.017   0.002   TYR I  91 
 ARG   0.005   0.000   ARG J  57 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.674 
Fit side-chains
REVERT: H  262 GLU cc_start: 0.6538 (tt0) cc_final: 0.6239 (mp0)
REVERT: I    1 MET cc_start: 0.7344 (mmm) cc_final: 0.7140 (mmm)
REVERT: I   29 LYS cc_start: 0.6908 (mtpt) cc_final: 0.5988 (pttp)
REVERT: I   62 LYS cc_start: 0.7588 (mtpp) cc_final: 0.7285 (mmtt)
REVERT: I   77 ARG cc_start: 0.6937 (mmp80) cc_final: 0.6393 (ptt180)
REVERT: I  189 LYS cc_start: 0.7096 (tttm) cc_final: 0.6863 (tptt)
REVERT: I  197 ARG cc_start: 0.7256 (mtp85) cc_final: 0.6607 (mtt90)
REVERT: I  223 ARG cc_start: 0.6618 (ttt-90) cc_final: 0.6191 (mpt180)
REVERT: J   41 LYS cc_start: 0.7619 (ttmt) cc_final: 0.7411 (ttmm)
REVERT: J  120 MET cc_start: 0.8103 (mtm) cc_final: 0.7821 (mtm)
REVERT: J  147 GLU cc_start: 0.7255 (pm20) cc_final: 0.6794 (pt0)
REVERT: J  188 ARG cc_start: 0.6255 (mpp-170) cc_final: 0.5596 (mmt90)
REVERT: J  219 LEU cc_start: 0.5955 (mm) cc_final: 0.5709 (tp)
  outliers start: 5
  outliers final: 1
  residues processed: 114
  average time/residue: 1.7165
  time to fit residues: 201.7676
Evaluate side-chains
  105 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   25 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0870
   chunk 27 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0870
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5197  Z= 0.169
  Angle     :  0.520   5.207   7033  Z= 0.270
  Chirality :  0.039   0.137    775
  Planarity :  0.004   0.038    901
  Dihedral  :  4.726  56.103    689
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.37 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.34), residues: 618
  helix:  2.02 (0.29), residues: 336
  sheet: -0.05 (1.04), residues: 20
  loop :  0.68 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J 132 
 HIS   0.006   0.001   HIS J 131 
 PHE   0.015   0.002   PHE I  30 
 TYR   0.016   0.002   TYR I  91 
 ARG   0.008   0.000   ARG I  63 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.606 
Fit side-chains
REVERT: H  262 GLU cc_start: 0.6530 (tt0) cc_final: 0.6218 (mp0)
REVERT: H  265 MET cc_start: 0.7681 (mmt) cc_final: 0.7407 (mmm)
REVERT: I   29 LYS cc_start: 0.6938 (mtpt) cc_final: 0.5976 (pttp)
REVERT: I   62 LYS cc_start: 0.7589 (mtpp) cc_final: 0.7291 (mmtt)
REVERT: I   77 ARG cc_start: 0.6920 (mmp80) cc_final: 0.6407 (ptt180)
REVERT: I  189 LYS cc_start: 0.7074 (tttm) cc_final: 0.6834 (tptt)
REVERT: I  197 ARG cc_start: 0.7255 (mtp85) cc_final: 0.6610 (mtt90)
REVERT: I  223 ARG cc_start: 0.6616 (ttt-90) cc_final: 0.6186 (mpt180)
REVERT: J   25 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.7072 (p)
REVERT: J   41 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7443 (ttmm)
REVERT: J  120 MET cc_start: 0.8094 (mtm) cc_final: 0.7827 (mtm)
REVERT: J  147 GLU cc_start: 0.7236 (pm20) cc_final: 0.6775 (pt0)
REVERT: J  188 ARG cc_start: 0.6213 (mpp-170) cc_final: 0.5934 (mpt180)
REVERT: J  219 LEU cc_start: 0.5942 (mm) cc_final: 0.5700 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 109
  average time/residue: 1.7042
  time to fit residues: 191.6314
Evaluate side-chains
  104 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   25 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 43 optimal weight:    0.0770
   chunk 33 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.0942

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5197  Z= 0.252
  Angle     :  0.596   5.257   7033  Z= 0.313
  Chirality :  0.041   0.142    775
  Planarity :  0.005   0.038    901
  Dihedral  :  4.907  56.173    689
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 11.91 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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 (0.34), residues: 618
  helix:  1.56 (0.28), residues: 345
  sheet: -0.18 (1.07), residues: 19
  loop :  0.50 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP J 132 
 HIS   0.009   0.002   HIS J 131 
 PHE   0.020   0.002   PHE I  30 
 TYR   0.020   0.002   TYR I  91 
 ARG   0.005   0.001   ARG I  63 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.641 
Fit side-chains
REVERT: H  262 GLU cc_start: 0.6521 (tt0) cc_final: 0.6226 (mp0)
REVERT: H  265 MET cc_start: 0.7671 (mmt) cc_final: 0.7393 (mmm)
REVERT: I   29 LYS cc_start: 0.6957 (mtpt) cc_final: 0.6021 (pttp)
REVERT: I   62 LYS cc_start: 0.7598 (mtpp) cc_final: 0.7292 (mmtt)
REVERT: I   77 ARG cc_start: 0.6994 (mmp80) cc_final: 0.6460 (ptt180)
REVERT: I  189 LYS cc_start: 0.7127 (tttm) cc_final: 0.6894 (tptt)
REVERT: I  197 ARG cc_start: 0.7303 (mtp85) cc_final: 0.6641 (mtt90)
REVERT: I  223 ARG cc_start: 0.6655 (ttt-90) cc_final: 0.6136 (mmt90)
REVERT: J  120 MET cc_start: 0.8164 (mtm) cc_final: 0.7890 (mtm)
REVERT: J  188 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.6017 (mpt180)
REVERT: J  219 LEU cc_start: 0.5986 (mm) cc_final: 0.5746 (tp)
  outliers start: 4
  outliers final: 0
  residues processed: 107
  average time/residue: 1.6738
  time to fit residues: 184.9168
Evaluate side-chains
  101 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  188 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5197  Z= 0.321
  Angle     :  0.663   5.769   7033  Z= 0.350
  Chirality :  0.043   0.152    775
  Planarity :  0.005   0.039    901
  Dihedral  :  5.040  55.392    689
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 12.27 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.20 (0.33), residues: 618
  helix:  1.24 (0.28), residues: 345
  sheet: -0.31 (1.08), residues: 19
  loop :  0.44 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP J 132 
 HIS   0.010   0.002   HIS J 131 
 PHE   0.020   0.003   PHE J 295 
 TYR   0.020   0.003   TYR I  91 
 ARG   0.004   0.001   ARG J 188 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.620 
Fit side-chains
REVERT: H  265 MET cc_start: 0.7681 (mmt) cc_final: 0.7386 (mmm)
REVERT: I    1 MET cc_start: 0.7353 (mmm) cc_final: 0.7144 (mmm)
REVERT: I   29 LYS cc_start: 0.6993 (mtpt) cc_final: 0.6036 (pttp)
REVERT: I   62 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7310 (mmtt)
REVERT: I   77 ARG cc_start: 0.7009 (mmp80) cc_final: 0.6481 (ptt180)
REVERT: I  189 LYS cc_start: 0.7170 (tttm) cc_final: 0.6929 (tptt)
REVERT: I  269 GLU cc_start: 0.6073 (tp30) cc_final: 0.5775 (tt0)
REVERT: J  120 MET cc_start: 0.8189 (mtm) cc_final: 0.7905 (mtm)
REVERT: J  188 ARG cc_start: 0.6311 (OUTLIER) cc_final: 0.6019 (mpt90)
  outliers start: 2
  outliers final: 1
  residues processed: 103
  average time/residue: 1.5936
  time to fit residues: 169.6401
Evaluate side-chains
  105 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue  188 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5197  Z= 0.209
  Angle     :  0.574   6.673   7033  Z= 0.297
  Chirality :  0.040   0.141    775
  Planarity :  0.005   0.039    901
  Dihedral  :  4.884  56.160    689
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 12.45 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.70 (0.34), residues: 618
  helix:  1.70 (0.28), residues: 337
  sheet: -0.38 (1.02), residues: 20
  loop :  0.65 (0.39), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP J 132 
 HIS   0.007   0.001   HIS J 131 
 PHE   0.017   0.002   PHE I  30 
 TYR   0.018   0.002   TYR I  91 
 ARG   0.005   0.000   ARG I  63 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.644 
Fit side-chains
REVERT: H  262 GLU cc_start: 0.6440 (tt0) cc_final: 0.6106 (mp0)
REVERT: H  265 MET cc_start: 0.7641 (mmt) cc_final: 0.7354 (mmm)
REVERT: I   29 LYS cc_start: 0.6973 (mtpt) cc_final: 0.5994 (pttp)
REVERT: I   62 LYS cc_start: 0.7605 (mtpp) cc_final: 0.7304 (mmtt)
REVERT: I   77 ARG cc_start: 0.6984 (mmp80) cc_final: 0.6505 (ptt180)
REVERT: I  189 LYS cc_start: 0.7094 (tttm) cc_final: 0.6857 (tptt)
REVERT: I  197 ARG cc_start: 0.7270 (mtp180) cc_final: 0.6587 (mtt90)
REVERT: I  269 GLU cc_start: 0.6045 (tp30) cc_final: 0.5783 (tt0)
REVERT: J   25 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7153 (p)
REVERT: J  120 MET cc_start: 0.8131 (mtm) cc_final: 0.7847 (mtm)
REVERT: J  147 GLU cc_start: 0.7249 (pm20) cc_final: 0.6776 (pt0)
REVERT: J  188 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.6017 (mpt180)
REVERT: J  219 LEU cc_start: 0.5962 (mm) cc_final: 0.5719 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 104
  average time/residue: 1.6167
  time to fit residues: 173.7230
Evaluate side-chains
  104 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue  188 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5197  Z= 0.232
  Angle     :  0.593   7.151   7033  Z= 0.309
  Chirality :  0.041   0.141    775
  Planarity :  0.005   0.039    901
  Dihedral  :  4.909  56.444    689
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.13 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 12.45 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.34), residues: 618
  helix:  1.53 (0.28), residues: 343
  sheet: -0.27 (1.07), residues: 19
  loop :  0.50 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP J 132 
 HIS   0.008   0.002   HIS J 131 
 PHE   0.019   0.002   PHE I  30 
 TYR   0.019   0.002   TYR I  91 
 ARG   0.004   0.000   ARG I  63 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.590 
Fit side-chains
REVERT: H  262 GLU cc_start: 0.6420 (tt0) cc_final: 0.6091 (mp0)
REVERT: H  265 MET cc_start: 0.7659 (mmt) cc_final: 0.7374 (mmm)
REVERT: I   29 LYS cc_start: 0.6972 (mtpt) cc_final: 0.6013 (pttp)
REVERT: I   62 LYS cc_start: 0.7601 (mtpp) cc_final: 0.7295 (mmtt)
REVERT: I   77 ARG cc_start: 0.6988 (mmp80) cc_final: 0.6520 (ptt180)
REVERT: I  189 LYS cc_start: 0.7120 (tttm) cc_final: 0.6884 (tptt)
REVERT: I  197 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6598 (mtt90)
REVERT: I  269 GLU cc_start: 0.6030 (tp30) cc_final: 0.5769 (tt0)
REVERT: J   25 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7167 (p)
REVERT: J  120 MET cc_start: 0.8155 (mtm) cc_final: 0.7860 (mtm)
REVERT: J  147 GLU cc_start: 0.7251 (pm20) cc_final: 0.6771 (pt0)
REVERT: J  188 ARG cc_start: 0.6220 (mpp-170) cc_final: 0.6013 (mpt180)
  outliers start: 2
  outliers final: 1
  residues processed: 103
  average time/residue: 1.6496
  time to fit residues: 175.3600
Evaluate side-chains
  105 residues out of total 554 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   25 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 43 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.202803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.174431 restraints weight = 2894.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 0.65
r_work: 0.3868 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 1.85 restraints_weight: 0.2500
r_work: 0.3573 rms_B_bonded: 4.50 restraints_weight: 0.1250
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5197  Z= 0.218
  Angle     :  0.585   7.239   7033  Z= 0.304
  Chirality :  0.040   0.140    775
  Planarity :  0.005   0.039    901
  Dihedral  :  4.901  57.111    689
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 12.82 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.54 (0.34), residues: 618
  helix:  1.58 (0.28), residues: 343
  sheet: -0.25 (1.07), residues: 19
  loop :  0.51 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP J 177 
 HIS   0.007   0.001   HIS J 131 
 PHE   0.018   0.002   PHE I  30 
 TYR   0.018   0.002   TYR I  91 
 ARG   0.009   0.001   ARG I  63 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3689.25 seconds
wall clock time: 66 minutes 2.74 seconds (3962.74 seconds total)