Starting phenix.real_space_refine
on Tue Feb 11 04:04:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1v_36805/02_2025/8k1v_36805.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1v_36805/02_2025/8k1v_36805.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1v_36805/02_2025/8k1v_36805.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1v_36805/02_2025/8k1v_36805.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1v_36805/02_2025/8k1v_36805.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1v_36805/02_2025/8k1v_36805.cif"
  }
  resolution = 3.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     K       5      8.98       5
     S      32      5.16       5
     C    2706      2.51       5
     N     616      2.21       5
     O     700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4059
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1921
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 4, 'TRANS': 237}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1921
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 4, 'TRANS': 237}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 110
          Unusual residues: {'  K': 5, 'Y01': 3}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
    Chain: "B"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 105
          Unusual residues: {'Y01': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 3.64, per 1000 atoms: 0.90
  Number of scatterers: 4059
  At special positions: 0
  Unit cell: (67.1, 71.5, 90.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       5     19.00
     S      32     16.00
     O     700      8.00
     N     616      7.00
     C    2706      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.21
  Conformation dependent library (CDL) restraints added in 485.3 milliseconds
  

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  896

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      87.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 53
      removed outlier: 5.615A  pdb=" N   ASP A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   HIS A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 70
      removed outlier: 3.718A  pdb=" N   ARG A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 75
    Processing helix  chain 'A' and resid 79 through 92
    Processing helix  chain 'A' and resid 103 through 147
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 155 through 183
    Processing helix  chain 'A' and resid 185 through 198
    Processing helix  chain 'A' and resid 212 through 217
    Processing helix  chain 'A' and resid 217 through 243
    Processing helix  chain 'A' and resid 244 through 247
    Processing helix  chain 'B' and resid 3 through 53
      removed outlier: 5.613A  pdb=" N   ASP B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   HIS B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 70
      removed outlier: 3.706A  pdb=" N   ARG B  60 " --> pdb=" O   SER B  56 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLN B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 75
    Processing helix  chain 'B' and resid 79 through 92
    Processing helix  chain 'B' and resid 103 through 147
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 155 through 183
    Processing helix  chain 'B' and resid 185 through 198
    Processing helix  chain 'B' and resid 212 through 217
    Processing helix  chain 'B' and resid 217 through 243
    Processing helix  chain 'B' and resid 244 through 247

    333 hydrogen bonds defined for protein.
    981 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.14

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 664
        1.33 -     1.45: 1092
        1.45 -     1.57: 2352
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 4156
  Sorted by residual:
  bond pdb=" C   ILE B 118 "
       pdb=" N   PRO B 119 "
    ideal  model  delta    sigma   weight residual
    1.335  1.343 -0.008 1.36e-02 5.41e+03 3.25e-01
  bond pdb=" C   ILE A 118 "
       pdb=" N   PRO A 119 "
    ideal  model  delta    sigma   weight residual
    1.335  1.343 -0.008 1.36e-02 5.41e+03 3.13e-01
  bond pdb=" C   GLU B  70 "
       pdb=" N   PRO B  71 "
    ideal  model  delta    sigma   weight residual
    1.335  1.341 -0.006 1.28e-02 6.10e+03 2.24e-01
  bond pdb=" N   LYS A 211 "
       pdb=" CA  LYS A 211 "
    ideal  model  delta    sigma   weight residual
    1.457  1.463 -0.006 1.29e-02 6.01e+03 2.08e-01
  bond pdb=" CA  LYS B 211 "
       pdb=" CB  LYS B 211 "
    ideal  model  delta    sigma   weight residual
    1.530  1.538 -0.008 1.69e-02 3.50e+03 2.07e-01
  ... (remaining 4151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 5577
        0.98 -     1.96: 48
        1.96 -     2.95: 7
        2.95 -     3.93: 6
        3.93 -     4.91: 6
  Bond angle restraints: 5644
  Sorted by residual:
  angle pdb=" C   THR A 210 "
        pdb=" N   LYS A 211 "
        pdb=" CA  LYS A 211 "
      ideal   model   delta    sigma   weight residual
     121.54  125.66   -4.12 1.91e+00 2.74e-01 4.66e+00
  angle pdb=" C   THR B 210 "
        pdb=" N   LYS B 211 "
        pdb=" CA  LYS B 211 "
      ideal   model   delta    sigma   weight residual
     121.54  125.63   -4.09 1.91e+00 2.74e-01 4.58e+00
  angle pdb=" N   GLY B 117 "
        pdb=" CA  GLY B 117 "
        pdb=" C   GLY B 117 "
      ideal   model   delta    sigma   weight residual
     113.18  116.68   -3.50 2.37e+00 1.78e-01 2.18e+00
  angle pdb=" N   GLY A 117 "
        pdb=" CA  GLY A 117 "
        pdb=" C   GLY A 117 "
      ideal   model   delta    sigma   weight residual
     113.18  116.61   -3.43 2.37e+00 1.78e-01 2.09e+00
  angle pdb=" CA  LYS A 211 "
        pdb=" CB  LYS A 211 "
        pdb=" CG  LYS A 211 "
      ideal   model   delta    sigma   weight residual
     114.10  116.55   -2.45 2.00e+00 2.50e-01 1.50e+00
  ... (remaining 5639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 2406
       16.01 -    32.03: 233
       32.03 -    48.04: 49
       48.04 -    64.06: 12
       64.06 -    80.07: 12
  Dihedral angle restraints: 2712
    sinusoidal: 1310
      harmonic: 1402
  Sorted by residual:
  dihedral pdb=" CG  ARG A   3 "
           pdb=" CD  ARG A   3 "
           pdb=" NE  ARG A   3 "
           pdb=" CZ  ARG A   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -139.67  -40.33     2      1.50e+01 4.44e-03 8.94e+00
  dihedral pdb=" CG  ARG B   3 "
           pdb=" CD  ARG B   3 "
           pdb=" NE  ARG B   3 "
           pdb=" CZ  ARG B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -139.74  -40.26     2      1.50e+01 4.44e-03 8.91e+00
  dihedral pdb=" CB  GLU B 130 "
           pdb=" CG  GLU B 130 "
           pdb=" CD  GLU B 130 "
           pdb=" OE1 GLU B 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   79.78  -79.78     1      3.00e+01 1.11e-03 8.77e+00
  ... (remaining 2709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.021: 451
       0.021 -    0.042: 82
       0.042 -    0.063: 79
       0.063 -    0.085: 20
       0.085 -    0.106: 18
  Chirality restraints: 650
  Sorted by residual:
  chirality pdb=" CA  VAL B 206 "
            pdb=" N   VAL B 206 "
            pdb=" C   VAL B 206 "
            pdb=" CB  VAL B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.80e-01
  chirality pdb=" CA  VAL A 206 "
            pdb=" N   VAL A 206 "
            pdb=" C   VAL A 206 "
            pdb=" CB  VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.10 2.00e-01 2.50e+01 2.73e-01
  chirality pdb=" CA  VAL A  76 "
            pdb=" N   VAL A  76 "
            pdb=" C   VAL A  76 "
            pdb=" CB  VAL A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.54   -0.10 2.00e-01 2.50e+01 2.64e-01
  ... (remaining 647 not shown)

  Planarity restraints: 664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 100 "    0.011 5.00e-02 4.00e+02   1.69e-02 4.58e-01
        pdb=" N   PRO A 101 "   -0.029 5.00e-02 4.00e+02
        pdb=" CA  PRO A 101 "    0.009 5.00e-02 4.00e+02
        pdb=" CD  PRO A 101 "    0.009 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 100 "   -0.010 5.00e-02 4.00e+02   1.52e-02 3.68e-01
        pdb=" N   PRO B 101 "    0.026 5.00e-02 4.00e+02
        pdb=" CA  PRO B 101 "   -0.008 5.00e-02 4.00e+02
        pdb=" CD  PRO B 101 "   -0.008 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 154 "    0.003 2.00e-02 2.50e+03   5.95e-03 3.54e-01
        pdb=" C   VAL A 154 "   -0.010 2.00e-02 2.50e+03
        pdb=" O   VAL A 154 "    0.004 2.00e-02 2.50e+03
        pdb=" N   SER A 155 "    0.003 2.00e-02 2.50e+03
  ... (remaining 661 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.85: 1400
        2.85 -     3.43: 4457
        3.43 -     4.00: 7154
        4.00 -     4.57: 10305
        4.57 -     5.14: 14285
  Nonbonded interactions: 37601
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  96 "
            pdb=" OG1 THR A 196 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" OD2 ASP B  58 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OD2 ASP A  58 "
            pdb=" OH  TYR B  52 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OH  TYR B  96 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" NZ  LYS A 144 "
            pdb=" O   ASP A 153 "
     model   vdw
     2.341 3.120
  ... (remaining 37596 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' and (resid 2 through 248 or resid 301 through 303))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.780
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.180
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
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      :  0.001   0.011   4156  Z= 0.075
  Angle     :  0.315   4.911   5644  Z= 0.164
  Chirality :  0.031   0.106    650
  Planarity :  0.001   0.017    664
  Dihedral  : 13.710  80.074   1816
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.96 (0.37), residues: 476
  helix:  4.59 (0.23), residues: 384
  sheet:  None (None), residues: 0
  loop :  0.62 (0.73), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 184 
 HIS   0.001   0.000   HIS A  72 
 PHE   0.004   0.000   PHE B 109 
 TYR   0.010   0.001   TYR B  18 
 ARG   0.001   0.000   ARG B  47 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A   35 MET cc_start: 0.8058 (ttp) cc_final: 0.7822 (mmm)
REVERT: A   42 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7922 (tppt)
REVERT: A   44 GLU cc_start: 0.8050 (tp30) cc_final: 0.7708 (tp30)
REVERT: A  173 ILE cc_start: 0.7809 (mt) cc_final: 0.7532 (mt)
REVERT: A  180 GLN cc_start: 0.7621 (mm110) cc_final: 0.6825 (tt0)
REVERT: A  182 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7076 (mm-30)
REVERT: B   35 MET cc_start: 0.8050 (ttp) cc_final: 0.7837 (mmm)
REVERT: B   44 GLU cc_start: 0.8068 (tp30) cc_final: 0.7600 (tp30)
REVERT: B  173 ILE cc_start: 0.7803 (mt) cc_final: 0.7525 (mt)
REVERT: B  180 GLN cc_start: 0.7533 (mm110) cc_final: 0.6732 (tt0)
REVERT: B  182 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7119 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2236
  time to fit residues: 30.5334
Evaluate side-chains
  95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.177228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.126124 restraints weight = 4581.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.28
r_work: 0.3236 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4156  Z= 0.221
  Angle     :  0.502   5.798   5644  Z= 0.264
  Chirality :  0.038   0.130    650
  Planarity :  0.003   0.018    664
  Dihedral  :  5.310  31.075    952
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  8.33 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.39 (0.38), residues: 476
  helix:  4.02 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  1.08 (0.87), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 184 
 HIS   0.001   0.000   HIS B 188 
 PHE   0.009   0.001   PHE B 223 
 TYR   0.021   0.002   TYR B  85 
 ARG   0.003   0.001   ARG A  36 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A   35 MET cc_start: 0.8457 (ttp) cc_final: 0.7883 (mmm)
REVERT: A   36 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7446 (mtp180)
REVERT: A   42 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7889 (tppt)
REVERT: A   44 GLU cc_start: 0.8138 (tp30) cc_final: 0.7871 (tp30)
REVERT: A   60 ARG cc_start: 0.8227 (tpp80) cc_final: 0.7957 (tpp80)
REVERT: A   69 SER cc_start: 0.8782 (p) cc_final: 0.8249 (p)
REVERT: A   73 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6884 (mpp80)
REVERT: A  180 GLN cc_start: 0.7626 (mm110) cc_final: 0.6993 (tt0)
REVERT: A  243 VAL cc_start: 0.7777 (t) cc_final: 0.7556 (t)
REVERT: B   35 MET cc_start: 0.8497 (ttp) cc_final: 0.8130 (mmm)
REVERT: B   36 ARG cc_start: 0.8340 (tpp80) cc_final: 0.7604 (mtp180)
REVERT: B   44 GLU cc_start: 0.8149 (tp30) cc_final: 0.7762 (tp30)
REVERT: B  180 GLN cc_start: 0.7660 (mm110) cc_final: 0.6958 (tt0)
  outliers start: 10
  outliers final: 4
  residues processed: 107
  average time/residue: 0.2195
  time to fit residues: 27.4511
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue  134 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    0.0970
   chunk 19 optimal weight:    0.3980
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A  33 HIS
B  33 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.176531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.124841 restraints weight = 4532.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.33
r_work: 0.3220 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4156  Z= 0.157
  Angle     :  0.470   5.616   5644  Z= 0.244
  Chirality :  0.035   0.101    650
  Planarity :  0.002   0.015    664
  Dihedral  :  4.905  30.883    952
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 11.03 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.24 (0.39), residues: 476
  helix:  3.90 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  1.06 (0.86), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP B  78 
 HIS   0.001   0.000   HIS B  72 
 PHE   0.007   0.001   PHE A  16 
 TYR   0.013   0.001   TYR B  85 
 ARG   0.003   0.000   ARG B  60 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7746 (mp)
REVERT: A   35 MET cc_start: 0.8472 (ttp) cc_final: 0.8072 (mtt)
REVERT: A   36 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7471 (mtp180)
REVERT: A   42 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7417 (tppt)
REVERT: A   44 GLU cc_start: 0.8159 (tp30) cc_final: 0.7853 (tp30)
REVERT: A   45 GLU cc_start: 0.7411 (pt0) cc_final: 0.6951 (pp20)
REVERT: A   60 ARG cc_start: 0.8318 (tpp80) cc_final: 0.8057 (tpp80)
REVERT: A  180 GLN cc_start: 0.7590 (mm110) cc_final: 0.6857 (tt0)
REVERT: A  243 VAL cc_start: 0.7822 (t) cc_final: 0.7611 (t)
REVERT: B   19 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7757 (mp)
REVERT: B   35 MET cc_start: 0.8493 (ttp) cc_final: 0.8081 (mmt)
REVERT: B   36 ARG cc_start: 0.8371 (tpp80) cc_final: 0.7686 (mtp180)
REVERT: B   44 GLU cc_start: 0.8161 (tp30) cc_final: 0.7752 (tp30)
REVERT: B   58 ASP cc_start: 0.8277 (m-30) cc_final: 0.8039 (t0)
REVERT: B  180 GLN cc_start: 0.7602 (mm110) cc_final: 0.6853 (tt0)
REVERT: B  243 VAL cc_start: 0.7828 (t) cc_final: 0.7612 (t)
  outliers start: 10
  outliers final: 6
  residues processed: 107
  average time/residue: 0.2332
  time to fit residues: 29.2737
Evaluate side-chains
  93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain B residue  206 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3810 r_free = 0.3810 target = 0.164486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.117267 restraints weight = 4549.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.26
r_work: 0.3099 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4156  Z= 0.197
  Angle     :  0.500   5.558   5644  Z= 0.263
  Chirality :  0.036   0.108    650
  Planarity :  0.002   0.014    664
  Dihedral  :  4.718  36.276    952
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.95 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.06 (0.38), residues: 476
  helix:  3.83 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.75 (0.81), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  78 
 HIS   0.000   0.000   HIS B  98 
 PHE   0.009   0.001   PHE A  16 
 TYR   0.019   0.002   TYR B  85 
 ARG   0.004   0.000   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7603 (mp)
REVERT: A   35 MET cc_start: 0.8573 (ttp) cc_final: 0.7962 (mmt)
REVERT: A   42 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7389 (tppt)
REVERT: A   44 GLU cc_start: 0.8137 (tp30) cc_final: 0.7820 (tp30)
REVERT: A   45 GLU cc_start: 0.7598 (pt0) cc_final: 0.7104 (pp20)
REVERT: A   60 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8159 (tpp80)
REVERT: A  180 GLN cc_start: 0.7521 (mm110) cc_final: 0.6981 (tt0)
REVERT: A  243 VAL cc_start: 0.7714 (t) cc_final: 0.7504 (t)
REVERT: B   19 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7527 (mp)
REVERT: B   31 SER cc_start: 0.8373 (p) cc_final: 0.8056 (m)
REVERT: B   35 MET cc_start: 0.8516 (ttp) cc_final: 0.7996 (mmt)
REVERT: B   36 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7595 (mtp180)
REVERT: B   44 GLU cc_start: 0.8136 (tp30) cc_final: 0.7729 (tp30)
REVERT: B   58 ASP cc_start: 0.8274 (m-30) cc_final: 0.7979 (t0)
REVERT: B  180 GLN cc_start: 0.7532 (mm110) cc_final: 0.6990 (tt0)
REVERT: B  243 VAL cc_start: 0.7690 (t) cc_final: 0.7489 (t)
  outliers start: 11
  outliers final: 6
  residues processed: 103
  average time/residue: 0.2382
  time to fit residues: 28.5624
Evaluate side-chains
  94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  206 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.164379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.117151 restraints weight = 4631.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.29
r_work: 0.3066 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.3971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4156  Z= 0.178
  Angle     :  0.508   5.980   5644  Z= 0.263
  Chirality :  0.035   0.110    650
  Planarity :  0.002   0.018    664
  Dihedral  :  4.680  39.176    952
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.67 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.02 (0.38), residues: 476
  helix:  3.80 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.75 (0.82), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 184 
 HIS   0.000   0.000   HIS B  72 
 PHE   0.008   0.001   PHE B 109 
 TYR   0.012   0.001   TYR B  85 
 ARG   0.004   0.001   ARG B  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7509 (mp)
REVERT: A   31 SER cc_start: 0.8400 (p) cc_final: 0.8044 (m)
REVERT: A   35 MET cc_start: 0.8606 (ttp) cc_final: 0.7851 (mmt)
REVERT: A   42 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7423 (tppt)
REVERT: A   44 GLU cc_start: 0.8059 (tp30) cc_final: 0.7746 (tp30)
REVERT: A   45 GLU cc_start: 0.7567 (pt0) cc_final: 0.7081 (pp20)
REVERT: A   60 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8132 (tpp80)
REVERT: A  180 GLN cc_start: 0.7505 (mm110) cc_final: 0.6985 (tt0)
REVERT: A  243 VAL cc_start: 0.7706 (t) cc_final: 0.7487 (t)
REVERT: B   19 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7621 (mp)
REVERT: B   31 SER cc_start: 0.8388 (p) cc_final: 0.8056 (m)
REVERT: B   35 MET cc_start: 0.8511 (ttp) cc_final: 0.7984 (mmt)
REVERT: B   36 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7568 (mtp180)
REVERT: B   44 GLU cc_start: 0.8144 (tp30) cc_final: 0.7745 (tp30)
REVERT: B  180 GLN cc_start: 0.7517 (mm110) cc_final: 0.6998 (tt0)
REVERT: B  243 VAL cc_start: 0.7684 (t) cc_final: 0.7461 (t)
  outliers start: 11
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2309
  time to fit residues: 27.5131
Evaluate side-chains
  99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  206 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 36 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0020
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.4588

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.165529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.117936 restraints weight = 4548.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.31
r_work: 0.3063 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   4156  Z= 0.155
  Angle     :  0.508   6.632   5644  Z= 0.257
  Chirality :  0.035   0.107    650
  Planarity :  0.002   0.018    664
  Dihedral  :  4.577  41.012    952
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.91 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.07 (0.38), residues: 476
  helix:  3.83 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.75 (0.82), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 184 
 HIS   0.000   0.000   HIS A  72 
 PHE   0.008   0.001   PHE B 109 
 TYR   0.014   0.001   TYR B 138 
 ARG   0.004   0.001   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.534 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7517 (mp)
REVERT: A   31 SER cc_start: 0.8393 (p) cc_final: 0.8074 (p)
REVERT: A   35 MET cc_start: 0.8580 (ttp) cc_final: 0.7802 (mmt)
REVERT: A   42 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7470 (tppt)
REVERT: A   44 GLU cc_start: 0.8055 (tp30) cc_final: 0.7739 (tp30)
REVERT: A   45 GLU cc_start: 0.7535 (pt0) cc_final: 0.7073 (pp20)
REVERT: A  180 GLN cc_start: 0.7372 (mm110) cc_final: 0.6837 (tt0)
REVERT: A  243 VAL cc_start: 0.7682 (t) cc_final: 0.7479 (t)
REVERT: B   19 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7528 (mp)
REVERT: B   31 SER cc_start: 0.8402 (p) cc_final: 0.8058 (m)
REVERT: B   35 MET cc_start: 0.8515 (ttp) cc_final: 0.7978 (mmt)
REVERT: B   36 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7572 (mtp180)
REVERT: B   44 GLU cc_start: 0.8145 (tp30) cc_final: 0.7755 (tp30)
REVERT: B  180 GLN cc_start: 0.7404 (mm110) cc_final: 0.6878 (tt0)
REVERT: B  243 VAL cc_start: 0.7614 (t) cc_final: 0.7402 (t)
  outliers start: 11
  outliers final: 9
  residues processed: 106
  average time/residue: 0.2404
  time to fit residues: 30.1429
Evaluate side-chains
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  206 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 17 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.162687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.114741 restraints weight = 4577.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.28
r_work: 0.3077 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4156  Z= 0.186
  Angle     :  0.537   6.353   5644  Z= 0.272
  Chirality :  0.036   0.111    650
  Planarity :  0.002   0.018    664
  Dihedral  :  4.642  41.833    952
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.87 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.04 (0.38), residues: 476
  helix:  3.81 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.74 (0.81), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  78 
 HIS   0.000   0.000   HIS A  72 
 PHE   0.008   0.001   PHE B 109 
 TYR   0.014   0.001   TYR A 138 
 ARG   0.004   0.000   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7518 (mp)
REVERT: A   31 SER cc_start: 0.8452 (p) cc_final: 0.8158 (p)
REVERT: A   35 MET cc_start: 0.8588 (ttp) cc_final: 0.7844 (mmt)
REVERT: A   42 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7949 (tppt)
REVERT: A   44 GLU cc_start: 0.8079 (tp30) cc_final: 0.7725 (tp30)
REVERT: A  180 GLN cc_start: 0.7418 (mm110) cc_final: 0.6882 (tt0)
REVERT: A  243 VAL cc_start: 0.7753 (t) cc_final: 0.7529 (t)
REVERT: B   19 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7578 (mp)
REVERT: B   31 SER cc_start: 0.8415 (p) cc_final: 0.8070 (m)
REVERT: B   35 MET cc_start: 0.8521 (ttp) cc_final: 0.7995 (mmt)
REVERT: B   36 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7612 (mtp180)
REVERT: B   44 GLU cc_start: 0.8205 (tp30) cc_final: 0.7854 (tp30)
REVERT: B  180 GLN cc_start: 0.7429 (mm110) cc_final: 0.6904 (tt0)
REVERT: B  243 VAL cc_start: 0.7738 (t) cc_final: 0.7512 (t)
  outliers start: 11
  outliers final: 9
  residues processed: 103
  average time/residue: 0.2403
  time to fit residues: 29.0006
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  206 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.160380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.112309 restraints weight = 4524.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.27
r_work: 0.3001 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4156  Z= 0.206
  Angle     :  0.555   6.702   5644  Z= 0.283
  Chirality :  0.036   0.113    650
  Planarity :  0.002   0.018    664
  Dihedral  :  4.776  43.089    952
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.87 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.95 (0.38), residues: 476
  helix:  3.77 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.60 (0.80), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 184 
 HIS   0.001   0.000   HIS B  98 
 PHE   0.009   0.001   PHE B  16 
 TYR   0.013   0.001   TYR B 138 
 ARG   0.004   0.001   ARG A  60 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7535 (mp)
REVERT: A   31 SER cc_start: 0.8421 (p) cc_final: 0.8115 (p)
REVERT: A   35 MET cc_start: 0.8617 (ttp) cc_final: 0.7845 (mmt)
REVERT: A   42 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7944 (tppt)
REVERT: A   44 GLU cc_start: 0.8089 (tp30) cc_final: 0.7643 (tp30)
REVERT: A  180 GLN cc_start: 0.7461 (mm110) cc_final: 0.6907 (tt0)
REVERT: A  243 VAL cc_start: 0.7652 (t) cc_final: 0.7414 (t)
REVERT: B   19 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7601 (mp)
REVERT: B   31 SER cc_start: 0.8417 (p) cc_final: 0.8009 (m)
REVERT: B   35 MET cc_start: 0.8529 (ttp) cc_final: 0.7961 (mmt)
REVERT: B   36 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7564 (mtp180)
REVERT: B   44 GLU cc_start: 0.8211 (tp30) cc_final: 0.7864 (tp30)
REVERT: B   60 ARG cc_start: 0.8296 (tpp80) cc_final: 0.8094 (tpp80)
REVERT: B  180 GLN cc_start: 0.7503 (mm110) cc_final: 0.6997 (tt0)
REVERT: B  243 VAL cc_start: 0.7636 (t) cc_final: 0.7396 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 104
  average time/residue: 0.2535
  time to fit residues: 30.5933
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  206 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3747 r_free = 0.3747 target = 0.159155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.111124 restraints weight = 4611.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.32
r_work: 0.2987 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4156  Z= 0.221
  Angle     :  0.563   7.735   5644  Z= 0.288
  Chirality :  0.037   0.118    650
  Planarity :  0.002   0.018    664
  Dihedral  :  4.872  43.955    952
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.38 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.86 (0.38), residues: 476
  helix:  3.70 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.60 (0.79), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  78 
 HIS   0.000   0.000   HIS A  72 
 PHE   0.010   0.001   PHE A 109 
 TYR   0.012   0.001   TYR A 138 
 ARG   0.004   0.000   ARG A  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7588 (mp)
REVERT: A   31 SER cc_start: 0.8418 (p) cc_final: 0.7984 (m)
REVERT: A   35 MET cc_start: 0.8632 (ttp) cc_final: 0.7861 (mmt)
REVERT: A   42 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7957 (tppt)
REVERT: A   44 GLU cc_start: 0.8148 (tp30) cc_final: 0.7764 (tp30)
REVERT: A  180 GLN cc_start: 0.7527 (mm110) cc_final: 0.6948 (tt0)
REVERT: A  243 VAL cc_start: 0.7703 (t) cc_final: 0.7464 (t)
REVERT: B   19 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7609 (mp)
REVERT: B   31 SER cc_start: 0.8463 (p) cc_final: 0.8065 (m)
REVERT: B   35 MET cc_start: 0.8545 (ttp) cc_final: 0.8004 (mmt)
REVERT: B   36 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7556 (mtp180)
REVERT: B   44 GLU cc_start: 0.8219 (tp30) cc_final: 0.7863 (tp30)
REVERT: B  180 GLN cc_start: 0.7523 (mm110) cc_final: 0.6964 (tt0)
REVERT: B  243 VAL cc_start: 0.7655 (t) cc_final: 0.7415 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 101
  average time/residue: 0.2240
  time to fit residues: 26.4472
Evaluate side-chains
  101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  206 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.157315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.110357 restraints weight = 4618.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.29
r_work: 0.2986 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.4786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4156  Z= 0.239
  Angle     :  0.564   6.850   5644  Z= 0.295
  Chirality :  0.037   0.117    650
  Planarity :  0.003   0.018    664
  Dihedral  :  4.999  44.372    952
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.12 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.70 (0.38), residues: 476
  helix:  3.63 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.36 (0.77), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  78 
 HIS   0.000   0.000   HIS A  72 
 PHE   0.009   0.001   PHE A  16 
 TYR   0.015   0.002   TYR B 138 
 ARG   0.005   0.001   ARG B  73 

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7636 (mp)
REVERT: A   31 SER cc_start: 0.8450 (p) cc_final: 0.8065 (m)
REVERT: A   35 MET cc_start: 0.8652 (ttp) cc_final: 0.7914 (mmt)
REVERT: A   42 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7952 (tppt)
REVERT: A   44 GLU cc_start: 0.8124 (tp30) cc_final: 0.7746 (tp30)
REVERT: A  180 GLN cc_start: 0.7536 (mm110) cc_final: 0.6952 (tt0)
REVERT: A  243 VAL cc_start: 0.7747 (t) cc_final: 0.7509 (t)
REVERT: B   19 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7642 (mp)
REVERT: B   31 SER cc_start: 0.8469 (p) cc_final: 0.8097 (m)
REVERT: B   35 MET cc_start: 0.8608 (ttp) cc_final: 0.7964 (mmt)
REVERT: B   36 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7544 (mtp180)
REVERT: B   44 GLU cc_start: 0.8235 (tp30) cc_final: 0.7872 (tp30)
REVERT: B  180 GLN cc_start: 0.7588 (mm110) cc_final: 0.7008 (tt0)
REVERT: B  243 VAL cc_start: 0.7730 (t) cc_final: 0.7491 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 102
  average time/residue: 0.2209
  time to fit residues: 26.3846
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  206 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.158185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.111571 restraints weight = 4602.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.28
r_work: 0.2991 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4156  Z= 0.210
  Angle     :  0.556   6.575   5644  Z= 0.285
  Chirality :  0.036   0.110    650
  Planarity :  0.003   0.019    664
  Dihedral  :  4.997  45.268    952
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.61 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.74 (0.38), residues: 476
  helix:  3.66 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.34 (0.77), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 184 
 HIS   0.000   0.000   HIS A  72 
 PHE   0.010   0.001   PHE A 109 
 TYR   0.014   0.002   TYR A 138 
 ARG   0.004   0.001   ARG B  73 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2052.43 seconds
wall clock time: 37 minutes 15.87 seconds (2235.87 seconds total)