Starting phenix.real_space_refine
on Sun Apr 27 12:30:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bt8_44881/04_2025/9bt8_44881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bt8_44881/04_2025/9bt8_44881.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bt8_44881/04_2025/9bt8_44881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bt8_44881/04_2025/9bt8_44881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bt8_44881/04_2025/9bt8_44881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bt8_44881/04_2025/9bt8_44881.cif"
  }
  resolution = 3.34
  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=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      16      5.16       5
     C    3611      2.51       5
     N     967      2.21       5
     O    1112      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 5712
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 439
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "H"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 908
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 2, 'TRANS': 114}
    Chain: "V"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 120
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "A"
      Number of atoms: 849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 849
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 2, 'TRANS': 108}
    Chain: "B"
      Number of atoms: 2596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2596
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 21, 'TRANS': 304}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 800
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98}
  Time building chain proxies: 4.26, per 1000 atoms: 0.75
  Number of scatterers: 5712
  At special positions: 0
  Unit cell: (60.48, 122.4, 102.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P       6     15.00
     O    1112      8.00
     N     967      7.00
     C    3611      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS B 120 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " 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: 1.31
  Conformation dependent library (CDL) restraints added in 645.6 milliseconds
  

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1356

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 14 sheets defined
      4.0% alpha, 42.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'H' and resid 31 through 33
      No H-bonds generated for 'chain 'H' and resid 31 through 33'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 4.088A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 64
      removed outlier: 3.520A  pdb=" N   LYS A  64 " --> pdb=" O   ASP A  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 61 through 64'
    Processing helix  chain 'A' and resid 86 through 90
    Processing helix  chain 'B' and resid 98 through 109
    Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 88
    Processing sheet with id=AA2, first strand: chain 'C' and resid 108 through 110
    Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 63
      removed outlier: 7.002A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   CYS H  99 " --> pdb=" O   GLN H 115 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   GLN H 115 " --> pdb=" O   CYS H  99 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   ARG H 101 " --> pdb=" O   TRP H 113 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   TRP H 113 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'V' and resid 361 through 364
    Processing sheet with id=AA6, first strand: chain 'A' and resid 4 through 7
      removed outlier: 4.215A  pdb=" N   GLN A   5 " --> pdb=" O   VAL A  23 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   VAL A  23 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER A  21 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.532A  pdb=" N   THR A 111 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   MET A  34 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   SER A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.875A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.819A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.875A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 9.819A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 188
    Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 208
      removed outlier: 3.538A  pdb=" N   VAL B 343 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 9.284A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LYS B 230 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   GLN B 237 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA B 239 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   LYS B 250 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE B 241 " --> pdb=" O   GLN B 248 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   GLN B 248 " --> pdb=" O   ILE B 241 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.612A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.907A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)

    218 hydrogen bonds defined for protein.
    573 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 1.59 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: 1829
        1.34 -     1.46: 1411
        1.46 -     1.58: 2547
        1.58 -     1.70: 22
        1.70 -     1.82: 23
  Bond restraints: 5832
  Sorted by residual:
  bond pdb=" OG1 TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.606  0.111 2.00e-02 2.50e+03 3.06e+01
  bond pdb=" OG1 TPO V 360 "
       pdb=" P   TPO V 360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" O3P TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.65e+01
  bond pdb=" O2P TPO V 359 "
       pdb=" P   TPO V 359 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.63e+01
  bond pdb=" O2P TPO V 360 "
       pdb=" P   TPO V 360 "
    ideal  model  delta    sigma   weight residual
    1.528  1.608 -0.080 2.00e-02 2.50e+03 1.61e+01
  ... (remaining 5827 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 7839
        2.53 -     5.06: 68
        5.06 -     7.59: 8
        7.59 -    10.12: 4
       10.12 -    12.65: 2
  Bond angle restraints: 7921
  Sorted by residual:
  angle pdb=" CB  TPO V 359 "
        pdb=" OG1 TPO V 359 "
        pdb=" P   TPO V 359 "
      ideal   model   delta    sigma   weight residual
     119.31  106.66   12.65 3.00e+00 1.11e-01 1.78e+01
  angle pdb=" CB  TPO V 360 "
        pdb=" OG1 TPO V 360 "
        pdb=" P   TPO V 360 "
      ideal   model   delta    sigma   weight residual
     119.31  107.34   11.97 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" OG1 TPO V 360 "
        pdb=" P   TPO V 360 "
        pdb=" O1P TPO V 360 "
      ideal   model   delta    sigma   weight residual
     100.43  109.72   -9.29 3.00e+00 1.11e-01 9.59e+00
  angle pdb=" CA  TYR B  63 "
        pdb=" C   TYR B  63 "
        pdb=" O   TYR B  63 "
      ideal   model   delta    sigma   weight residual
     119.08  122.16   -3.08 1.03e+00 9.43e-01 8.96e+00
  angle pdb=" OG1 TPO V 359 "
        pdb=" P   TPO V 359 "
        pdb=" O1P TPO V 359 "
      ideal   model   delta    sigma   weight residual
     100.43  109.32   -8.89 3.00e+00 1.11e-01 8.79e+00
  ... (remaining 7916 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3016
       17.83 -    35.66: 366
       35.66 -    53.49: 78
       53.49 -    71.32: 16
       71.32 -    89.15: 6
  Dihedral angle restraints: 3482
    sinusoidal: 1367
      harmonic: 2115
  Sorted by residual:
  dihedral pdb=" CA  VAL C 111 "
           pdb=" C   VAL C 111 "
           pdb=" N   ASN C 112 "
           pdb=" CA  ASN C 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.42  -21.58     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CB  CYS C  95 "
           pdb=" SG  CYS C  95 "
           pdb=" SG  CYS B 120 "
           pdb=" CB  CYS B 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -55.95  -30.05     1      1.00e+01 1.00e-02 1.29e+01
  dihedral pdb=" CA  LEU B  79 "
           pdb=" C   LEU B  79 "
           pdb=" N   PHE B  80 "
           pdb=" CA  PHE B  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.58  -17.42     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 3479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 516
       0.029 -    0.058: 243
       0.058 -    0.087: 67
       0.087 -    0.116: 45
       0.116 -    0.144: 22
  Chirality restraints: 893
  Sorted by residual:
  chirality pdb=" CB  VAL C 111 "
            pdb=" CA  VAL C 111 "
            pdb=" CG1 VAL C 111 "
            pdb=" CG2 VAL C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  ILE L  49 "
            pdb=" N   ILE L  49 "
            pdb=" C   ILE L  49 "
            pdb=" CB  ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  ASP H 111 "
            pdb=" N   ASP H 111 "
            pdb=" C   ASP H 111 "
            pdb=" CB  ASP H 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 890 not shown)

  Planarity restraints: 1000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  16 "    0.044 5.00e-02 4.00e+02   6.62e-02 7.01e+00
        pdb=" N   PRO H  17 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO H  17 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H  17 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  44 "    0.040 5.00e-02 4.00e+02   6.04e-02 5.84e+00
        pdb=" N   PRO B  45 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B  45 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  45 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 107 "    0.006 2.00e-02 2.50e+03   1.22e-02 2.99e+00
        pdb=" CG  TYR H 107 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 107 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 107 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 107 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 107 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 107 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H 107 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 997 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1411
        2.79 -     3.32: 4562
        3.32 -     3.85: 8562
        3.85 -     4.37: 9874
        4.37 -     4.90: 18352
  Nonbonded interactions: 42761
  Sorted by model distance:
  nonbonded pdb=" OG  SER H  36 "
            pdb=" O   ILE H  54 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OG  SER B  13 "
            pdb=" OD1 ASN B  15 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   ALA B 263 "
            pdb=" OG  SER B 266 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   SER H  66 "
            pdb=" NH2 ARG H  70 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" ND2 ASN C 135 "
            pdb=" O   ARG B  76 "
     model   vdw
     2.328 3.120
  ... (remaining 42756 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.770
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.111   5835  Z= 0.227
  Angle     :  0.645  12.650   7927  Z= 0.318
  Chirality :  0.043   0.144    893
  Planarity :  0.005   0.066   1000
  Dihedral  : 16.428  89.153   2117
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 25.44 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.41 (0.32), residues: 700
  helix:  1.19 (1.59), residues: 11
  sheet:  0.48 (0.32), residues: 294
  loop : -0.91 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  50 
 HIS   0.005   0.001   HIS C 122 
 PHE   0.012   0.001   PHE A  29 
 TYR   0.029   0.002   TYR H 107 
 ARG   0.007   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25585 (  207)
  hydrogen bonds       : angle      10.00188 (  573)
  SS BOND              : bond        0.00043 (    3)
  SS BOND              : angle       0.38650 (    6)
  covalent geometry    : bond        0.00501 ( 5832)
  covalent geometry    : angle       0.64482 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.658 
Fit side-chains
REVERT: H  107 TYR cc_start: 0.7548 (t80) cc_final: 0.7344 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1999
  time to fit residues: 24.0927
Evaluate side-chains
  91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 29 optimal weight:    0.2980
   chunk 18 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 54 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
C 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.117674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.097814 restraints weight = 7918.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.27
r_work: 0.3167 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5835  Z= 0.106
  Angle     :  0.531   8.478   7927  Z= 0.277
  Chirality :  0.043   0.161    893
  Planarity :  0.004   0.038   1000
  Dihedral  :  4.284  21.438    810
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 24.80 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.18 (0.32), residues: 700
  helix:  1.83 (1.76), residues: 11
  sheet:  0.81 (0.33), residues: 285
  loop : -0.89 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  50 
 HIS   0.004   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.013   0.001   TYR C  90 
 ARG   0.002   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  207)
  hydrogen bonds       : angle       6.35174 (  573)
  SS BOND              : bond        0.00162 (    3)
  SS BOND              : angle       0.62996 (    6)
  covalent geometry    : bond        0.00237 ( 5832)
  covalent geometry    : angle       0.53133 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.805 
Fit side-chains
REVERT: B  110 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8092 (tm-30)
REVERT: B  232 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7880 (mttp)
REVERT: L   80 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8059 (mt0)
  outliers start: 17
  outliers final: 12
  residues processed: 104
  average time/residue: 0.2474
  time to fit residues: 33.1415
Evaluate side-chains
  96 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.117486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.096513 restraints weight = 7950.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 2.46
r_work: 0.2870 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5835  Z= 0.145
  Angle     :  0.540   8.666   7927  Z= 0.281
  Chirality :  0.042   0.136    893
  Planarity :  0.004   0.035   1000
  Dihedral  :  4.341  22.105    810
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.80 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.22 (0.32), residues: 700
  helix:  1.52 (1.69), residues: 11
  sheet:  0.77 (0.32), residues: 296
  loop : -0.95 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.009   0.001   HIS C 122 
 PHE   0.012   0.001   PHE A  29 
 TYR   0.017   0.001   TYR C 136 
 ARG   0.003   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03571 (  207)
  hydrogen bonds       : angle       5.85938 (  573)
  SS BOND              : bond        0.00081 (    3)
  SS BOND              : angle       1.09052 (    6)
  covalent geometry    : bond        0.00346 ( 5832)
  covalent geometry    : angle       0.53896 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.626 
Fit side-chains
REVERT: H  107 TYR cc_start: 0.7203 (t80) cc_final: 0.6761 (t80)
REVERT: B  110 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7879 (tm-30)
REVERT: B  232 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7736 (mttt)
REVERT: B  244 PHE cc_start: 0.8823 (m-10) cc_final: 0.8519 (m-10)
REVERT: L   80 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7852 (mt0)
  outliers start: 23
  outliers final: 16
  residues processed: 109
  average time/residue: 0.1855
  time to fit residues: 26.0782
Evaluate side-chains
  103 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 56 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 52 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS
B 280 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.118845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.097777 restraints weight = 8055.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.50
r_work: 0.2875 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5835  Z= 0.122
  Angle     :  0.514   8.551   7927  Z= 0.266
  Chirality :  0.042   0.141    893
  Planarity :  0.004   0.043   1000
  Dihedral  :  4.265  25.649    810
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.80 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.18 (0.32), residues: 700
  helix:  1.29 (1.69), residues: 11
  sheet:  0.88 (0.32), residues: 296
  loop : -0.99 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  50 
 HIS   0.008   0.001   HIS C 122 
 PHE   0.012   0.001   PHE A  29 
 TYR   0.015   0.001   TYR C 136 
 ARG   0.008   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03112 (  207)
  hydrogen bonds       : angle       5.49981 (  573)
  SS BOND              : bond        0.00103 (    3)
  SS BOND              : angle       0.77969 (    6)
  covalent geometry    : bond        0.00290 ( 5832)
  covalent geometry    : angle       0.51423 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 85
  time to evaluate  : 0.669 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8667 (t80) cc_final: 0.8358 (t80)
REVERT: H  107 TYR cc_start: 0.7340 (t80) cc_final: 0.6832 (t80)
REVERT: B  110 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7836 (tm-30)
REVERT: B  232 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7680 (mttp)
REVERT: B  244 PHE cc_start: 0.8809 (m-10) cc_final: 0.8542 (m-10)
REVERT: L   80 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7790 (mt0)
  outliers start: 28
  outliers final: 21
  residues processed: 108
  average time/residue: 0.2230
  time to fit residues: 30.9386
Evaluate side-chains
  105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 50 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0040
   overall best weight:    1.0596

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

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.115738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.094846 restraints weight = 7936.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.43
r_work: 0.2887 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5835  Z= 0.220
  Angle     :  0.614   8.974   7927  Z= 0.318
  Chirality :  0.045   0.137    893
  Planarity :  0.004   0.044   1000
  Dihedral  :  4.712  23.894    810
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 24.64 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.36 (0.32), residues: 700
  helix:  1.18 (1.70), residues: 11
  sheet:  0.75 (0.32), residues: 296
  loop : -1.11 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.011   0.002   HIS C 122 
 PHE   0.016   0.002   PHE H 105 
 TYR   0.024   0.002   TYR C 136 
 ARG   0.009   0.001   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03641 (  207)
  hydrogen bonds       : angle       5.67178 (  573)
  SS BOND              : bond        0.00059 (    3)
  SS BOND              : angle       0.62866 (    6)
  covalent geometry    : bond        0.00539 ( 5832)
  covalent geometry    : angle       0.61442 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 87
  time to evaluate  : 0.634 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8840 (t80) cc_final: 0.8624 (t80)
REVERT: B  110 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8015 (tm-30)
REVERT: B  232 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7821 (mttp)
REVERT: B  244 PHE cc_start: 0.8852 (m-10) cc_final: 0.8614 (m-10)
REVERT: B  255 MET cc_start: 0.8652 (tpt) cc_final: 0.8428 (tpt)
REVERT: L   80 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8132 (mt0)
  outliers start: 33
  outliers final: 25
  residues processed: 114
  average time/residue: 0.1904
  time to fit residues: 27.9255
Evaluate side-chains
  108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.115152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.094465 restraints weight = 7955.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.38
r_work: 0.2928 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5835  Z= 0.165
  Angle     :  0.558   8.682   7927  Z= 0.288
  Chirality :  0.043   0.138    893
  Planarity :  0.004   0.049   1000
  Dihedral  :  4.610  27.569    810
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 26.09 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.35 (0.32), residues: 700
  helix:  1.20 (1.71), residues: 11
  sheet:  0.78 (0.32), residues: 296
  loop : -1.13 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.007   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.019   0.001   TYR C 136 
 ARG   0.010   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  207)
  hydrogen bonds       : angle       5.52819 (  573)
  SS BOND              : bond        0.00083 (    3)
  SS BOND              : angle       0.58668 (    6)
  covalent geometry    : bond        0.00401 ( 5832)
  covalent geometry    : angle       0.55777 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 86
  time to evaluate  : 0.718 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8846 (t80) cc_final: 0.8635 (t80)
REVERT: H   92 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8212 (pt0)
REVERT: H  107 TYR cc_start: 0.7487 (t80) cc_final: 0.7176 (t80)
REVERT: A   69 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8743 (tt)
REVERT: B  110 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: B  232 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7894 (mttp)
REVERT: B  244 PHE cc_start: 0.8827 (m-10) cc_final: 0.8574 (m-10)
REVERT: L   80 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7990 (mt0)
  outliers start: 31
  outliers final: 24
  residues processed: 112
  average time/residue: 0.1941
  time to fit residues: 27.8792
Evaluate side-chains
  110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 19 optimal weight:    0.0010
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 52 optimal weight:    0.2980
   chunk 10 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0970
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.3784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.117656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.097058 restraints weight = 7872.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.35
r_work: 0.3056 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5835  Z= 0.107
  Angle     :  0.519   8.480   7927  Z= 0.265
  Chirality :  0.042   0.139    893
  Planarity :  0.004   0.051   1000
  Dihedral  :  4.386  33.771    810
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 27.54 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.27 (0.32), residues: 700
  helix:  1.25 (1.71), residues: 11
  sheet:  0.86 (0.32), residues: 296
  loop : -1.09 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  50 
 HIS   0.006   0.001   HIS C 122 
 PHE   0.012   0.001   PHE A  29 
 TYR   0.014   0.001   TYR C 136 
 ARG   0.011   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02862 (  207)
  hydrogen bonds       : angle       5.28493 (  573)
  SS BOND              : bond        0.00090 (    3)
  SS BOND              : angle       1.53253 (    6)
  covalent geometry    : bond        0.00253 ( 5832)
  covalent geometry    : angle       0.51749 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.903 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8829 (t80) cc_final: 0.8570 (t80)
REVERT: H  107 TYR cc_start: 0.7437 (t80) cc_final: 0.6974 (t80)
REVERT: B  110 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8099 (tm-30)
REVERT: B  232 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7827 (mttp)
REVERT: B  244 PHE cc_start: 0.8866 (m-10) cc_final: 0.8596 (m-10)
REVERT: L   80 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7817 (mt0)
  outliers start: 27
  outliers final: 20
  residues processed: 107
  average time/residue: 0.2311
  time to fit residues: 31.6169
Evaluate side-chains
  106 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 41 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS
A  73 ASN
B 280 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.116261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.096324 restraints weight = 7918.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 2.29
r_work: 0.2921 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5835  Z= 0.139
  Angle     :  0.542   8.635   7927  Z= 0.279
  Chirality :  0.042   0.139    893
  Planarity :  0.004   0.033   1000
  Dihedral  :  4.492  36.734    810
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 27.05 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.32 (0.31), residues: 700
  helix:  1.34 (1.73), residues: 11
  sheet:  0.85 (0.32), residues: 296
  loop : -1.15 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  50 
 HIS   0.010   0.001   HIS C 122 
 PHE   0.014   0.001   PHE A  29 
 TYR   0.016   0.001   TYR C 136 
 ARG   0.006   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03024 (  207)
  hydrogen bonds       : angle       5.30450 (  573)
  SS BOND              : bond        0.00073 (    3)
  SS BOND              : angle       1.42020 (    6)
  covalent geometry    : bond        0.00338 ( 5832)
  covalent geometry    : angle       0.54047 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.703 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8843 (t80) cc_final: 0.8591 (t80)
REVERT: H  107 TYR cc_start: 0.7358 (t80) cc_final: 0.6911 (t80)
REVERT: A   43 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8455 (mtpp)
REVERT: A   69 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8763 (tt)
REVERT: B  110 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: B  232 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7897 (mttp)
REVERT: L   80 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7958 (mt0)
  outliers start: 30
  outliers final: 24
  residues processed: 107
  average time/residue: 0.1929
  time to fit residues: 26.6138
Evaluate side-chains
  109 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.117469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.096836 restraints weight = 7844.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.36
r_work: 0.2882 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5835  Z= 0.125
  Angle     :  0.525   8.582   7927  Z= 0.269
  Chirality :  0.042   0.140    893
  Planarity :  0.004   0.033   1000
  Dihedral  :  4.533  42.564    810
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 27.05 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.31 (0.31), residues: 700
  helix:  1.33 (1.73), residues: 11
  sheet:  0.82 (0.32), residues: 298
  loop : -1.13 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.010   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.016   0.001   TYR C 136 
 ARG   0.006   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02918 (  207)
  hydrogen bonds       : angle       5.24093 (  573)
  SS BOND              : bond        0.00086 (    3)
  SS BOND              : angle       1.23245 (    6)
  covalent geometry    : bond        0.00302 ( 5832)
  covalent geometry    : angle       0.52382 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.721 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8841 (t80) cc_final: 0.8597 (t80)
REVERT: H  107 TYR cc_start: 0.7492 (t80) cc_final: 0.6949 (t80)
REVERT: A   43 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8415 (mtpp)
REVERT: B  110 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8058 (tm-30)
REVERT: B  232 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7822 (mttp)
REVERT: L   80 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7904 (mt0)
  outliers start: 29
  outliers final: 25
  residues processed: 107
  average time/residue: 0.2299
  time to fit residues: 31.9769
Evaluate side-chains
  108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0870
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.116399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.096223 restraints weight = 7979.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.34
r_work: 0.3124 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5835  Z= 0.136
  Angle     :  0.549   8.643   7927  Z= 0.281
  Chirality :  0.043   0.204    893
  Planarity :  0.004   0.033   1000
  Dihedral  :  4.631  46.312    810
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 27.38 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.34 (0.31), residues: 700
  helix:  1.32 (1.73), residues: 11
  sheet:  0.82 (0.32), residues: 298
  loop : -1.16 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  50 
 HIS   0.011   0.001   HIS C 122 
 PHE   0.013   0.001   PHE A  29 
 TYR   0.016   0.001   TYR C 136 
 ARG   0.005   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02950 (  207)
  hydrogen bonds       : angle       5.25798 (  573)
  SS BOND              : bond        0.00083 (    3)
  SS BOND              : angle       1.17108 (    6)
  covalent geometry    : bond        0.00331 ( 5832)
  covalent geometry    : angle       0.54812 ( 7921)

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

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

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1400 Ramachandran restraints generated.
    700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.623 
Fit side-chains
REVERT: C   92 TYR cc_start: 0.8853 (t80) cc_final: 0.8624 (t80)
REVERT: H  107 TYR cc_start: 0.7524 (t80) cc_final: 0.7031 (t80)
REVERT: A   43 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8457 (mtpp)
REVERT: A   69 ILE cc_start: 0.8787 (tt) cc_final: 0.8536 (tt)
REVERT: B  110 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8137 (tm-30)
REVERT: B  232 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7890 (mttp)
REVERT: L   80 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7931 (mt0)
  outliers start: 27
  outliers final: 26
  residues processed: 106
  average time/residue: 0.1813
  time to fit residues: 25.0934
Evaluate side-chains
  110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue   76 ASN
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   80 GLN
Chi-restraints excluded: chain L residue   95 VAL
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.117307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.096009 restraints weight = 8016.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 2.49
r_work: 0.2853 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2708 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5835  Z= 0.155
  Angle     :  0.558   8.684   7927  Z= 0.286
  Chirality :  0.043   0.172    893
  Planarity :  0.004   0.060   1000
  Dihedral  :  4.851  50.791    810
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 27.05 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.37 (0.31), residues: 700
  helix:  1.32 (1.73), residues: 11
  sheet:  0.79 (0.32), residues: 298
  loop : -1.18 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  36 
 HIS   0.011   0.001   HIS C 122 
 PHE   0.014   0.001   PHE A  29 
 TYR   0.018   0.001   TYR C 136 
 ARG   0.014   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  207)
  hydrogen bonds       : angle       5.31487 (  573)
  SS BOND              : bond        0.00066 (    3)
  SS BOND              : angle       1.15152 (    6)
  covalent geometry    : bond        0.00377 ( 5832)
  covalent geometry    : angle       0.55764 ( 7921)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3441.34 seconds
wall clock time: 60 minutes 47.06 seconds (3647.06 seconds total)