Starting phenix.real_space_refine
on Fri Aug 22 15:07:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5o_37299/08_2025/8w5o_37299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5o_37299/08_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_37299/08_2025/8w5o_37299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5o_37299/08_2025/8w5o_37299.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5o_37299/08_2025/8w5o_37299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5o_37299/08_2025/8w5o_37299.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.23, per 1000 atoms: 0.26
  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: 0.28
  Conformation dependent library (CDL) restraints added in 190.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.16
  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: 0.48

  Time building geometry restraints manager: 0.41 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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.530
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.260
-------------------------------------------------------------------------------
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 : 24.87
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG H  70 
 TYR   0.040   0.003   TYR H 113 
 PHE   0.023   0.004   PHE L  74 
 TRP   0.055   0.005   TRP L  97 
 HIS   0.003   0.001   HIS L  37 

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

*********************** 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  : 0.194 
Fit side-chains
   revert: symmetry clash
   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: 0.8209 (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: 0.8551 (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: 0.8622 (tm-30)
REVERT: b   46 LYS cc_start: 0.8428 (mttp) cc_final: 0.8096 (mttm)
REVERT: b  123 ASP cc_start: 0.8592 (t0) cc_final: 0.8298 (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: 0.8283 (mmtm)
REVERT: B   24 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7648 (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: 0.8927 (m110)
REVERT: A   22 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8046 (p0)
REVERT: A   30 ASN cc_start: 0.8035 (p0) cc_final: 0.7344 (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: 0.8973 (p)
REVERT: A   54 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8146 (mt0)
REVERT: A   57 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7069 (ptt180)
REVERT: A   63 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8891 (tttp)
REVERT: A   65 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7950 (tm-30)
REVERT: A   68 ILE cc_start: 0.8973 (mt) cc_final: 0.8751 (mt)
REVERT: A   72 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8469 (p)
REVERT: A   98 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8569 (pp30)
REVERT: A  103 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8652 (mt-10)
  outliers start: 58
  outliers final: 30
  residues processed: 246
  average time/residue: 0.0840
  time to fit residues: 24.6336
Evaluate side-chains
  184 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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 54 optimal weight:    5.9990
   chunk 24 optimal weight:    0.4980
   chunk 48 optimal weight:    6.9990
   chunk 56 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0770
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.9144

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

Flipped N/Q/H residues before XYZ refinement:
H  77 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 = 0.3427 r_free = 0.3427 target = 0.094495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.075063 restraints weight = 10640.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.078111 restraints weight = 4861.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.080176 restraints weight = 3002.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.081615 restraints weight = 2201.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.082552 restraints weight = 1784.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.110   4778  Z= 0.166
  Angle     :  0.803  16.039   6500  Z= 0.399
  Chirality :  0.050   0.246    758
  Planarity :  0.011   0.172    848
  Dihedral  : 11.962 101.464    752
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  :  5.57 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  8.08 %
    Allowed  : 19.81 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.03 (0.32), residues: 610
  helix: -0.12 (0.61), residues: 75
  sheet: -2.14 (0.30), residues: 249
  loop : -2.31 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 109 
 TYR   0.020   0.001   TYR H 113 
 PHE   0.019   0.002   PHE b 107 
 TRP   0.020   0.002   TRP L  97 
 HIS   0.003   0.001   HIS L  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 4778)
  covalent geometry    : angle       0.80260 ( 6500)
  hydrogen bonds       : bond        0.04184 (  143)
  hydrogen bonds       : angle       6.35116 (  375)

*********************** 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
  215 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 173
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7454 (ptt90) cc_final: 0.5059 (mtt-85)
REVERT: H   92 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8676 (mm-30)
REVERT: H  104 TYR cc_start: 0.8794 (m-80) cc_final: 0.8579 (m-80)
REVERT: H  116 ASP cc_start: 0.8819 (p0) cc_final: 0.8281 (p0)
REVERT: H  117 TYR cc_start: 0.9020 (m-80) cc_final: 0.8488 (m-10)
REVERT: L   20 GLU cc_start: 0.8164 (mp0) cc_final: 0.7959 (pm20)
REVERT: L   21 ARG cc_start: 0.8304 (ptm-80) cc_final: 0.7780 (ptm-80)
REVERT: L   92 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7343 (tm-30)
REVERT: L   93 GLN cc_start: 0.8867 (pp30) cc_final: 0.7792 (pp30)
REVERT: L  106 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8477 (mmmm)
REVERT: b   37 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8536 (tm-30)
REVERT: b   87 GLN cc_start: 0.8619 (mm110) cc_final: 0.8376 (mm110)
REVERT: b  123 ASP cc_start: 0.8759 (t0) cc_final: 0.8502 (t0)
REVERT: b  129 ASN cc_start: 0.8515 (m110) cc_final: 0.8141 (m-40)
REVERT: B   24 ARG cc_start: 0.8574 (mtp-110) cc_final: 0.7317 (tpt170)
REVERT: B   45 GLU cc_start: 0.6816 (pm20) cc_final: 0.6606 (pm20)
REVERT: B  104 GLU cc_start: 0.8277 (pt0) cc_final: 0.7951 (pt0)
REVERT: B  127 GLN cc_start: 0.8312 (mp10) cc_final: 0.7824 (mp10)
REVERT: A   37 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8704 (tm-30)
REVERT: A   54 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7752 (mt0)
REVERT: A   57 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6886 (ptt180)
REVERT: A   59 ARG cc_start: 0.7626 (ptp90) cc_final: 0.7413 (ptt-90)
REVERT: A   77 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7995 (m-40)
REVERT: A   91 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6963 (m-30)
REVERT: A   98 GLN cc_start: 0.8898 (pt0) cc_final: 0.8553 (pt0)
REVERT: A  102 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7806 (t0)
REVERT: A  103 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8503 (mt-10)
  outliers start: 42
  outliers final: 24
  residues processed: 202
  average time/residue: 0.0748
  time to fit residues: 18.3829
Evaluate side-chains
  174 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
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   89 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   41 GLN
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  116 LEU
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   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 33 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    6.3388

-------------------------------------------------------------------------------
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
A  10 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.096663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.076135 restraints weight = 10542.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.078902 restraints weight = 5484.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.080788 restraints weight = 3730.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.081778 restraints weight = 2942.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.082761 restraints weight = 2571.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.081   4778  Z= 0.328
  Angle     :  0.855  14.082   6500  Z= 0.438
  Chirality :  0.052   0.245    758
  Planarity :  0.010   0.163    848
  Dihedral  : 10.029  84.041    707
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.34 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 20.96 %
    Favored  : 70.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.89 (0.32), residues: 610
  helix: -0.02 (0.56), residues: 76
  sheet: -1.85 (0.32), residues: 237
  loop : -2.46 (0.32), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 109 
 TYR   0.032   0.002   TYR H 113 
 PHE   0.019   0.003   PHE L  74 
 TRP   0.023   0.003   TRP L  97 
 HIS   0.008   0.003   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00736 ( 4778)
  covalent geometry    : angle       0.85499 ( 6500)
  hydrogen bonds       : bond        0.04456 (  143)
  hydrogen bonds       : angle       6.31821 (  375)

*********************** 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
  184 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 140
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.8163 (ptt90) cc_final: 0.5407 (mtt-85)
REVERT: H   92 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8410 (mm-30)
REVERT: L   21 ARG cc_start: 0.8540 (ptm-80) cc_final: 0.7993 (ptm-80)
REVERT: L   92 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7889 (tm-30)
REVERT: L  106 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8630 (mmmm)
REVERT: L  107 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9254 (tt)
REVERT: b   10 ASN cc_start: 0.8586 (m-40) cc_final: 0.8372 (p0)
REVERT: b   16 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8421 (mmtp)
REVERT: b   37 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8533 (tm-30)
REVERT: b   65 GLN cc_start: 0.8014 (tt0) cc_final: 0.7806 (tt0)
REVERT: b   67 LYS cc_start: 0.8171 (mttp) cc_final: 0.7859 (mttp)
REVERT: b  115 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9092 (tt)
REVERT: b  121 LEU cc_start: 0.9459 (tp) cc_final: 0.9073 (tp)
REVERT: b  129 ASN cc_start: 0.8893 (m110) cc_final: 0.8553 (m-40)
REVERT: B   24 ARG cc_start: 0.8687 (mtp-110) cc_final: 0.8096 (tpt170)
REVERT: B   69 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7176 (tm-30)
REVERT: B  104 GLU cc_start: 0.8286 (pt0) cc_final: 0.7942 (pt0)
REVERT: B  116 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9228 (tt)
REVERT: B  127 GLN cc_start: 0.8454 (mp10) cc_final: 0.7888 (mp10)
REVERT: A    6 VAL cc_start: 0.7915 (t) cc_final: 0.7496 (p)
REVERT: A   54 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7860 (mt0)
REVERT: A   60 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7692 (tptp)
REVERT: A   67 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8373 (mtpp)
REVERT: A  102 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7821 (t70)
REVERT: A  103 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8364 (mt-10)
  outliers start: 44
  outliers final: 32
  residues processed: 170
  average time/residue: 0.0787
  time to fit residues: 16.1799
Evaluate side-chains
  170 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 131
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
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   89 LEU
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   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  115 LEU
Chi-restraints excluded: chain b residue  116 LEU
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   69 GLN
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   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   60 LYS
Chi-restraints excluded: chain A residue   66 VAL
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  121 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 25 optimal weight:   10.0000
   chunk 8 optimal weight:    0.4980
   chunk 3 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0040
   chunk 55 optimal weight:   30.0000
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    0.3980
   chunk 24 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 30 optimal weight:   20.0000
   overall best weight:    1.9796

-------------------------------------------------------------------------------
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**
L  37 HIS
B  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.091505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.072300 restraints weight = 10765.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.075270 restraints weight = 4970.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.077332 restraints weight = 3084.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.078733 restraints weight = 2256.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.079646 restraints weight = 1834.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.5006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   4778  Z= 0.154
  Angle     :  0.741  11.571   6500  Z= 0.375
  Chirality :  0.049   0.234    758
  Planarity :  0.009   0.152    848
  Dihedral  :  8.979  87.735    702
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  5.08 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 22.50 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.56 (0.32), residues: 610
  helix:  0.48 (0.57), residues: 76
  sheet: -1.69 (0.31), residues: 246
  loop : -2.27 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 101 
 TYR   0.020   0.001   TYR H 113 
 PHE   0.013   0.002   PHE H  30 
 TRP   0.012   0.001   TRP L  97 
 HIS   0.005   0.002   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4778)
  covalent geometry    : angle       0.74061 ( 6500)
  hydrogen bonds       : bond        0.03175 (  143)
  hydrogen bonds       : angle       5.57416 (  375)

*********************** 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
  193 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 154
  time to evaluate  : 0.111 
Fit side-chains
REVERT: H   47 ARG cc_start: 0.7343 (ptt90) cc_final: 0.4872 (mtt-85)
REVERT: H   92 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8564 (mm-30)
REVERT: H  116 ASP cc_start: 0.8671 (p0) cc_final: 0.8306 (p0)
REVERT: L   21 ARG cc_start: 0.8324 (ptm-80) cc_final: 0.7647 (ptm-80)
REVERT: L   52 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8233 (ptmt)
REVERT: L   78 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7945 (tp)
REVERT: L   92 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7293 (tm-30)
REVERT: L   93 GLN cc_start: 0.8816 (pp30) cc_final: 0.7612 (pp30)
REVERT: L  105 THR cc_start: 0.8192 (m) cc_final: 0.7888 (m)
REVERT: L  106 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8409 (mmmm)
REVERT: b   14 ASP cc_start: 0.8153 (p0) cc_final: 0.7714 (p0)
REVERT: b   37 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8520 (tm-30)
REVERT: b   46 LYS cc_start: 0.8295 (mttp) cc_final: 0.7734 (mttm)
REVERT: b   65 GLN cc_start: 0.7985 (tt0) cc_final: 0.7756 (tt0)
REVERT: b   67 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7617 (mttp)
REVERT: b  129 ASN cc_start: 0.8681 (m110) cc_final: 0.8297 (m-40)
REVERT: B   24 ARG cc_start: 0.8768 (mtp-110) cc_final: 0.7642 (tpt170)
REVERT: B   96 PHE cc_start: 0.8971 (m-10) cc_final: 0.8724 (m-10)
REVERT: B  127 GLN cc_start: 0.8537 (mp10) cc_final: 0.7892 (mp10)
REVERT: A   16 LYS cc_start: 0.9507 (OUTLIER) cc_final: 0.9130 (mmtm)
REVERT: A   17 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8782 (mp10)
REVERT: A   54 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7647 (mt0)
REVERT: A   62 TYR cc_start: 0.8980 (m-80) cc_final: 0.8609 (m-10)
REVERT: A  102 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8020 (t0)
REVERT: A  103 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8608 (mt-10)
  outliers start: 39
  outliers final: 26
  residues processed: 176
  average time/residue: 0.0695
  time to fit residues: 15.0419
Evaluate side-chains
  173 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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   71 ILE
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain H residue  111 VAL
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 b residue   32 VAL
Chi-restraints excluded: chain b residue   67 LYS
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   22 ASN
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   16 LYS
Chi-restraints excluded: chain A residue   17 GLN
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   66 VAL
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  121 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 1 optimal weight:    0.4980
   overall best weight:    2.6384

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

Flipped N/Q/H residues before XYZ refinement:
b  70 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 = 0.3357 r_free = 0.3357 target = 0.090202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.070968 restraints weight = 10956.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.073904 restraints weight = 5080.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.075911 restraints weight = 3162.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.077268 restraints weight = 2328.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.078190 restraints weight = 1910.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.5253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   4778  Z= 0.171
  Angle     :  0.749  10.236   6500  Z= 0.380
  Chirality :  0.048   0.231    758
  Planarity :  0.009   0.146    848
  Dihedral  :  7.652  59.792    693
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  7.38 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 22.69 %
    Favored  : 68.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.32), residues: 610
  helix:  0.63 (0.58), residues: 76
  sheet: -1.44 (0.32), residues: 241
  loop : -2.33 (0.33), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b  24 
 TYR   0.020   0.002   TYR H 113 
 PHE   0.011   0.002   PHE H  30 
 TRP   0.008   0.001   TRP L  97 
 HIS   0.005   0.002   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 4778)
  covalent geometry    : angle       0.74857 ( 6500)
  hydrogen bonds       : bond        0.03193 (  143)
  hydrogen bonds       : angle       5.36352 (  375)

*********************** 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
  189 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 145
  time to evaluate  : 0.109 
Fit side-chains
REVERT: H   47 ARG cc_start: 0.7429 (ptt90) cc_final: 0.4977 (mtt-85)
REVERT: H   92 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8454 (mm-30)
REVERT: H  116 ASP cc_start: 0.8791 (p0) cc_final: 0.8393 (p0)
REVERT: H  117 TYR cc_start: 0.9095 (m-80) cc_final: 0.8777 (m-80)
REVERT: L   21 ARG cc_start: 0.8273 (ptm-80) cc_final: 0.7560 (ptm-80)
REVERT: L   40 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8118 (tt0)
REVERT: L   52 LYS cc_start: 0.8310 (ttpp) cc_final: 0.8030 (ptmt)
REVERT: L   92 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7322 (tm-30)
REVERT: L   93 GLN cc_start: 0.8843 (pp30) cc_final: 0.7870 (pp30)
REVERT: L  105 THR cc_start: 0.8165 (m) cc_final: 0.7773 (m)
REVERT: L  106 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8453 (mmmm)
REVERT: b   10 ASN cc_start: 0.9053 (m-40) cc_final: 0.8672 (p0)
REVERT: b   14 ASP cc_start: 0.8900 (p0) cc_final: 0.8481 (p0)
REVERT: b   37 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8563 (tm-30)
REVERT: b   59 ARG cc_start: 0.8800 (ptp90) cc_final: 0.8592 (ptp90)
REVERT: b   65 GLN cc_start: 0.8022 (tt0) cc_final: 0.7726 (tt0)
REVERT: b   67 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7595 (mttp)
REVERT: b  122 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7657 (tp)
REVERT: b  129 ASN cc_start: 0.8686 (m110) cc_final: 0.8298 (m110)
REVERT: B   24 ARG cc_start: 0.8812 (mtp-110) cc_final: 0.7684 (tpt170)
REVERT: B  115 LEU cc_start: 0.8851 (tt) cc_final: 0.8607 (tt)
REVERT: B  127 GLN cc_start: 0.8751 (mp10) cc_final: 0.8120 (mp10)
REVERT: A   16 LYS cc_start: 0.9521 (mmtm) cc_final: 0.9079 (mmpt)
REVERT: A   17 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8718 (mp10)
REVERT: A   54 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7493 (mt0)
REVERT: A   60 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7822 (tptt)
REVERT: A   69 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6754 (tm130)
REVERT: A  102 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8041 (t0)
REVERT: A  103 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8686 (mt-10)
REVERT: A  129 ASN cc_start: 0.8451 (m-40) cc_final: 0.8221 (m-40)
  outliers start: 44
  outliers final: 30
  residues processed: 174
  average time/residue: 0.0748
  time to fit residues: 15.7517
Evaluate side-chains
  179 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 141
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
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   89 LEU
Chi-restraints excluded: chain H residue  111 VAL
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   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   67 LYS
Chi-restraints excluded: chain b residue   75 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  132 TYR
Chi-restraints excluded: chain B residue   22 ASN
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   17 GLN
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   60 LYS
Chi-restraints excluded: chain A residue   66 VAL
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  121 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
b  70 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.090222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.070834 restraints weight = 11164.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.073751 restraints weight = 5234.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.075768 restraints weight = 3270.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.077144 restraints weight = 2414.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.077892 restraints weight = 1975.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   4778  Z= 0.186
  Angle     :  0.744   9.333   6500  Z= 0.377
  Chirality :  0.049   0.228    758
  Planarity :  0.009   0.141    848
  Dihedral  :  7.576  57.043    693
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  6.39 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  9.23 %
    Allowed  : 22.88 %
    Favored  : 67.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.33), residues: 610
  helix:  0.70 (0.58), residues: 76
  sheet: -1.33 (0.33), residues: 241
  loop : -2.24 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b  24 
 TYR   0.020   0.002   TYR H 113 
 PHE   0.010   0.002   PHE H  30 
 TRP   0.006   0.002   TRP H 118 
 HIS   0.005   0.002   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 4778)
  covalent geometry    : angle       0.74370 ( 6500)
  hydrogen bonds       : bond        0.03205 (  143)
  hydrogen bonds       : angle       5.32018 (  375)

*********************** 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
  198 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 150
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7510 (ptt90) cc_final: 0.5052 (mtt-85)
REVERT: H   92 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8324 (mm-30)
REVERT: H  116 ASP cc_start: 0.8863 (p0) cc_final: 0.8550 (p0)
REVERT: L   21 ARG cc_start: 0.8319 (ptm-80) cc_final: 0.7564 (ptm-80)
REVERT: L   40 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8059 (tt0)
REVERT: L   52 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8125 (ptmt)
REVERT: L   92 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7513 (tm-30)
REVERT: L  105 THR cc_start: 0.8217 (m) cc_final: 0.7922 (m)
REVERT: L  106 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8365 (mmmm)
REVERT: b   10 ASN cc_start: 0.9142 (m-40) cc_final: 0.8821 (p0)
REVERT: b   14 ASP cc_start: 0.9012 (p0) cc_final: 0.8636 (p0)
REVERT: b   17 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8677 (tp-100)
REVERT: b   37 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8557 (tm-30)
REVERT: b   46 LYS cc_start: 0.8292 (mttm) cc_final: 0.7908 (mttm)
REVERT: b   59 ARG cc_start: 0.8763 (ptp90) cc_final: 0.8482 (ptp90)
REVERT: b   65 GLN cc_start: 0.8041 (tt0) cc_final: 0.7710 (tt0)
REVERT: b   67 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7608 (mttp)
REVERT: b  122 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7679 (tp)
REVERT: b  129 ASN cc_start: 0.8758 (m110) cc_final: 0.8397 (m110)
REVERT: B   24 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.7648 (tpt170)
REVERT: B  115 LEU cc_start: 0.8845 (tt) cc_final: 0.8602 (tt)
REVERT: B  127 GLN cc_start: 0.8786 (mp10) cc_final: 0.8069 (mp10)
REVERT: A   16 LYS cc_start: 0.9516 (mmtm) cc_final: 0.9070 (mmpt)
REVERT: A   17 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8697 (mp10)
REVERT: A   69 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6829 (tm130)
REVERT: A  102 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8243 (t70)
REVERT: A  103 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8621 (mt-10)
REVERT: A  129 ASN cc_start: 0.8484 (m-40) cc_final: 0.8239 (m-40)
  outliers start: 48
  outliers final: 35
  residues processed: 180
  average time/residue: 0.0698
  time to fit residues: 15.3113
Evaluate side-chains
  186 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 145
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
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   89 LEU
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   67 LYS
Chi-restraints excluded: chain b residue   75 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  132 TYR
Chi-restraints excluded: chain B residue   22 ASN
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    6 VAL
Chi-restraints excluded: chain A residue   17 GLN
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   60 LYS
Chi-restraints excluded: chain A residue   66 VAL
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  121 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0070
   chunk 30 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   overall best weight:    3.1804

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.090556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.070981 restraints weight = 10745.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.073896 restraints weight = 5057.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.075886 restraints weight = 3172.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.077262 restraints weight = 2345.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.078202 restraints weight = 1921.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.5619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   4778  Z= 0.188
  Angle     :  0.747  10.004   6500  Z= 0.378
  Chirality :  0.048   0.225    758
  Planarity :  0.009   0.137    848
  Dihedral  :  7.210  55.841    690
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  6.72 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 24.04 %
    Favored  : 67.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.20 (0.33), residues: 610
  helix:  0.63 (0.57), residues: 76
  sheet: -1.15 (0.34), residues: 238
  loop : -2.29 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b  24 
 TYR   0.019   0.002   TYR H 113 
 PHE   0.021   0.002   PHE B  96 
 TRP   0.007   0.001   TRP H  50 
 HIS   0.005   0.002   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 4778)
  covalent geometry    : angle       0.74710 ( 6500)
  hydrogen bonds       : bond        0.03223 (  143)
  hydrogen bonds       : angle       5.26025 (  375)

*********************** 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
  198 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 154
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7466 (ptt90) cc_final: 0.5032 (mtt-85)
REVERT: H  116 ASP cc_start: 0.8932 (p0) cc_final: 0.8618 (p0)
REVERT: L   21 ARG cc_start: 0.8329 (ptm-80) cc_final: 0.7545 (ptm-80)
REVERT: L   40 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8046 (tt0)
REVERT: L   52 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8062 (ptmt)
REVERT: L   92 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7519 (tm-30)
REVERT: L  105 THR cc_start: 0.8125 (m) cc_final: 0.7702 (m)
REVERT: L  106 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8247 (mmmm)
REVERT: b   10 ASN cc_start: 0.9144 (m-40) cc_final: 0.8852 (p0)
REVERT: b   14 ASP cc_start: 0.9057 (p0) cc_final: 0.8711 (p0)
REVERT: b   17 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8719 (tp-100)
REVERT: b   37 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8547 (tm-30)
REVERT: b   46 LYS cc_start: 0.8149 (mttm) cc_final: 0.7681 (mttm)
REVERT: b   67 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7491 (mttp)
REVERT: b  122 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7637 (tp)
REVERT: b  129 ASN cc_start: 0.8759 (m110) cc_final: 0.8423 (m110)
REVERT: B   24 ARG cc_start: 0.8809 (mtp-110) cc_final: 0.7621 (tpt170)
REVERT: B   59 ARG cc_start: 0.8103 (ptt180) cc_final: 0.7847 (ptt180)
REVERT: B  115 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8583 (tt)
REVERT: B  127 GLN cc_start: 0.8772 (mp10) cc_final: 0.8019 (mp10)
REVERT: A   16 LYS cc_start: 0.9505 (mmtm) cc_final: 0.9168 (mmpt)
REVERT: A   17 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8697 (mp10)
REVERT: A   69 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6749 (tm130)
REVERT: A  102 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8151 (t70)
REVERT: A  103 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8596 (mt-10)
REVERT: A  129 ASN cc_start: 0.8467 (m-40) cc_final: 0.8207 (m-40)
  outliers start: 44
  outliers final: 33
  residues processed: 179
  average time/residue: 0.0757
  time to fit residues: 16.5230
Evaluate side-chains
  185 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 145
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
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   71 ILE
Chi-restraints excluded: chain H residue   89 LEU
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   67 LYS
Chi-restraints excluded: chain b residue   75 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  132 TYR
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue    6 VAL
Chi-restraints excluded: chain A residue   17 GLN
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   66 VAL
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  121 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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  10 ASN
A  10 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.091051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.071309 restraints weight = 10984.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.074234 restraints weight = 5097.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.076260 restraints weight = 3178.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.077632 restraints weight = 2347.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.078553 restraints weight = 1922.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.5763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   4778  Z= 0.169
  Angle     :  0.744   7.944   6500  Z= 0.378
  Chirality :  0.049   0.221    758
  Planarity :  0.008   0.133    848
  Dihedral  :  6.927  53.939    690
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  6.23 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 25.77 %
    Favored  : 65.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.33), residues: 610
  helix:  0.74 (0.57), residues: 76
  sheet: -1.06 (0.34), residues: 235
  loop : -2.24 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  96 
 TYR   0.016   0.002   TYR A  89 
 PHE   0.014   0.002   PHE B  94 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.004   0.002   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 4778)
  covalent geometry    : angle       0.74446 ( 6500)
  hydrogen bonds       : bond        0.03105 (  143)
  hydrogen bonds       : angle       5.12938 (  375)

*********************** 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
  194 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 150
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7461 (ptt90) cc_final: 0.5035 (mtt-85)
REVERT: H   60 TYR cc_start: 0.8396 (m-80) cc_final: 0.8086 (m-80)
REVERT: H  116 ASP cc_start: 0.8952 (p0) cc_final: 0.8660 (p0)
REVERT: L   21 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.7696 (ptm-80)
REVERT: L   40 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.7950 (tt0)
REVERT: L   52 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8034 (ptmt)
REVERT: L   92 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: L   96 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.7973 (mmm-85)
REVERT: L  105 THR cc_start: 0.8125 (m) cc_final: 0.7693 (m)
REVERT: L  106 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8054 (mmmm)
REVERT: b   10 ASN cc_start: 0.9144 (m-40) cc_final: 0.8873 (p0)
REVERT: b   14 ASP cc_start: 0.9016 (p0) cc_final: 0.8697 (p0)
REVERT: b   17 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8713 (tp-100)
REVERT: b  122 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7651 (tp)
REVERT: b  129 ASN cc_start: 0.8768 (m110) cc_final: 0.8421 (m110)
REVERT: B   24 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.7625 (tpt170)
REVERT: B   59 ARG cc_start: 0.8051 (ptt180) cc_final: 0.7837 (ptt180)
REVERT: B  115 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8594 (tt)
REVERT: B  127 GLN cc_start: 0.8747 (mp10) cc_final: 0.8058 (mp10)
REVERT: B  128 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8653 (mm)
REVERT: A   16 LYS cc_start: 0.9492 (mmtm) cc_final: 0.9142 (mmpt)
REVERT: A   17 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8646 (mp10)
REVERT: A   68 ILE cc_start: 0.8256 (mt) cc_final: 0.8048 (mp)
REVERT: A   69 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6613 (tm130)
REVERT: A  102 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8152 (t70)
REVERT: A  103 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8664 (mt-10)
REVERT: A  129 ASN cc_start: 0.8485 (m-40) cc_final: 0.8213 (m-40)
  outliers start: 44
  outliers final: 28
  residues processed: 173
  average time/residue: 0.0771
  time to fit residues: 16.2504
Evaluate side-chains
  181 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 146
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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   71 ILE
Chi-restraints excluded: chain H residue  111 VAL
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   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   75 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  132 TYR
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   17 GLN
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   66 VAL
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  121 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 51 optimal weight:   20.0000
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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  65 GLN ** 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 = 0.3383 r_free = 0.3383 target = 0.092257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.072413 restraints weight = 10753.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.075392 restraints weight = 5065.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.077413 restraints weight = 3176.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.078796 restraints weight = 2358.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.079672 restraints weight = 1939.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.5937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   4778  Z= 0.154
  Angle     :  0.749   7.907   6500  Z= 0.381
  Chirality :  0.048   0.217    758
  Planarity :  0.008   0.131    848
  Dihedral  :  6.718  51.809    690
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  5.74 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  7.31 %
    Allowed  : 26.35 %
    Favored  : 66.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.33), residues: 610
  helix:  0.71 (0.56), residues: 76
  sheet: -0.94 (0.34), residues: 235
  loop : -2.18 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  96 
 TYR   0.017   0.001   TYR A  89 
 PHE   0.022   0.002   PHE B  96 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.004   0.002   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 4778)
  covalent geometry    : angle       0.74937 ( 6500)
  hydrogen bonds       : bond        0.03001 (  143)
  hydrogen bonds       : angle       5.05280 (  375)

*********************** 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
  190 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 152
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7401 (ptt90) cc_final: 0.5033 (mtt-85)
REVERT: H   60 TYR cc_start: 0.8375 (m-80) cc_final: 0.8041 (m-80)
REVERT: H  116 ASP cc_start: 0.8921 (p0) cc_final: 0.8646 (p0)
REVERT: L   21 ARG cc_start: 0.8454 (ptm-80) cc_final: 0.7727 (ptm-80)
REVERT: L   40 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7981 (tt0)
REVERT: L   52 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8057 (ptmt)
REVERT: L   92 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: L  105 THR cc_start: 0.8134 (m) cc_final: 0.7669 (m)
REVERT: L  106 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8050 (mmmm)
REVERT: b   10 ASN cc_start: 0.9189 (m-40) cc_final: 0.8864 (p0)
REVERT: b   14 ASP cc_start: 0.9027 (p0) cc_final: 0.8721 (p0)
REVERT: b   17 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8704 (tp-100)
REVERT: b  129 ASN cc_start: 0.8767 (m110) cc_final: 0.8425 (m110)
REVERT: B   24 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.7593 (tpt170)
REVERT: B   59 ARG cc_start: 0.7908 (ptt180) cc_final: 0.7679 (ptt180)
REVERT: B  115 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8592 (tt)
REVERT: B  127 GLN cc_start: 0.8798 (mp10) cc_final: 0.8116 (mp10)
REVERT: B  128 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8547 (mm)
REVERT: A   16 LYS cc_start: 0.9510 (mmtm) cc_final: 0.9151 (mmpt)
REVERT: A   17 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8663 (mp10)
REVERT: A  102 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7800 (t0)
REVERT: A  129 ASN cc_start: 0.8476 (m-40) cc_final: 0.8177 (m-40)
  outliers start: 38
  outliers final: 29
  residues processed: 174
  average time/residue: 0.0649
  time to fit residues: 13.9101
Evaluate side-chains
  178 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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   71 ILE
Chi-restraints excluded: chain H residue  111 VAL
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   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  122 ILE
Chi-restraints excluded: chain b residue  125 ILE
Chi-restraints excluded: chain b residue  132 TYR
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   17 GLN
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   66 VAL
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  102 ASP
Chi-restraints excluded: chain A residue  121 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0770
   chunk 16 optimal weight:    0.7980
   overall best weight:    2.1342

-------------------------------------------------------------------------------
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  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  10 ASN
A  10 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.091763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.072016 restraints weight = 11051.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.074981 restraints weight = 5139.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.076982 restraints weight = 3224.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.078340 restraints weight = 2401.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.079171 restraints weight = 1982.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.6053

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     :  0.749   8.522   6500  Z= 0.378
  Chirality :  0.048   0.210    758
  Planarity :  0.008   0.131    848
  Dihedral  :  6.370  52.458    686
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  6.23 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  7.31 %
    Allowed  : 26.73 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.33), residues: 610
  helix:  0.93 (0.58), residues: 76
  sheet: -0.83 (0.35), residues: 235
  loop : -2.14 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  96 
 TYR   0.021   0.002   TYR H 105 
 PHE   0.012   0.002   PHE H  30 
 TRP   0.009   0.001   TRP L  97 
 HIS   0.004   0.002   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 4778)
  covalent geometry    : angle       0.74863 ( 6500)
  hydrogen bonds       : bond        0.03016 (  143)
  hydrogen bonds       : angle       5.02266 (  375)

********************** 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
  184 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 146
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 ARG cc_start: 0.7415 (ptt90) cc_final: 0.5031 (mtt-85)
REVERT: H  116 ASP cc_start: 0.8926 (p0) cc_final: 0.8666 (p0)
REVERT: L   40 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8029 (tt0)
REVERT: L   52 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8049 (ptmt)
REVERT: L   92 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: L   96 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.7854 (mmm-85)
REVERT: L  105 THR cc_start: 0.8193 (m) cc_final: 0.7736 (m)
REVERT: L  106 LYS cc_start: 0.8514 (mmmt) cc_final: 0.7983 (mmmm)
REVERT: b   10 ASN cc_start: 0.9189 (m-40) cc_final: 0.8873 (p0)
REVERT: b   14 ASP cc_start: 0.9047 (p0) cc_final: 0.8544 (p0)
REVERT: b   17 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8444 (tp-100)
REVERT: b   67 LYS cc_start: 0.7897 (mmtp) cc_final: 0.7373 (mmtm)
REVERT: b  129 ASN cc_start: 0.8785 (m110) cc_final: 0.8432 (m110)
REVERT: B   10 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8595 (p0)
REVERT: B   24 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.7599 (tpt170)
REVERT: B   59 ARG cc_start: 0.8040 (ptt180) cc_final: 0.7827 (ptt180)
REVERT: B  115 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8583 (tt)
REVERT: B  127 GLN cc_start: 0.8606 (mp10) cc_final: 0.8061 (mp10)
REVERT: B  128 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8450 (mm)
REVERT: A   16 LYS cc_start: 0.9474 (mmtm) cc_final: 0.9119 (mmpt)
REVERT: A   17 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8623 (mp10)
REVERT: A   69 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6577 (tm130)
REVERT: A  102 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7745 (t0)
REVERT: A  129 ASN cc_start: 0.8468 (m-40) cc_final: 0.8168 (m-40)
  outliers start: 38
  outliers final: 27
  residues processed: 169
  average time/residue: 0.0692
  time to fit residues: 14.2425
Evaluate side-chains
  176 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 142
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
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 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  122 ILE
Chi-restraints excluded: chain b residue  125 ILE
Chi-restraints excluded: chain b residue  132 TYR
Chi-restraints excluded: chain B residue   10 ASN
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain A residue    2 LYS
Chi-restraints excluded: chain A residue   17 GLN
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   66 VAL
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  102 ASP
Chi-restraints excluded: chain A residue  121 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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  65 GLN
** B  10 ASN ** 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 = 0.3379 r_free = 0.3379 target = 0.091791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.072307 restraints weight = 10901.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.075223 restraints weight = 5016.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.077228 restraints weight = 3125.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.078576 restraints weight = 2315.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.079402 restraints weight = 1903.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.6077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.131   4778  Z= 0.253
  Angle     :  1.200  59.185   6500  Z= 0.708
  Chirality :  0.056   0.808    758
  Planarity :  0.009   0.130    848
  Dihedral  :  6.398  52.429    686
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  6.23 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  7.31 %
    Allowed  : 26.73 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.84 (0.33), residues: 610
  helix:  0.94 (0.58), residues: 76
  sheet: -0.83 (0.34), residues: 235
  loop : -2.15 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  96 
 TYR   0.018   0.002   TYR A  89 
 PHE   0.011   0.002   PHE B  94 
 TRP   0.008   0.001   TRP L  97 
 HIS   0.004   0.002   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 4778)
  covalent geometry    : angle       1.20037 ( 6500)
  hydrogen bonds       : bond        0.03046 (  143)
  hydrogen bonds       : angle       5.03683 (  375)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 916.43 seconds
wall clock time: 16 minutes 26.58 seconds (986.58 seconds total)