Starting phenix.real_space_refine
on Sat May 10 20:46:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b3k_44143/05_2025/9b3k_44143.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b3k_44143/05_2025/9b3k_44143.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b3k_44143/05_2025/9b3k_44143.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b3k_44143/05_2025/9b3k_44143.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b3k_44143/05_2025/9b3k_44143.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b3k_44143/05_2025/9b3k_44143.cif"
  }
  resolution = 2.56
  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=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 960 atoms to isotropic.
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      27      5.16       5
     C    3940      2.51       5
     N     972      2.21       5
     O    1124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6063
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "Z"
      Number of atoms: 2833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 2833
          Classifications: {'peptide': 370}
          Link IDs: {'PTRANS': 13, 'TRANS': 356}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1687
          Classifications: {'peptide': 224}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 212}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1543
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 203, 1540
          Classifications: {'peptide': 203}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 203, 1540
          Classifications: {'peptide': 203}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 1563
  Time building chain proxies: 5.06, per 1000 atoms: 0.83
  Number of scatterers: 6063
  At special positions: 0
  Unit cell: (66.825, 65.175, 129.525, 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      27     16.00
     O    1124      8.00
     N     972      7.00
     C    3940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  48 " - pdb=" SG  CYS H 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 181 " - pdb=" SG  CYS H 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  47 " - pdb=" SG  CYS L 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 158 " - pdb=" SG  CYS L 218 " distance=2.03

  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: 1.55
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 12 sheets defined
      46.0% alpha, 31.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'Z' and resid 3 through 21
      removed outlier: 3.561A  pdb=" N   GLY Z  20 " --> pdb=" O   PHE Z  16 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 22 through 24
      No H-bonds generated for 'chain 'Z' and resid 22 through 24'
    Processing helix  chain 'Z' and resid 25 through 34
    Processing helix  chain 'Z' and resid 36 through 66
      removed outlier: 4.217A  pdb=" N   PHE Z  47 " --> pdb=" O   LEU Z  43 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ALA Z  48 " --> pdb=" O   VAL Z  44 " (cutoff:3.500A)
      Proline residue:  Z  56  - end of helix
    Processing helix  chain 'Z' and resid 66 through 88
      removed outlier: 3.709A  pdb=" N   ILE Z  70 " --> pdb=" O   GLY Z  66 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 90 through 119
      Proline residue:  Z 110  - end of helix
    Processing helix  chain 'Z' and resid 124 through 150
      Proline residue:  Z 144  - end of helix
    Processing helix  chain 'Z' and resid 156 through 177
    Processing helix  chain 'Z' and resid 204 through 224
      removed outlier: 3.740A  pdb=" N   ALA Z 220 " --> pdb=" O   PHE Z 216 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   PHE Z 221 " --> pdb=" O   GLY Z 217 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU Z 224 " --> pdb=" O   ALA Z 220 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 224 through 234
      removed outlier: 3.559A  pdb=" N   ASN Z 234 " --> pdb=" O   ALA Z 230 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 236 through 258
    Processing helix  chain 'Z' and resid 258 through 266
    Processing helix  chain 'Z' and resid 267 through 288
    Processing helix  chain 'Z' and resid 291 through 302
      removed outlier: 3.779A  pdb=" N   VAL Z 301 " --> pdb=" O   LEU Z 297 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 303 through 321
      removed outlier: 3.696A  pdb=" N   ARG Z 310 " --> pdb=" O   PHE Z 306 " (cutoff:3.500A)
      Proline residue:  Z 311  - end of helix
    Processing helix  chain 'Z' and resid 324 through 352
      Proline residue:  Z 344  - end of helix
      removed outlier: 3.579A  pdb=" N   ALA Z 349 " --> pdb=" O   LEU Z 345 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 356 through 384
    Processing helix  chain 'H' and resid 113 through 117
      removed outlier: 3.672A  pdb=" N   THR H 117 " --> pdb=" O   ALA H 114 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 228 through 230
      No H-bonds generated for 'chain 'H' and resid 228 through 230'
    Processing helix  chain 'L' and resid 103 through 107
      removed outlier: 3.999A  pdb=" N   PHE L 107 " --> pdb=" O   PRO L 104 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 145 through 152
      removed outlier: 3.689A  pdb=" N   GLY L 152 " --> pdb=" O   GLN L 148 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 207 through 212
      removed outlier: 3.629A  pdb=" N   LYS L 212 " --> pdb=" O   ALA L 208 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 29 through 33
    Processing sheet with id=AA2, first strand: chain 'H' and resid 84 through 86
      removed outlier: 6.637A  pdb=" N   TRP H  62 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   SER H  76 " --> pdb=" O   ILE H  60 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE H  60 " --> pdb=" O   SER H  76 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   SER H  78 " --> pdb=" O   SER H  58 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   SER H  58 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 84 through 86
      removed outlier: 6.637A  pdb=" N   TRP H  62 " --> pdb=" O   VAL H  74 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   SER H  76 " --> pdb=" O   ILE H  60 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE H  60 " --> pdb=" O   SER H  76 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   SER H  78 " --> pdb=" O   SER H  58 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   SER H  58 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   CYS H 122 " --> pdb=" O   TRP H 145 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   TRP H 145 " --> pdb=" O   CYS H 122 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ARG H 124 " --> pdb=" O   ASP H 143 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA H 132 " --> pdb=" O   VAL H 135 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 161 through 165
      removed outlier: 3.785A  pdb=" N   GLY H 180 " --> pdb=" O   LEU H 165 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   TYR H 217 " --> pdb=" O   ASP H 185 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 161 through 165
      removed outlier: 3.785A  pdb=" N   GLY H 180 " --> pdb=" O   LEU H 165 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   TYR H 217 " --> pdb=" O   ASP H 185 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 191 through 195
      removed outlier: 4.017A  pdb=" N   TYR H 235 " --> pdb=" O   VAL H 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 31
    Processing sheet with id=AA8, first strand: chain 'L' and resid 34 through 37
      removed outlier: 6.430A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 34 through 37
    Processing sheet with id=AB1, first strand: chain 'L' and resid 140 through 142
      removed outlier: 3.664A  pdb=" N   VAL L 157 " --> pdb=" O   PHE L 142 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   TYR L 197 " --> pdb=" O   ASN L 162 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 169 through 169
    Processing sheet with id=AB3, first strand: chain 'L' and resid 169 through 169

    421 hydrogen bonds defined for protein.
    1182 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: 2.02

  Time building geometry restraints manager: 1.84 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: 1846
        1.34 -     1.46: 1409
        1.46 -     1.58: 2907
        1.58 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 6207
  Sorted by residual:
  bond pdb=" C   VAL H 135 "
       pdb=" N   GLY H 136 "
    ideal  model  delta    sigma   weight residual
    1.328  1.310  0.018 1.31e-02 5.83e+03 1.89e+00
  bond pdb=" N   TRP H 133 "
       pdb=" CA  TRP H 133 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.12e+00
  bond pdb=" CB  ASP H 143 "
       pdb=" CG  ASP H 143 "
    ideal  model  delta    sigma   weight residual
    1.516  1.490  0.026 2.50e-02 1.60e+03 1.04e+00
  bond pdb=" CG  PRO Z 311 "
       pdb=" CD  PRO Z 311 "
    ideal  model  delta    sigma   weight residual
    1.503  1.475  0.028 3.40e-02 8.65e+02 6.92e-01
  bond pdb=" CB  PRO Z 207 "
       pdb=" CG  PRO Z 207 "
    ideal  model  delta    sigma   weight residual
    1.492  1.452  0.040 5.00e-02 4.00e+02 6.28e-01
  ... (remaining 6202 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 8250
        1.71 -     3.42: 141
        3.42 -     5.13: 19
        5.13 -     6.85: 10
        6.85 -     8.56: 1
  Bond angle restraints: 8421
  Sorted by residual:
  angle pdb=" N   VAL Z 153 "
        pdb=" CA  VAL Z 153 "
        pdb=" C   VAL Z 153 "
      ideal   model   delta    sigma   weight residual
     112.96  108.86    4.10 1.00e+00 1.00e+00 1.68e+01
  angle pdb=" N   GLU H 189 "
        pdb=" CA  GLU H 189 "
        pdb=" C   GLU H 189 "
      ideal   model   delta    sigma   weight residual
     109.81  116.19   -6.38 2.21e+00 2.05e-01 8.34e+00
  angle pdb=" N   VAL H 135 "
        pdb=" CA  VAL H 135 "
        pdb=" C   VAL H 135 "
      ideal   model   delta    sigma   weight residual
     109.34  103.45    5.89 2.08e+00 2.31e-01 8.02e+00
  angle pdb=" C   TRP H 133 "
        pdb=" CA  TRP H 133 "
        pdb=" CB  TRP H 133 "
      ideal   model   delta    sigma   weight residual
     110.42  116.05   -5.63 1.99e+00 2.53e-01 8.00e+00
  angle pdb=" CA  LEU L 199 "
        pdb=" CB  LEU L 199 "
        pdb=" CG  LEU L 199 "
      ideal   model   delta    sigma   weight residual
     116.30  124.86   -8.56 3.50e+00 8.16e-02 5.98e+00
  ... (remaining 8416 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3134
       17.86 -    35.71: 362
       35.71 -    53.57: 101
       53.57 -    71.43: 26
       71.43 -    89.28: 6
  Dihedral angle restraints: 3629
    sinusoidal: 1351
      harmonic: 2278
  Sorted by residual:
  dihedral pdb=" CB  CYS H 181 "
           pdb=" SG  CYS H 181 "
           pdb=" SG  CYS H 237 "
           pdb=" CB  CYS H 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.73   63.73     1      1.00e+01 1.00e-02 5.35e+01
  dihedral pdb=" CA  GLU H 189 "
           pdb=" C   GLU H 189 "
           pdb=" N   PRO H 190 "
           pdb=" CA  PRO H 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.86   27.14     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CB  CYS H  48 "
           pdb=" SG  CYS H  48 "
           pdb=" SG  CYS H 122 "
           pdb=" CB  CYS H 122 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.29   34.71     1      1.00e+01 1.00e-02 1.71e+01
  ... (remaining 3626 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 719
       0.043 -    0.086: 184
       0.086 -    0.129: 57
       0.129 -    0.172: 5
       0.172 -    0.215: 2
  Chirality restraints: 967
  Sorted by residual:
  chirality pdb=" CB  VAL Z 233 "
            pdb=" CA  VAL Z 233 "
            pdb=" CG1 VAL Z 233 "
            pdb=" CG2 VAL Z 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  THR Z 206 "
            pdb=" N   THR Z 206 "
            pdb=" C   THR Z 206 "
            pdb=" CB  THR Z 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CB  THR Z 206 "
            pdb=" CA  THR Z 206 "
            pdb=" OG1 THR Z 206 "
            pdb=" CG2 THR Z 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.36e-01
  ... (remaining 964 not shown)

  Planarity restraints: 1045
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 189 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.12e+00
        pdb=" N   PRO H 190 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO H 190 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO H 190 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL H 135 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" C   VAL H 135 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL H 135 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY H 136 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA H 132 "    0.007 2.00e-02 2.50e+03   1.36e-02 1.86e+00
        pdb=" C   ALA H 132 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ALA H 132 "    0.009 2.00e-02 2.50e+03
        pdb=" N   TRP H 133 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1042 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 470
        2.74 -     3.28: 5767
        3.28 -     3.82: 10480
        3.82 -     4.36: 12452
        4.36 -     4.90: 21514
  Nonbonded interactions: 50683
  Sorted by model distance:
  nonbonded pdb=" O   SER H  81 "
            pdb=" OG  SER H  81 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OD2 ASP L 194 "
            pdb=" OG1 THR L 196 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   SER H 111 "
            pdb=" OG  SER H 111 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OG  SER Z  81 "
            pdb=" O   SER Z  97 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   SER L  54 "
            pdb=" NH2 ARG L  90 "
     model   vdw
     2.290 3.120
  ... (remaining 50678 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=0.12 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:             2.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.810
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
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      :  0.004   0.040   6211  Z= 0.176
  Angle     :  0.586   8.558   8429  Z= 0.305
  Chirality :  0.043   0.215    967
  Planarity :  0.004   0.044   1045
  Dihedral  : 17.050  89.284   2165
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.02 %
    Favored  : 71.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.31), residues: 780
  helix:  2.26 (0.29), residues: 343
  sheet:  1.21 (0.36), residues: 207
  loop : -0.92 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 139 
 HIS   0.002   0.001   HIS H 241 
 PHE   0.021   0.002   PHE Z 335 
 TYR   0.011   0.002   TYR H 121 
 ARG   0.002   0.000   ARG H  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10059 (  385)
  hydrogen bonds       : angle       5.22859 ( 1182)
  SS BOND              : bond        0.00162 (    4)
  SS BOND              : angle       0.68730 (    8)
  covalent geometry    : bond        0.00414 ( 6207)
  covalent geometry    : angle       0.58552 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.614 
Fit side-chains
REVERT: L   48 ARG cc_start: 0.7132 (mpt90) cc_final: 0.6915 (mmt180)
  outliers start: 29
  outliers final: 28
  residues processed: 103
  average time/residue: 0.9803
  time to fit residues: 106.8647
Evaluate side-chains
  102 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue    5 ILE
Chi-restraints excluded: chain Z residue   26 LEU
Chi-restraints excluded: chain Z residue   79 SER
Chi-restraints excluded: chain Z residue  153 VAL
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  209 ILE
Chi-restraints excluded: chain Z residue  229 THR
Chi-restraints excluded: chain Z residue  267 SER
Chi-restraints excluded: chain Z residue  309 ILE
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue   58 SER
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   81 SER
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue  101 SER
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  118 SER
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  155 SER
Chi-restraints excluded: chain L residue  159 LEU
Chi-restraints excluded: chain L residue  200 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.2980
   chunk 59 optimal weight:    0.0060
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
Z 128 ASN
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.163068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.117478 restraints weight = 7887.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.36
r_work: 0.3127 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.0571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6211  Z= 0.133
  Angle     :  0.554   8.353   8429  Z= 0.289
  Chirality :  0.041   0.169    967
  Planarity :  0.004   0.045   1045
  Dihedral  :  7.158  53.634    879
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 22.67 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  1.89 (0.31), residues: 780
  helix:  2.54 (0.29), residues: 344
  sheet:  1.45 (0.37), residues: 197
  loop : -0.93 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 133 
 HIS   0.003   0.001   HIS Z 155 
 PHE   0.017   0.001   PHE Z 335 
 TYR   0.010   0.001   TYR H 121 
 ARG   0.002   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04031 (  385)
  hydrogen bonds       : angle       4.22978 ( 1182)
  SS BOND              : bond        0.00154 (    4)
  SS BOND              : angle       0.55307 (    8)
  covalent geometry    : bond        0.00303 ( 6207)
  covalent geometry    : angle       0.55368 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.710 
Fit side-chains
REVERT: L   48 ARG cc_start: 0.7526 (mpt90) cc_final: 0.7183 (mmt180)
  outliers start: 24
  outliers final: 12
  residues processed: 93
  average time/residue: 1.0660
  time to fit residues: 104.6222
Evaluate side-chains
  81 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue  153 VAL
Chi-restraints excluded: chain Z residue  309 ILE
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain H residue  253 GLU
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  145 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 42 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 1 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0870
   chunk 3 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.165725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.120543 restraints weight = 7898.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.40
r_work: 0.3166 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.0934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6211  Z= 0.107
  Angle     :  0.513   6.375   8429  Z= 0.267
  Chirality :  0.040   0.168    967
  Planarity :  0.004   0.043   1045
  Dihedral  :  5.702  55.306    857
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 23.42 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  2.05 (0.31), residues: 780
  helix:  2.66 (0.29), residues: 345
  sheet:  1.50 (0.37), residues: 197
  loop : -0.81 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 133 
 HIS   0.003   0.001   HIS Z 155 
 PHE   0.014   0.001   PHE Z  16 
 TYR   0.008   0.001   TYR H 121 
 ARG   0.002   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  385)
  hydrogen bonds       : angle       3.99735 ( 1182)
  SS BOND              : bond        0.00138 (    4)
  SS BOND              : angle       0.47262 (    8)
  covalent geometry    : bond        0.00237 ( 6207)
  covalent geometry    : angle       0.51346 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.705 
Fit side-chains
REVERT: H   91 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7452 (tmtt)
REVERT: H  154 PHE cc_start: 0.6423 (m-80) cc_final: 0.6052 (m-10)
REVERT: L   48 ARG cc_start: 0.7479 (mpt90) cc_final: 0.6835 (mmt90)
REVERT: L  199 LEU cc_start: 0.8016 (tt) cc_final: 0.7707 (tm)
  outliers start: 18
  outliers final: 10
  residues processed: 95
  average time/residue: 1.0891
  time to fit residues: 109.1660
Evaluate side-chains
  87 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue  140 PHE
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  297 LEU
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue   91 LYS
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue  145 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.162716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.117240 restraints weight = 9504.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.79
r_work: 0.3101 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.0797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6211  Z= 0.149
  Angle     :  0.555   6.496   8429  Z= 0.289
  Chirality :  0.042   0.208    967
  Planarity :  0.005   0.082   1045
  Dihedral  :  5.480  53.097    850
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.67 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  1.94 (0.31), residues: 780
  helix:  2.57 (0.28), residues: 344
  sheet:  1.52 (0.38), residues: 196
  loop : -0.93 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 139 
 HIS   0.003   0.001   HIS Z 155 
 PHE   0.022   0.002   PHE Z 335 
 TYR   0.010   0.001   TYR H 121 
 ARG   0.002   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  385)
  hydrogen bonds       : angle       4.10788 ( 1182)
  SS BOND              : bond        0.00160 (    4)
  SS BOND              : angle       0.55205 (    8)
  covalent geometry    : bond        0.00348 ( 6207)
  covalent geometry    : angle       0.55450 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.624 
Fit side-chains
REVERT: Z  310 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7386 (mtt180)
REVERT: H   72 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8691 (tt0)
REVERT: H   91 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7453 (tmtt)
REVERT: H  154 PHE cc_start: 0.6476 (m-80) cc_final: 0.6043 (m-10)
REVERT: L   48 ARG cc_start: 0.7522 (mpt90) cc_final: 0.7189 (mmt180)
REVERT: L  199 LEU cc_start: 0.8032 (tt) cc_final: 0.7685 (tm)
  outliers start: 28
  outliers final: 13
  residues processed: 95
  average time/residue: 0.9890
  time to fit residues: 99.3842
Evaluate side-chains
  89 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue  153 VAL
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  209 ILE
Chi-restraints excluded: chain Z residue  310 ARG
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   72 GLU
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue   91 LYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  157 ILE
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue  124 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 76 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0570
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.163692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.117684 restraints weight = 8216.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.37
r_work: 0.3137 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6211  Z= 0.124
  Angle     :  0.528   6.448   8429  Z= 0.275
  Chirality :  0.041   0.185    967
  Planarity :  0.004   0.085   1045
  Dihedral  :  5.409  52.356    850
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.82 %
    Favored  : 72.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  2.00 (0.31), residues: 780
  helix:  2.61 (0.29), residues: 345
  sheet:  1.51 (0.38), residues: 196
  loop : -0.83 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 139 
 HIS   0.003   0.001   HIS Z 155 
 PHE   0.016   0.001   PHE Z 335 
 TYR   0.010   0.001   TYR H 121 
 ARG   0.002   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  385)
  hydrogen bonds       : angle       4.02227 ( 1182)
  SS BOND              : bond        0.00149 (    4)
  SS BOND              : angle       0.48691 (    8)
  covalent geometry    : bond        0.00284 ( 6207)
  covalent geometry    : angle       0.52785 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 0.722 
Fit side-chains
REVERT: H   91 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7473 (tmtt)
REVERT: L   48 ARG cc_start: 0.7517 (mpt90) cc_final: 0.7210 (mmt180)
REVERT: L  199 LEU cc_start: 0.8019 (tt) cc_final: 0.7666 (tm)
  outliers start: 28
  outliers final: 18
  residues processed: 95
  average time/residue: 1.0963
  time to fit residues: 109.9463
Evaluate side-chains
  91 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue    5 ILE
Chi-restraints excluded: chain Z residue   65 LEU
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  209 ILE
Chi-restraints excluded: chain Z residue  287 VAL
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue   69 LYS
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue   91 LYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  182 LEU
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue  118 SER
Chi-restraints excluded: chain L residue  124 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.161348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.114615 restraints weight = 6254.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.00
r_work: 0.3119 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.0781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6211  Z= 0.177
  Angle     :  0.580   6.514   8429  Z= 0.302
  Chirality :  0.043   0.181    967
  Planarity :  0.005   0.077   1045
  Dihedral  :  5.587  53.584    850
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 22.82 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  1.80 (0.31), residues: 780
  helix:  2.44 (0.28), residues: 344
  sheet:  1.47 (0.38), residues: 196
  loop : -0.98 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 139 
 HIS   0.003   0.001   HIS Z 155 
 PHE   0.022   0.002   PHE Z 335 
 TYR   0.012   0.002   TYR H 121 
 ARG   0.002   0.000   ARG L  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04529 (  385)
  hydrogen bonds       : angle       4.19634 ( 1182)
  SS BOND              : bond        0.00161 (    4)
  SS BOND              : angle       0.56247 (    8)
  covalent geometry    : bond        0.00420 ( 6207)
  covalent geometry    : angle       0.58025 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.635 
Fit side-chains
REVERT: Z  310 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7447 (mtt180)
REVERT: H   72 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8674 (tt0)
REVERT: H   91 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7469 (tmtt)
REVERT: L   48 ARG cc_start: 0.7571 (mpt90) cc_final: 0.7257 (mmt180)
REVERT: L  199 LEU cc_start: 0.8058 (tt) cc_final: 0.7702 (tm)
  outliers start: 30
  outliers final: 18
  residues processed: 93
  average time/residue: 1.0878
  time to fit residues: 106.9415
Evaluate side-chains
  92 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue   65 LEU
Chi-restraints excluded: chain Z residue  153 VAL
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  209 ILE
Chi-restraints excluded: chain Z residue  310 ARG
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue   72 GLU
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue   91 LYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  157 ILE
Chi-restraints excluded: chain H residue  182 LEU
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue  118 SER
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  159 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0060
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0770
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 74 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.4354

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

Flipped N/Q/H residues before XYZ refinement:
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.164146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.118471 restraints weight = 7860.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.32
r_work: 0.3144 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6211  Z= 0.116
  Angle     :  0.533   7.268   8429  Z= 0.274
  Chirality :  0.041   0.176    967
  Planarity :  0.004   0.072   1045
  Dihedral  :  5.360  51.248    850
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.17 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  2.00 (0.31), residues: 780
  helix:  2.63 (0.29), residues: 345
  sheet:  1.49 (0.37), residues: 196
  loop : -0.86 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 139 
 HIS   0.003   0.001   HIS Z 155 
 PHE   0.016   0.001   PHE Z  16 
 TYR   0.010   0.001   TYR H 121 
 ARG   0.002   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  385)
  hydrogen bonds       : angle       3.98998 ( 1182)
  SS BOND              : bond        0.00147 (    4)
  SS BOND              : angle       0.48674 (    8)
  covalent geometry    : bond        0.00258 ( 6207)
  covalent geometry    : angle       0.53264 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.681 
Fit side-chains
REVERT: Z  310 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7344 (mtt180)
REVERT: H   91 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7467 (tmtt)
REVERT: H  154 PHE cc_start: 0.6524 (m-80) cc_final: 0.6204 (m-10)
REVERT: L   48 ARG cc_start: 0.7552 (mpt90) cc_final: 0.7207 (mmt180)
REVERT: L  199 LEU cc_start: 0.8024 (tt) cc_final: 0.7662 (tm)
  outliers start: 22
  outliers final: 17
  residues processed: 90
  average time/residue: 1.0675
  time to fit residues: 101.6044
Evaluate side-chains
  92 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue    5 ILE
Chi-restraints excluded: chain Z residue   65 LEU
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  209 ILE
Chi-restraints excluded: chain Z residue  287 VAL
Chi-restraints excluded: chain Z residue  310 ARG
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue   91 LYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  182 LEU
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   33 SER
Chi-restraints excluded: chain L residue  118 SER
Chi-restraints excluded: chain L residue  124 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.160616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.115229 restraints weight = 8178.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.50
r_work: 0.3077 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6211  Z= 0.203
  Angle     :  0.605   7.481   8429  Z= 0.314
  Chirality :  0.044   0.184    967
  Planarity :  0.005   0.072   1045
  Dihedral  :  5.534  54.822    849
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.57 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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 (0.31), residues: 780
  helix:  2.36 (0.28), residues: 344
  sheet:  1.40 (0.37), residues: 196
  loop : -1.03 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 139 
 HIS   0.003   0.001   HIS H 241 
 PHE   0.023   0.002   PHE Z 335 
 TYR   0.012   0.002   TYR H 121 
 ARG   0.002   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 (  385)
  hydrogen bonds       : angle       4.25590 ( 1182)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       0.59709 (    8)
  covalent geometry    : bond        0.00488 ( 6207)
  covalent geometry    : angle       0.60518 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.698 
Fit side-chains
REVERT: Z    1 MET cc_start: 0.5154 (OUTLIER) cc_final: 0.4338 (tpp)
REVERT: Z  310 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7467 (mtt180)
REVERT: H   91 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7474 (tmtt)
REVERT: H  154 PHE cc_start: 0.6664 (m-80) cc_final: 0.6264 (m-10)
REVERT: L   48 ARG cc_start: 0.7613 (mpt90) cc_final: 0.7282 (mmt180)
REVERT: L  191 ASP cc_start: 0.6967 (t70) cc_final: 0.6610 (t0)
REVERT: L  199 LEU cc_start: 0.8018 (tt) cc_final: 0.7652 (tm)
  outliers start: 27
  outliers final: 18
  residues processed: 94
  average time/residue: 1.0328
  time to fit residues: 102.5492
Evaluate side-chains
  95 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue    1 MET
Chi-restraints excluded: chain Z residue   65 LEU
Chi-restraints excluded: chain Z residue  153 VAL
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  209 ILE
Chi-restraints excluded: chain Z residue  310 ARG
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue   91 LYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  157 ILE
Chi-restraints excluded: chain H residue  182 LEU
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue  118 SER
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  159 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 76 optimal weight:    9.9990
   chunk 41 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   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 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.162294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.116462 restraints weight = 8173.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.38
r_work: 0.3119 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.0872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6211  Z= 0.144
  Angle     :  0.562   7.293   8429  Z= 0.291
  Chirality :  0.042   0.231    967
  Planarity :  0.004   0.070   1045
  Dihedral  :  5.421  52.878    849
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 24.02 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  1.81 (0.31), residues: 780
  helix:  2.45 (0.29), residues: 346
  sheet:  1.44 (0.37), residues: 196
  loop : -0.96 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 139 
 HIS   0.003   0.001   HIS Z 155 
 PHE   0.019   0.001   PHE Z  16 
 TYR   0.010   0.001   TYR H 121 
 ARG   0.002   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  385)
  hydrogen bonds       : angle       4.11510 ( 1182)
  SS BOND              : bond        0.00153 (    4)
  SS BOND              : angle       0.50880 (    8)
  covalent geometry    : bond        0.00335 ( 6207)
  covalent geometry    : angle       0.56192 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.708 
Fit side-chains
REVERT: Z  157 MET cc_start: 0.8012 (tpp) cc_final: 0.7734 (tpp)
REVERT: Z  310 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7426 (mtt180)
REVERT: H   72 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8693 (tt0)
REVERT: H   91 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7478 (tmtt)
REVERT: H  154 PHE cc_start: 0.6600 (m-80) cc_final: 0.6177 (m-10)
REVERT: L   48 ARG cc_start: 0.7617 (mpt90) cc_final: 0.7273 (mmt180)
REVERT: L  199 LEU cc_start: 0.7978 (tt) cc_final: 0.7606 (tm)
  outliers start: 25
  outliers final: 17
  residues processed: 88
  average time/residue: 1.0859
  time to fit residues: 100.9189
Evaluate side-chains
  90 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue    5 ILE
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  209 ILE
Chi-restraints excluded: chain Z residue  310 ARG
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue   72 GLU
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue   91 LYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  157 ILE
Chi-restraints excluded: chain H residue  182 LEU
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue  118 SER
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  159 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 30 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:
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.162721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117644 restraints weight = 9777.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.80
r_work: 0.3108 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.0922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6211  Z= 0.137
  Angle     :  0.556   7.141   8429  Z= 0.288
  Chirality :  0.042   0.219    967
  Planarity :  0.004   0.069   1045
  Dihedral  :  5.348  52.354    849
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 24.17 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  1.88 (0.31), residues: 780
  helix:  2.53 (0.29), residues: 346
  sheet:  1.44 (0.37), residues: 196
  loop : -0.94 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 139 
 HIS   0.003   0.001   HIS Z 155 
 PHE   0.018   0.001   PHE Z 335 
 TYR   0.010   0.001   TYR H 121 
 ARG   0.002   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  385)
  hydrogen bonds       : angle       4.06427 ( 1182)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       0.49821 (    8)
  covalent geometry    : bond        0.00316 ( 6207)
  covalent geometry    : angle       0.55596 ( 8421)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.723 
Fit side-chains
REVERT: Z  310 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7385 (mtt180)
REVERT: H   72 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8696 (tt0)
REVERT: H   91 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7469 (tmtt)
REVERT: H  154 PHE cc_start: 0.6507 (m-80) cc_final: 0.6069 (m-10)
REVERT: L   48 ARG cc_start: 0.7579 (mpt90) cc_final: 0.7234 (mmt180)
REVERT: L  199 LEU cc_start: 0.8048 (tt) cc_final: 0.7676 (tm)
  outliers start: 23
  outliers final: 19
  residues processed: 88
  average time/residue: 1.0695
  time to fit residues: 99.2773
Evaluate side-chains
  93 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Z residue   12 ILE
Chi-restraints excluded: chain Z residue  206 THR
Chi-restraints excluded: chain Z residue  209 ILE
Chi-restraints excluded: chain Z residue  287 VAL
Chi-restraints excluded: chain Z residue  309 ILE
Chi-restraints excluded: chain Z residue  310 ARG
Chi-restraints excluded: chain Z residue  353 VAL
Chi-restraints excluded: chain H residue   28 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue   72 GLU
Chi-restraints excluded: chain H residue   74 VAL
Chi-restraints excluded: chain H residue   90 VAL
Chi-restraints excluded: chain H residue   91 LYS
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  152 THR
Chi-restraints excluded: chain H residue  157 ILE
Chi-restraints excluded: chain H residue  182 LEU
Chi-restraints excluded: chain H residue  191 VAL
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue  118 SER
Chi-restraints excluded: chain L residue  124 GLN
Chi-restraints excluded: chain L residue  159 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0030
   chunk 63 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.3796

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

Flipped N/Q/H residues before XYZ refinement:
** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.160241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.113709 restraints weight = 6451.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.87
r_work: 0.3131 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.0884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6211  Z= 0.213
  Angle     :  0.619   7.394   8429  Z= 0.322
  Chirality :  0.045   0.222    967
  Planarity :  0.005   0.070   1045
  Dihedral  :  5.595  54.710    849
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 24.17 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    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:  1.62 (0.31), residues: 780
  helix:  2.29 (0.28), residues: 344
  sheet:  1.36 (0.37), residues: 196
  loop : -1.06 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H 139 
 HIS   0.003   0.001   HIS H 241 
 PHE   0.024   0.002   PHE Z 335 
 TYR   0.011   0.002   TYR Z 292 
 ARG   0.003   0.000   ARG H 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04913 (  385)
  hydrogen bonds       : angle       4.28352 ( 1182)
  SS BOND              : bond        0.00170 (    4)
  SS BOND              : angle       0.59279 (    8)
  covalent geometry    : bond        0.00512 ( 6207)
  covalent geometry    : angle       0.61859 ( 8421)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5608.47 seconds
wall clock time: 97 minutes 20.44 seconds (5840.44 seconds total)