Starting phenix.real_space_refine
on Thu Jun  5 00:51:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5o_37299/06_2025/8w5o_37299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5o_37299/06_2025/8w5o_37299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5o_37299/06_2025/8w5o_37299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5o_37299/06_2025/8w5o_37299.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5o_37299/06_2025/8w5o_37299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5o_37299/06_2025/8w5o_37299.cif"
  }
  resolution = 3.6
  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=   0.007 sd=   0.080
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2924      2.51       5
     N     825      2.21       5
     O     934      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4697
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 949
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "L"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 800
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 6, 'TRANS': 98}
    Chain: "b"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 993
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 980
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 980
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 8, 'TRANS': 122}
    Chain: "A"
      Number of atoms: 975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 975
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 8, 'TRANS': 121}
  Time building chain proxies: 3.67, per 1000 atoms: 0.78
  Number of scatterers: 4697
  At special positions: 0
  Unit cell: (83.16, 112.2, 99, 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      14     16.00
     O     934      8.00
     N     825      7.00
     C    2924      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 612.5 milliseconds
  

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1150

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      13.9% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'H' and resid 31 through 35
      removed outlier: 3.553A  pdb=" N   TYR H  35 " --> pdb=" O   PHE H  32 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 101 through 117
    Processing helix  chain 'b' and resid 118 through 126
    Processing helix  chain 'B' and resid 101 through 117
    Processing helix  chain 'B' and resid 118 through 126
    Processing helix  chain 'A' and resid 101 through 118
      removed outlier: 3.518A  pdb=" N   VAL A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA A 117 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   SER A 118 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 128
    Processing sheet with id=AA1, first strand: chain 'H' and resid 21 through 25
      removed outlier: 3.709A  pdb=" N   CYS H  25 " --> pdb=" O   LEU H  82 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU H  82 " --> pdb=" O   CYS H  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 62
      removed outlier: 6.714A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 8 through 9
      removed outlier: 3.808A  pdb=" N   LEU L  76 " --> pdb=" O   PHE L  24 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 56 through 57
      removed outlier: 6.919A  pdb=" N   TRP L  38 " --> pdb=" O   LEU L  50 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   LYS L  52 " --> pdb=" O   ILE L  36 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   ILE L  36 " --> pdb=" O   LYS L  52 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLN L  92 " --> pdb=" O   HIS L  37 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'b' and resid 6 through 9
      removed outlier: 6.036A  pdb=" N   SER b  36 " --> pdb=" O   PRO b  23 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLY b  25 " --> pdb=" O   SER b  34 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   SER b  34 " --> pdb=" O   GLY b  25 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 9
      removed outlier: 6.036A  pdb=" N   SER B  36 " --> pdb=" O   PRO B  23 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLY B  25 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   SER B  34 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 74
      removed outlier: 7.075A  pdb=" N   THR B  72 " --> pdb=" O   THR B  85 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   THR B  85 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER B  83 " --> pdb=" O   CYS B  74 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 6 through 8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 34 through 36

    143 hydrogen bonds defined for protein.
    375 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: 1.05

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 789
        1.29 -     1.42: 1174
        1.42 -     1.55: 2790
        1.55 -     1.68: 7
        1.68 -     1.81: 18
  Bond restraints: 4778
  Sorted by residual:
  bond pdb=" C   VAL A  52 "
       pdb=" O   VAL A  52 "
    ideal  model  delta    sigma   weight residual
    1.237  1.160  0.077 1.10e-02 8.26e+03 4.87e+01
  bond pdb=" C   GLN A  69 "
       pdb=" O   GLN A  69 "
    ideal  model  delta    sigma   weight residual
    1.235  1.159  0.076 1.13e-02 7.83e+03 4.58e+01
  bond pdb=" C   VAL A  64 "
       pdb=" O   VAL A  64 "
    ideal  model  delta    sigma   weight residual
    1.238  1.169  0.069 1.06e-02 8.90e+03 4.18e+01
  bond pdb=" C   GLN L  93 "
       pdb=" O   GLN L  93 "
    ideal  model  delta    sigma   weight residual
    1.235  1.157  0.078 1.22e-02 6.72e+03 4.09e+01
  bond pdb=" C   GLN A  65 "
       pdb=" O   GLN A  65 "
    ideal  model  delta    sigma   weight residual
    1.235  1.157  0.077 1.22e-02 6.72e+03 4.02e+01
  ... (remaining 4773 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.61: 6468
        8.61 -    17.21: 28
       17.21 -    25.82: 1
       25.82 -    34.43: 2
       34.43 -    43.03: 1
  Bond angle restraints: 6500
  Sorted by residual:
  angle pdb=" C   ASP b  81 "
        pdb=" N   PRO b  82 "
        pdb=" CA  PRO b  82 "
      ideal   model   delta    sigma   weight residual
     119.84  148.45  -28.61 1.25e+00 6.40e-01 5.24e+02
  angle pdb=" C   ASP b  81 "
        pdb=" N   PRO b  82 "
        pdb=" CD  PRO b  82 "
      ideal   model   delta    sigma   weight residual
     125.00   81.97   43.03 4.10e+00 5.95e-02 1.10e+02
  angle pdb=" C   ASN A  70 "
        pdb=" N   PRO A  71 "
        pdb=" CA  PRO A  71 "
      ideal   model   delta    sigma   weight residual
     119.84  131.98  -12.14 1.25e+00 6.40e-01 9.44e+01
  angle pdb=" N   ALA A  43 "
        pdb=" CA  ALA A  43 "
        pdb=" C   ALA A  43 "
      ideal   model   delta    sigma   weight residual
     112.88  125.25  -12.37 1.29e+00 6.01e-01 9.20e+01
  angle pdb=" N   LYS A  60 "
        pdb=" CA  LYS A  60 "
        pdb=" C   LYS A  60 "
      ideal   model   delta    sigma   weight residual
     111.74  123.62  -11.88 1.35e+00 5.49e-01 7.74e+01
  ... (remaining 6495 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 2617
       17.07 -    34.13: 183
       34.13 -    51.20: 79
       51.20 -    68.26: 18
       68.26 -    85.32: 4
  Dihedral angle restraints: 2901
    sinusoidal: 1111
      harmonic: 1790
  Sorted by residual:
  dihedral pdb=" CA  ASP H 112 "
           pdb=" C   ASP H 112 "
           pdb=" N   TYR H 113 "
           pdb=" CA  TYR H 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.06  -36.94     0      5.00e+00 4.00e-02 5.46e+01
  dihedral pdb=" N   TRP L  97 "
           pdb=" C   TRP L  97 "
           pdb=" CA  TRP L  97 "
           pdb=" CB  TRP L  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.62  -16.82     0      2.50e+00 1.60e-01 4.52e+01
  dihedral pdb=" C   TRP L  97 "
           pdb=" N   TRP L  97 "
           pdb=" CA  TRP L  97 "
           pdb=" CB  TRP L  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.70   15.10     0      2.50e+00 1.60e-01 3.65e+01
  ... (remaining 2898 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.172: 699
       0.172 -    0.345: 45
       0.345 -    0.517: 11
       0.517 -    0.689: 1
       0.689 -    0.861: 2
  Chirality restraints: 758
  Sorted by residual:
  chirality pdb=" CA  TRP L  97 "
            pdb=" N   TRP L  97 "
            pdb=" C   TRP L  97 "
            pdb=" CB  TRP L  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.65    0.86 2.00e-01 2.50e+01 1.86e+01
  chirality pdb=" CA  GLU H  92 "
            pdb=" N   GLU H  92 "
            pdb=" C   GLU H  92 "
            pdb=" CB  GLU H  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.36e+01
  chirality pdb=" CA  ASN b  77 "
            pdb=" N   ASN b  77 "
            pdb=" C   ASN b  77 "
            pdb=" CB  ASN b  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.88e+00
  ... (remaining 755 not shown)

  Planarity restraints: 848
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  81 "    0.120 5.00e-02 4.00e+02   1.80e-01 5.16e+01
        pdb=" N   PRO B  82 "   -0.310 5.00e-02 4.00e+02
        pdb=" CA  PRO B  82 "    0.116 5.00e-02 4.00e+02
        pdb=" CD  PRO B  82 "    0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  81 "   -0.106 5.00e-02 4.00e+02   1.60e-01 4.08e+01
        pdb=" N   PRO A  82 "    0.276 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "   -0.093 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "   -0.078 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP b  81 "    0.108 5.00e-02 4.00e+02   1.40e-01 3.16e+01
        pdb=" N   PRO b  82 "   -0.236 5.00e-02 4.00e+02
        pdb=" CA  PRO b  82 "    0.104 5.00e-02 4.00e+02
        pdb=" CD  PRO b  82 "    0.025 5.00e-02 4.00e+02
  ... (remaining 845 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 6
        1.93 -     2.67: 385
        2.67 -     3.42: 6307
        3.42 -     4.16: 10163
        4.16 -     4.90: 17330
  Nonbonded interactions: 34191
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 104 "
            pdb=" NH2 ARG A  86 "
     model   vdw
     1.189 3.120
  nonbonded pdb=" CZ2 TRP L  97 "
            pdb=" OG  SER b  79 "
     model   vdw
     1.366 3.340
  nonbonded pdb=" OD2 ASP B 126 "
            pdb=" NH2 ARG A 109 "
     model   vdw
     1.531 3.120
  nonbonded pdb=" CD  GLU B 104 "
            pdb=" NH2 ARG A  86 "
     model   vdw
     1.697 3.350
  nonbonded pdb=" CE2 TRP L  97 "
            pdb=" OG  SER b  79 "
     model   vdw
     1.865 3.260
  ... (remaining 34186 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 2 through 131)
  selection = (chain 'b' and resid 2 through 131)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.850
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
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      :  0.016   0.094   4778  Z= 1.069
  Angle     :  1.884  43.032   6500  Z= 1.121
  Chirality :  0.110   0.861    758
  Planarity :  0.014   0.180    848
  Dihedral  : 15.015  85.325   1751
  Min Nonbonded Distance : 1.189

Molprobity Statistics.
  All-atom Clashscore : 24.97
  Ramachandran Plot:
    Outliers :  1.64 %
    Allowed  :  6.72 %
    Favored  : 91.64 %
  Rotamer:
    Outliers : 11.15 %
    Allowed  : 11.35 %
    Favored  : 77.50 %
  Cbeta Deviations :  2.96 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -3.64 (0.30), residues: 610
  helix: -0.90 (0.54), residues: 70
  sheet: -2.45 (0.28), residues: 263
  loop : -2.67 (0.32), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.005   TRP L  97 
 HIS   0.003   0.001   HIS L  37 
 PHE   0.023   0.004   PHE L  74 
 TYR   0.040   0.003   TYR H 113 
 ARG   0.007   0.001   ARG H  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22654 (  143)
  hydrogen bonds       : angle       9.68809 (  375)
  covalent geometry    : bond        0.01570 ( 4778)
  covalent geometry    : angle       1.88380 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 205
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7894 (ptt90) cc_final: 0.5520 (mtt-85)
REVERT: H  117 TYR cc_start: 0.8467 (m-80) cc_final: 0.8210 (m-10)
REVERT: L   50 LEU cc_start: 0.9148 (mt) cc_final: 0.8788 (mp)
REVERT: L   70 SER cc_start: 0.8934 (t) cc_final: 0.8552 (p)
REVERT: L   92 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8453 (tm-30)
REVERT: L  106 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8687 (mmmm)
REVERT: b   37 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8620 (tm-30)
REVERT: b   46 LYS cc_start: 0.8428 (mttp) cc_final: 0.8095 (mttm)
REVERT: b   63 LYS cc_start: 0.8505 (tmtt) cc_final: 0.8014 (ttmt)
REVERT: b  123 ASP cc_start: 0.8592 (t0) cc_final: 0.8302 (t0)
REVERT: b  129 ASN cc_start: 0.8875 (m110) cc_final: 0.8666 (m-40)
REVERT: B   16 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8282 (mmtm)
REVERT: B   24 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7649 (tpt170)
REVERT: B   46 LYS cc_start: 0.8387 (mttp) cc_final: 0.8166 (mttm)
REVERT: B   98 GLN cc_start: 0.8692 (tt0) cc_final: 0.8363 (tp40)
REVERT: B  129 ASN cc_start: 0.9337 (m110) cc_final: 0.8925 (m110)
REVERT: A   22 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8045 (p0)
REVERT: A   30 ASN cc_start: 0.8035 (p0) cc_final: 0.7343 (p0)
REVERT: A   32 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8279 (m)
REVERT: A   34 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8665 (t)
REVERT: A   53 SER cc_start: 0.9358 (m) cc_final: 0.8978 (p)
REVERT: A   54 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8148 (mt0)
REVERT: A   57 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7070 (ptt180)
REVERT: A   63 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8893 (tttp)
REVERT: A   65 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7947 (tm-30)
REVERT: A   68 ILE cc_start: 0.8973 (mt) cc_final: 0.8752 (mt)
REVERT: A   72 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (p)
REVERT: A   98 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8568 (pp30)
REVERT: A  103 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8651 (mt-10)
  outliers start: 58
  outliers final: 30
  residues processed: 246
  average time/residue: 0.2247
  time to fit residues: 65.4277
Evaluate side-chains
  182 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 143
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   90 LYS
Chi-restraints excluded: chain H residue   92 GLU
Chi-restraints excluded: chain L residue   95 TYR
Chi-restraints excluded: chain L residue  107 LEU
Chi-restraints excluded: chain b residue   80 CYS
Chi-restraints excluded: chain B residue   74 CYS
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue    7 THR
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 LYS
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue   56 SER
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue   65 GLN
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   74 CYS
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue   89 TYR
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  128 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  10 ASN
B 129 ASN
A  70 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.089673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.070328 restraints weight = 10902.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.073185 restraints weight = 5113.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.075151 restraints weight = 3223.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.099   4778  Z= 0.284
  Angle     :  0.881  16.457   6500  Z= 0.447
  Chirality :  0.053   0.260    758
  Planarity :  0.011   0.174    848
  Dihedral  : 12.547  98.639    752
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  7.54 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  9.04 %
    Allowed  : 20.19 %
    Favored  : 70.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -3.10 (0.31), residues: 610
  helix: -0.32 (0.58), residues: 75
  sheet: -2.12 (0.32), residues: 233
  loop : -2.42 (0.32), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP L  97 
 HIS   0.004   0.001   HIS L  37 
 PHE   0.018   0.003   PHE b 107 
 TYR   0.028   0.002   TYR H 113 
 ARG   0.008   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04892 (  143)
  hydrogen bonds       : angle       6.69309 (  375)
  covalent geometry    : bond        0.00655 ( 4778)
  covalent geometry    : angle       0.88073 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 158
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7476 (ptt90) cc_final: 0.4945 (mtt-85)
REVERT: H   92 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8706 (mm-30)
REVERT: H  101 ARG cc_start: 0.7654 (tpm170) cc_final: 0.7362 (mmm-85)
REVERT: H  116 ASP cc_start: 0.8750 (p0) cc_final: 0.8128 (p0)
REVERT: L   20 GLU cc_start: 0.8173 (mp0) cc_final: 0.7810 (pm20)
REVERT: L   52 LYS cc_start: 0.8498 (tttt) cc_final: 0.8283 (ptmt)
REVERT: L   92 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: L   93 GLN cc_start: 0.8921 (pp30) cc_final: 0.7727 (pp30)
REVERT: L  106 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8521 (mmmm)
REVERT: b   37 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: b   87 GLN cc_start: 0.8617 (mm110) cc_final: 0.8357 (mm110)
REVERT: b  123 ASP cc_start: 0.8774 (t0) cc_final: 0.8482 (t0)
REVERT: b  128 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8626 (mm)
REVERT: b  129 ASN cc_start: 0.8641 (m110) cc_final: 0.8238 (m-40)
REVERT: B   24 ARG cc_start: 0.8733 (mtp-110) cc_final: 0.7730 (tpt170)
REVERT: B   69 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6910 (tm-30)
REVERT: B  104 GLU cc_start: 0.8371 (pt0) cc_final: 0.8080 (pt0)
REVERT: B  127 GLN cc_start: 0.8394 (mp10) cc_final: 0.7766 (mp10)
REVERT: A   34 SER cc_start: 0.8532 (m) cc_final: 0.8298 (t)
REVERT: A   37 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8709 (tm-30)
REVERT: A   54 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7766 (mt0)
REVERT: A   57 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6961 (ptt180)
REVERT: A   69 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6952 (tm-30)
REVERT: A   77 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7958 (m-40)
REVERT: A  102 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7644 (t70)
REVERT: A  103 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8831 (mt-10)
  outliers start: 47
  outliers final: 28
  residues processed: 192
  average time/residue: 0.1968
  time to fit residues: 45.8138
Evaluate side-chains
  176 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   30 PHE
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  115 MET
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   95 TYR
Chi-restraints excluded: chain L residue  107 LEU
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue   80 CYS
Chi-restraints excluded: chain b residue   93 THR
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain b residue  128 LEU
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue   74 CYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue   57 ARG
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   74 CYS
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  122 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 55 optimal weight:   30.0000
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** L   9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  70 ASN
** B  69 GLN ** 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 = 0.3356 r_free = 0.3356 target = 0.090498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.070547 restraints weight = 10815.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.073190 restraints weight = 5688.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.074987 restraints weight = 3839.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.4603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.083   4778  Z= 0.301
  Angle     :  0.854  13.651   6500  Z= 0.434
  Chirality :  0.052   0.249    758
  Planarity :  0.010   0.161    848
  Dihedral  : 10.738  84.029    715
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.18 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  8.85 %
    Allowed  : 21.35 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -2.94 (0.32), residues: 610
  helix: -0.00 (0.57), residues: 75
  sheet: -2.02 (0.32), residues: 234
  loop : -2.37 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP L  97 
 HIS   0.001   0.000   HIS L  37 
 PHE   0.017   0.003   PHE L  74 
 TYR   0.028   0.002   TYR H 113 
 ARG   0.005   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04442 (  143)
  hydrogen bonds       : angle       6.33297 (  375)
  covalent geometry    : bond        0.00682 ( 4778)
  covalent geometry    : angle       0.85374 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 144
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7934 (ptt90) cc_final: 0.5224 (mtt-85)
REVERT: H   92 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8426 (mm-30)
REVERT: L   20 GLU cc_start: 0.8145 (mp0) cc_final: 0.7945 (pm20)
REVERT: L   41 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8668 (tp40)
REVERT: L   92 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: L  106 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8644 (mmmm)
REVERT: b   14 ASP cc_start: 0.8290 (p0) cc_final: 0.7865 (p0)
REVERT: b   37 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8567 (tm-30)
REVERT: b   46 LYS cc_start: 0.8609 (mttm) cc_final: 0.8149 (mttm)
REVERT: b   67 LYS cc_start: 0.8341 (mptt) cc_final: 0.7864 (mptt)
REVERT: b  122 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8105 (tp)
REVERT: b  123 ASP cc_start: 0.8859 (t0) cc_final: 0.8583 (t0)
REVERT: b  128 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8874 (mm)
REVERT: b  129 ASN cc_start: 0.8850 (m110) cc_final: 0.8433 (m110)
REVERT: B   24 ARG cc_start: 0.8796 (mtp-110) cc_final: 0.8012 (tpt170)
REVERT: B  104 GLU cc_start: 0.8422 (pt0) cc_final: 0.8206 (pt0)
REVERT: B  116 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9203 (tt)
REVERT: B  127 GLN cc_start: 0.8551 (mp10) cc_final: 0.7780 (mp10)
REVERT: A   34 SER cc_start: 0.8669 (m) cc_final: 0.8437 (t)
REVERT: A   37 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8498 (tm-30)
REVERT: A   54 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.7902 (mt0)
REVERT: A  102 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7418 (t70)
REVERT: A  103 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8451 (mt-10)
  outliers start: 46
  outliers final: 34
  residues processed: 175
  average time/residue: 0.1917
  time to fit residues: 40.8848
Evaluate side-chains
  174 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 134
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  115 MET
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   41 GLN
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   61 THR
Chi-restraints excluded: chain L residue   81 VAL
Chi-restraints excluded: chain L residue   95 TYR
Chi-restraints excluded: chain L residue  107 LEU
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue   50 VAL
Chi-restraints excluded: chain b residue   75 THR
Chi-restraints excluded: chain b residue   93 THR
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain b residue  122 ILE
Chi-restraints excluded: chain b residue  125 ILE
Chi-restraints excluded: chain b residue  128 LEU
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   74 CYS
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   16 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  122 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 51 optimal weight:    0.0270
   chunk 39 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    3.6044

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.089804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.069772 restraints weight = 10914.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.072679 restraints weight = 5132.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.074682 restraints weight = 3239.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083   4778  Z= 0.204
  Angle     :  0.770  11.508   6500  Z= 0.392
  Chirality :  0.050   0.238    758
  Planarity :  0.009   0.151    848
  Dihedral  :  9.767  85.975    709
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  6.72 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  8.27 %
    Allowed  : 24.62 %
    Favored  : 67.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -2.79 (0.32), residues: 610
  helix:  0.28 (0.58), residues: 76
  sheet: -1.84 (0.32), residues: 236
  loop : -2.40 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H  50 
 HIS   0.002   0.001   HIS H  63 
 PHE   0.013   0.002   PHE A  96 
 TYR   0.023   0.002   TYR H 113 
 ARG   0.005   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  143)
  hydrogen bonds       : angle       5.87733 (  375)
  covalent geometry    : bond        0.00485 ( 4778)
  covalent geometry    : angle       0.77050 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 142
  time to evaluate  : 0.539 
Fit side-chains
REVERT: H   47 ARG cc_start: 0.7241 (ptt90) cc_final: 0.4759 (mtt-85)
REVERT: H   92 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8630 (mm-30)
REVERT: L   92 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7656 (tm-30)
REVERT: L  106 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8413 (mmmm)
REVERT: b   14 ASP cc_start: 0.8528 (p0) cc_final: 0.7784 (p0)
REVERT: b   16 LYS cc_start: 0.9181 (mmmm) cc_final: 0.8786 (mmmm)
REVERT: b   37 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8479 (tm-30)
REVERT: b   67 LYS cc_start: 0.7947 (mptt) cc_final: 0.7469 (mptt)
REVERT: b  123 ASP cc_start: 0.8817 (t0) cc_final: 0.8544 (t0)
REVERT: b  128 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8667 (mm)
REVERT: b  129 ASN cc_start: 0.8620 (m110) cc_final: 0.8101 (m110)
REVERT: B   24 ARG cc_start: 0.8861 (mtp-110) cc_final: 0.7684 (tpt170)
REVERT: B   45 GLU cc_start: 0.7051 (pm20) cc_final: 0.6803 (pm20)
REVERT: B  116 LEU cc_start: 0.9422 (mt) cc_final: 0.9120 (tt)
REVERT: B  127 GLN cc_start: 0.8680 (mp10) cc_final: 0.8126 (mp10)
REVERT: A    6 VAL cc_start: 0.8015 (t) cc_final: 0.7621 (m)
REVERT: A   34 SER cc_start: 0.8520 (m) cc_final: 0.8234 (t)
REVERT: A   37 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8366 (tm-30)
REVERT: A   47 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7805 (ptp90)
REVERT: A   54 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7449 (mt0)
REVERT: A   69 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6965 (tm130)
REVERT: A  103 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8728 (mt-10)
  outliers start: 43
  outliers final: 27
  residues processed: 173
  average time/residue: 0.1902
  time to fit residues: 39.9163
Evaluate side-chains
  165 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   61 THR
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   81 VAL
Chi-restraints excluded: chain L residue   95 TYR
Chi-restraints excluded: chain L residue  107 LEU
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue   75 THR
Chi-restraints excluded: chain b residue   80 CYS
Chi-restraints excluded: chain b residue   93 THR
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain b residue  128 LEU
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   74 CYS
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  58 ASN
B  10 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.087370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.067417 restraints weight = 11189.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.070241 restraints weight = 5323.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.072181 restraints weight = 3397.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.5190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.077   4778  Z= 0.296
  Angle     :  0.821  10.589   6500  Z= 0.424
  Chirality :  0.051   0.234    758
  Planarity :  0.009   0.146    848
  Dihedral  :  9.257  86.016    699
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.51 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  9.62 %
    Allowed  : 24.42 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.17 %

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: -2.74 (0.32), residues: 610
  helix:  0.13 (0.58), residues: 76
  sheet: -1.71 (0.33), residues: 227
  loop : -2.41 (0.32), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  50 
 HIS   0.002   0.001   HIS H  63 
 PHE   0.013   0.002   PHE H  32 
 TYR   0.029   0.002   TYR H 113 
 ARG   0.004   0.001   ARG H  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04016 (  143)
  hydrogen bonds       : angle       6.01490 (  375)
  covalent geometry    : bond        0.00672 ( 4778)
  covalent geometry    : angle       0.82112 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 144
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7287 (ptt90) cc_final: 0.4808 (mtt-85)
REVERT: H   92 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: L   40 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8259 (tm-30)
REVERT: L   92 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7812 (tm-30)
REVERT: L  106 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8375 (mmmm)
REVERT: b   14 ASP cc_start: 0.8562 (p0) cc_final: 0.7867 (p0)
REVERT: b   16 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8766 (mmmm)
REVERT: b   37 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8400 (tm-30)
REVERT: b   67 LYS cc_start: 0.8062 (mptt) cc_final: 0.7476 (mptt)
REVERT: b  121 LEU cc_start: 0.9226 (tp) cc_final: 0.8837 (tp)
REVERT: b  123 ASP cc_start: 0.8706 (t0) cc_final: 0.8417 (t0)
REVERT: b  129 ASN cc_start: 0.8731 (m110) cc_final: 0.8202 (m110)
REVERT: B   24 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.7752 (tpt170)
REVERT: B   45 GLU cc_start: 0.7039 (pm20) cc_final: 0.6723 (pm20)
REVERT: B  116 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9216 (tt)
REVERT: B  127 GLN cc_start: 0.8718 (mp10) cc_final: 0.7997 (mp10)
REVERT: A   34 SER cc_start: 0.8642 (m) cc_final: 0.8336 (t)
REVERT: A   37 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8782 (tm-30)
REVERT: A   47 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7878 (ptp90)
REVERT: A   54 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7410 (mt0)
REVERT: A   67 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7851 (mtpp)
REVERT: A   69 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7146 (tm130)
REVERT: A  102 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7822 (t70)
REVERT: A  103 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8684 (mt-10)
REVERT: A  129 ASN cc_start: 0.8512 (m-40) cc_final: 0.8276 (m-40)
  outliers start: 50
  outliers final: 35
  residues processed: 179
  average time/residue: 0.1894
  time to fit residues: 41.0321
Evaluate side-chains
  180 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 139
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue  111 VAL
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  115 MET
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   61 THR
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   81 VAL
Chi-restraints excluded: chain L residue   95 TYR
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue   50 VAL
Chi-restraints excluded: chain b residue   75 THR
Chi-restraints excluded: chain b residue   80 CYS
Chi-restraints excluded: chain b residue   93 THR
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain b residue  125 ILE
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue   74 CYS
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  128 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 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 = 0.3377 r_free = 0.3377 target = 0.092274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.072189 restraints weight = 10666.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.075148 restraints weight = 5040.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.077171 restraints weight = 3188.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.5451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   4778  Z= 0.145
  Angle     :  0.762   9.278   6500  Z= 0.382
  Chirality :  0.048   0.222    758
  Planarity :  0.009   0.141    848
  Dihedral  :  8.167  89.387    697
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  5.08 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 29.04 %
    Favored  : 65.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -2.44 (0.33), residues: 610
  helix:  0.58 (0.58), residues: 76
  sheet: -1.55 (0.33), residues: 241
  loop : -2.26 (0.33), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  50 
 HIS   0.004   0.002   HIS L  37 
 PHE   0.012   0.002   PHE A  96 
 TYR   0.016   0.001   TYR B  99 
 ARG   0.003   0.000   ARG b  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03029 (  143)
  hydrogen bonds       : angle       5.32083 (  375)
  covalent geometry    : bond        0.00373 ( 4778)
  covalent geometry    : angle       0.76190 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7128 (ptt90) cc_final: 0.4854 (mtt-85)
REVERT: H   68 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8346 (mmmt)
REVERT: H   92 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8642 (mm-30)
REVERT: L   40 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7803 (tt0)
REVERT: L   92 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7772 (tm-30)
REVERT: L  105 THR cc_start: 0.7882 (m) cc_final: 0.7444 (m)
REVERT: L  106 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8256 (mmmm)
REVERT: b   10 ASN cc_start: 0.9212 (m-40) cc_final: 0.8853 (p0)
REVERT: b   14 ASP cc_start: 0.8818 (p0) cc_final: 0.8129 (p0)
REVERT: b   16 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8825 (mmmm)
REVERT: b   37 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8551 (tm-30)
REVERT: b   67 LYS cc_start: 0.7755 (mptt) cc_final: 0.7277 (mptt)
REVERT: b  123 ASP cc_start: 0.8624 (t0) cc_final: 0.8388 (t0)
REVERT: b  129 ASN cc_start: 0.8605 (m110) cc_final: 0.8086 (m110)
REVERT: B   10 ASN cc_start: 0.8874 (p0) cc_final: 0.8615 (p0)
REVERT: B   24 ARG cc_start: 0.8759 (mtp-110) cc_final: 0.7383 (tpt170)
REVERT: B   45 GLU cc_start: 0.6992 (pm20) cc_final: 0.6724 (pm20)
REVERT: B  127 GLN cc_start: 0.8763 (mp10) cc_final: 0.8025 (mp10)
REVERT: B  128 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8665 (mm)
REVERT: B  129 ASN cc_start: 0.9286 (m-40) cc_final: 0.8842 (m-40)
REVERT: A    6 VAL cc_start: 0.7893 (t) cc_final: 0.7610 (m)
REVERT: A   34 SER cc_start: 0.8629 (m) cc_final: 0.8211 (t)
REVERT: A   37 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8733 (tm-30)
REVERT: A  103 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8505 (mt-10)
REVERT: A  127 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8505 (mm110)
REVERT: A  129 ASN cc_start: 0.8422 (m-40) cc_final: 0.8163 (m-40)
  outliers start: 27
  outliers final: 19
  residues processed: 171
  average time/residue: 0.2122
  time to fit residues: 44.4820
Evaluate side-chains
  169 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   41 GLN
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   61 THR
Chi-restraints excluded: chain L residue   81 VAL
Chi-restraints excluded: chain L residue   95 TYR
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue   75 THR
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.091488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.071314 restraints weight = 10739.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.074249 restraints weight = 5065.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.076276 restraints weight = 3180.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.5640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   4778  Z= 0.156
  Angle     :  0.740   8.110   6500  Z= 0.375
  Chirality :  0.048   0.219    758
  Planarity :  0.008   0.135    848
  Dihedral  :  6.804  51.626    688
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  6.07 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 28.08 %
    Favored  : 65.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -2.21 (0.33), residues: 610
  helix:  0.72 (0.58), residues: 76
  sheet: -1.27 (0.34), residues: 237
  loop : -2.22 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  50 
 HIS   0.002   0.001   HIS L  37 
 PHE   0.015   0.002   PHE H  30 
 TYR   0.017   0.001   TYR H 105 
 ARG   0.003   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03091 (  143)
  hydrogen bonds       : angle       5.15250 (  375)
  covalent geometry    : bond        0.00392 ( 4778)
  covalent geometry    : angle       0.74048 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7057 (ptt90) cc_final: 0.4716 (mtt-85)
REVERT: H   68 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8374 (mmmt)
REVERT: H   85 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7664 (tp-100)
REVERT: H   92 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8677 (mm-30)
REVERT: L   40 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7758 (tt0)
REVERT: L   92 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7761 (tm-30)
REVERT: L  105 THR cc_start: 0.7993 (m) cc_final: 0.7588 (m)
REVERT: L  106 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8230 (mmmm)
REVERT: b   10 ASN cc_start: 0.9245 (m-40) cc_final: 0.8908 (p0)
REVERT: b   14 ASP cc_start: 0.8724 (p0) cc_final: 0.8046 (p0)
REVERT: b   16 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8734 (mmmm)
REVERT: b   37 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: b   67 LYS cc_start: 0.7690 (mptt) cc_final: 0.7219 (mptt)
REVERT: b  123 ASP cc_start: 0.8646 (t0) cc_final: 0.8363 (t0)
REVERT: b  129 ASN cc_start: 0.8617 (m110) cc_final: 0.8087 (m110)
REVERT: B   24 ARG cc_start: 0.8770 (mtp-110) cc_final: 0.7554 (tpt170)
REVERT: B   45 GLU cc_start: 0.7098 (pm20) cc_final: 0.6795 (pm20)
REVERT: B   59 ARG cc_start: 0.8104 (ptt180) cc_final: 0.7855 (ptt180)
REVERT: B  127 GLN cc_start: 0.8720 (mp10) cc_final: 0.8027 (mp10)
REVERT: B  128 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8490 (mm)
REVERT: B  129 ASN cc_start: 0.9214 (m-40) cc_final: 0.8878 (m-40)
REVERT: A    6 VAL cc_start: 0.7808 (t) cc_final: 0.7517 (m)
REVERT: A   34 SER cc_start: 0.8517 (m) cc_final: 0.8084 (t)
REVERT: A   37 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8698 (tm-30)
REVERT: A   47 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7670 (ptt-90)
REVERT: A  103 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8650 (mt-10)
REVERT: A  127 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8542 (mm110)
REVERT: A  129 ASN cc_start: 0.8476 (m-40) cc_final: 0.8198 (m-40)
  outliers start: 33
  outliers final: 21
  residues processed: 174
  average time/residue: 0.2147
  time to fit residues: 45.2566
Evaluate side-chains
  174 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  115 MET
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   41 GLN
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   61 THR
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   81 VAL
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue   75 THR
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  128 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 37 optimal weight:   20.0000
   chunk 30 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0870
   chunk 29 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   overall best weight:    3.8166

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.089981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.069470 restraints weight = 10878.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.072394 restraints weight = 5163.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.074359 restraints weight = 3273.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.5698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   4778  Z= 0.212
  Angle     :  0.782  10.784   6500  Z= 0.392
  Chirality :  0.049   0.216    758
  Planarity :  0.008   0.134    848
  Dihedral  :  6.829  50.327    686
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  7.38 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 27.69 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -2.35 (0.33), residues: 610
  helix:  0.51 (0.57), residues: 76
  sheet: -1.38 (0.33), residues: 244
  loop : -2.26 (0.33), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  50 
 HIS   0.003   0.001   HIS H  63 
 PHE   0.014   0.002   PHE b 107 
 TYR   0.020   0.002   TYR H 113 
 ARG   0.003   0.000   ARG H  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  143)
  hydrogen bonds       : angle       5.31987 (  375)
  covalent geometry    : bond        0.00503 ( 4778)
  covalent geometry    : angle       0.78162 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7048 (ptt90) cc_final: 0.4765 (mtt-85)
REVERT: L   40 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8114 (tt0)
REVERT: L   92 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: L  105 THR cc_start: 0.8153 (m) cc_final: 0.7791 (m)
REVERT: L  106 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8051 (mmmm)
REVERT: b   10 ASN cc_start: 0.9184 (m-40) cc_final: 0.8851 (p0)
REVERT: b   14 ASP cc_start: 0.8739 (p0) cc_final: 0.8021 (p0)
REVERT: b   16 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8691 (mmmm)
REVERT: b   37 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8635 (tm-30)
REVERT: b   67 LYS cc_start: 0.7797 (mptt) cc_final: 0.7267 (mptt)
REVERT: b  123 ASP cc_start: 0.8605 (t0) cc_final: 0.8379 (t0)
REVERT: b  129 ASN cc_start: 0.8710 (m110) cc_final: 0.8211 (m110)
REVERT: B   24 ARG cc_start: 0.8816 (mtp-110) cc_final: 0.7541 (tpt170)
REVERT: B   59 ARG cc_start: 0.8129 (ptt180) cc_final: 0.7782 (ptt180)
REVERT: B  127 GLN cc_start: 0.8726 (mp10) cc_final: 0.8050 (mp10)
REVERT: B  128 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8560 (mm)
REVERT: B  129 ASN cc_start: 0.9302 (m-40) cc_final: 0.8948 (m-40)
REVERT: A   14 ASP cc_start: 0.8658 (p0) cc_final: 0.8385 (p0)
REVERT: A   34 SER cc_start: 0.8618 (m) cc_final: 0.8200 (t)
REVERT: A   37 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8728 (tm-30)
REVERT: A   47 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7832 (ptt-90)
REVERT: A  103 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8677 (mt-10)
REVERT: A  121 LEU cc_start: 0.9226 (tp) cc_final: 0.8946 (tt)
REVERT: A  127 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8520 (mm110)
REVERT: A  129 ASN cc_start: 0.8477 (m-40) cc_final: 0.8189 (m-40)
  outliers start: 33
  outliers final: 27
  residues processed: 171
  average time/residue: 0.2252
  time to fit residues: 46.7878
Evaluate side-chains
  178 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   30 PHE
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue  111 VAL
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  115 MET
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   61 THR
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   81 VAL
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue   75 THR
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain b residue  125 ILE
Chi-restraints excluded: chain b residue  132 TYR
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  128 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 33 optimal weight:    0.4980
   chunk 16 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
L  37 HIS
B  10 ASN
A  10 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.093584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.072886 restraints weight = 10737.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.075901 restraints weight = 5086.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.077950 restraints weight = 3229.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.5933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   4778  Z= 0.144
  Angle     :  0.766  10.125   6500  Z= 0.380
  Chirality :  0.048   0.201    758
  Planarity :  0.008   0.130    848
  Dihedral  :  6.363  47.123    686
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.57 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 29.23 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -2.07 (0.33), residues: 610
  helix:  0.38 (0.56), residues: 77
  sheet: -1.05 (0.34), residues: 235
  loop : -2.12 (0.33), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  50 
 HIS   0.003   0.002   HIS L  37 
 PHE   0.015   0.002   PHE b 107 
 TYR   0.012   0.001   TYR H 105 
 ARG   0.003   0.000   ARG b  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02925 (  143)
  hydrogen bonds       : angle       4.95913 (  375)
  covalent geometry    : bond        0.00375 ( 4778)
  covalent geometry    : angle       0.76578 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.6906 (ptt90) cc_final: 0.4708 (mtt-85)
REVERT: H   85 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7604 (tp-100)
REVERT: H   90 LYS cc_start: 0.8881 (tppt) cc_final: 0.8495 (tmmt)
REVERT: H  105 TYR cc_start: 0.8783 (p90) cc_final: 0.8376 (p90)
REVERT: L   40 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7883 (tt0)
REVERT: L   75 THR cc_start: 0.8611 (t) cc_final: 0.8340 (m)
REVERT: L   92 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: L  105 THR cc_start: 0.8013 (m) cc_final: 0.7581 (m)
REVERT: L  106 LYS cc_start: 0.8424 (mmmt) cc_final: 0.7919 (mmmm)
REVERT: b   10 ASN cc_start: 0.9248 (m-40) cc_final: 0.8931 (p0)
REVERT: b   14 ASP cc_start: 0.8666 (p0) cc_final: 0.7946 (p0)
REVERT: b   16 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8794 (mmmm)
REVERT: b   37 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8528 (tm-30)
REVERT: b   67 LYS cc_start: 0.7669 (mptt) cc_final: 0.7210 (mptt)
REVERT: b  123 ASP cc_start: 0.8599 (t0) cc_final: 0.8349 (t0)
REVERT: b  129 ASN cc_start: 0.8648 (m110) cc_final: 0.8173 (m110)
REVERT: B   24 ARG cc_start: 0.8681 (mtp-110) cc_final: 0.7354 (tpt170)
REVERT: B   37 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8294 (tp40)
REVERT: B   59 ARG cc_start: 0.8168 (ptt180) cc_final: 0.7904 (ptt180)
REVERT: B  127 GLN cc_start: 0.8656 (mp10) cc_final: 0.8194 (mp10)
REVERT: B  128 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8517 (mm)
REVERT: B  129 ASN cc_start: 0.9329 (m-40) cc_final: 0.9017 (m-40)
REVERT: A   14 ASP cc_start: 0.8601 (p0) cc_final: 0.8349 (p0)
REVERT: A   34 SER cc_start: 0.8472 (m) cc_final: 0.8025 (t)
REVERT: A   37 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8644 (tm-30)
REVERT: A  103 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8699 (mt-10)
REVERT: A  121 LEU cc_start: 0.9157 (tp) cc_final: 0.8864 (tp)
REVERT: A  129 ASN cc_start: 0.8451 (m-40) cc_final: 0.8163 (m-40)
  outliers start: 28
  outliers final: 18
  residues processed: 171
  average time/residue: 0.2200
  time to fit residues: 45.8883
Evaluate side-chains
  171 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   30 PHE
Chi-restraints excluded: chain H residue  101 ARG
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   81 VAL
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  128 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
L  79 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.087852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.067680 restraints weight = 10961.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.070500 restraints weight = 5294.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.072458 restraints weight = 3380.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.5862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070   4778  Z= 0.293
  Angle     :  0.865   9.501   6500  Z= 0.435
  Chirality :  0.051   0.197    758
  Planarity :  0.008   0.132    848
  Dihedral  :  7.153  51.803    686
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  9.51 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 29.23 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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: -2.29 (0.32), residues: 610
  helix:  0.14 (0.56), residues: 77
  sheet: -1.11 (0.35), residues: 225
  loop : -2.30 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H  39 
 HIS   0.004   0.002   HIS H  63 
 PHE   0.021   0.003   PHE b 107 
 TYR   0.029   0.002   TYR H 113 
 ARG   0.007   0.001   ARG b  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  143)
  hydrogen bonds       : angle       5.50217 (  375)
  covalent geometry    : bond        0.00669 ( 4778)
  covalent geometry    : angle       0.86455 ( 6500)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7143 (ptt90) cc_final: 0.4804 (mtt-85)
REVERT: H   65 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6746 (m-30)
REVERT: H   90 LYS cc_start: 0.8862 (tppt) cc_final: 0.8451 (tmmt)
REVERT: L   40 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8180 (tm-30)
REVERT: L   92 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7616 (tm-30)
REVERT: L  106 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8096 (mmmm)
REVERT: b   10 ASN cc_start: 0.9229 (m-40) cc_final: 0.8848 (p0)
REVERT: b   14 ASP cc_start: 0.8716 (p0) cc_final: 0.8081 (p0)
REVERT: b   16 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8688 (mmmm)
REVERT: b   37 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8484 (tm-30)
REVERT: b   67 LYS cc_start: 0.7876 (mptt) cc_final: 0.7295 (mptt)
REVERT: b  123 ASP cc_start: 0.8607 (t0) cc_final: 0.8388 (t0)
REVERT: b  129 ASN cc_start: 0.8721 (m110) cc_final: 0.8247 (m110)
REVERT: B   24 ARG cc_start: 0.8842 (mtp-110) cc_final: 0.7733 (tpt170)
REVERT: B  127 GLN cc_start: 0.8742 (mp10) cc_final: 0.8008 (mp10)
REVERT: A   34 SER cc_start: 0.8595 (m) cc_final: 0.8297 (t)
REVERT: A   47 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7725 (ptt-90)
REVERT: A  103 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8840 (mt-10)
REVERT: A  121 LEU cc_start: 0.9216 (tp) cc_final: 0.8936 (tp)
REVERT: A  127 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8414 (mm110)
REVERT: A  129 ASN cc_start: 0.8471 (m-40) cc_final: 0.8167 (m-40)
  outliers start: 29
  outliers final: 24
  residues processed: 162
  average time/residue: 0.2105
  time to fit residues: 41.7581
Evaluate side-chains
  162 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   10 SER
Chi-restraints excluded: chain H residue   30 PHE
Chi-restraints excluded: chain H residue   65 ASP
Chi-restraints excluded: chain H residue   71 ILE
Chi-restraints excluded: chain H residue  113 TYR
Chi-restraints excluded: chain H residue  115 MET
Chi-restraints excluded: chain L residue    5 ILE
Chi-restraints excluded: chain L residue   40 GLN
Chi-restraints excluded: chain L residue   46 SER
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   81 VAL
Chi-restraints excluded: chain b residue   32 VAL
Chi-restraints excluded: chain b residue   75 THR
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain b residue  132 TYR
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   93 THR
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  128 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0050
   chunk 51 optimal weight:    9.9990
   chunk 1 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 56 optimal weight:    7.9990
   chunk 4 optimal weight:    0.4980
   chunk 8 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
B  10 ASN
A  10 ASN
A  87 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.093851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.073195 restraints weight = 10732.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.076247 restraints weight = 5006.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.078372 restraints weight = 3132.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.6143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   4778  Z= 0.144
  Angle     :  0.800  10.457   6500  Z= 0.396
  Chirality :  0.048   0.193    758
  Planarity :  0.008   0.127    848
  Dihedral  :  6.206  47.210    686
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.92 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 31.15 %
    Favored  : 64.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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 (0.33), residues: 610
  helix:  0.61 (0.56), residues: 77
  sheet: -0.98 (0.34), residues: 236
  loop : -2.15 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L  97 
 HIS   0.004   0.002   HIS H  63 
 PHE   0.021   0.002   PHE b 107 
 TYR   0.011   0.001   TYR H 105 
 ARG   0.007   0.001   ARG b  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02792 (  143)
  hydrogen bonds       : angle       4.96911 (  375)
  covalent geometry    : bond        0.00370 ( 4778)
  covalent geometry    : angle       0.80020 ( 6500)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2104.56 seconds
wall clock time: 37 minutes 32.20 seconds (2252.20 seconds total)