Starting phenix.real_space_refine
on Fri Aug 22 14:22:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1v_36805/08_2025/8k1v_36805.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1v_36805/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1v_36805/08_2025/8k1v_36805.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1v_36805/08_2025/8k1v_36805.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1v_36805/08_2025/8k1v_36805.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1v_36805/08_2025/8k1v_36805.map"
  }
  resolution = 3.48
  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=   0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.12, per 1000 atoms: 0.28
  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: 0.26
  Conformation dependent library (CDL) restraints added in 91.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.09
  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: 0.58

  Time building geometry restraints manager: 0.34 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 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:             0.700
  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:                    0.010
  Process input model:                     5.500
  Find NCS groups from input model:        0.060
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.650
-------------------------------------------------------------------------------
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= 0.069
  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 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:  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
 ARG   0.001   0.000   ARG B  47 
 TYR   0.010   0.001   TYR B  18 
 PHE   0.004   0.000   PHE B 109 
 TRP   0.001   0.000   TRP B 184 
 HIS   0.001   0.000   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00115 ( 4156)
  covalent geometry    : angle       0.31478 ( 5644)
  hydrogen bonds       : bond        0.09497 (  333)
  hydrogen bonds       : angle       3.99682 (  981)

*********************** 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  : 0.129 
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: 0.0965
  time to fit residues: 13.2103
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  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.180060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.128934 restraints weight = 4635.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.34
r_work: 0.3246 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4156  Z= 0.131
  Angle     :  0.487   5.743   5644  Z= 0.256
  Chirality :  0.037   0.126    650
  Planarity :  0.003   0.019    664
  Dihedral  :  5.369  31.456    952
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  8.09 %
    Favored  : 89.46 %
  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:  5.40 (0.39), residues: 476
  helix:  4.03 (0.23), residues: 390
  sheet:  None (None), residues: 0
  loop :  1.03 (0.88), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  60 
 TYR   0.017   0.001   TYR B  85 
 PHE   0.009   0.001   PHE B 223 
 TRP   0.003   0.001   TRP A  78 
 HIS   0.001   0.000   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 4156)
  covalent geometry    : angle       0.48680 ( 5644)
  hydrogen bonds       : bond        0.03601 (  333)
  hydrogen bonds       : angle       3.49588 (  981)

*********************** 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
  113 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   35 MET cc_start: 0.8444 (ttp) cc_final: 0.7965 (mmm)
REVERT: A   36 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7457 (mtp180)
REVERT: A   42 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7898 (tppt)
REVERT: A   44 GLU cc_start: 0.8133 (tp30) cc_final: 0.7886 (tp30)
REVERT: A   60 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7914 (tpp80)
REVERT: A   69 SER cc_start: 0.8824 (p) cc_final: 0.8263 (p)
REVERT: A   73 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.6860 (mpp80)
REVERT: A  180 GLN cc_start: 0.7620 (mm110) cc_final: 0.6857 (tt0)
REVERT: B   35 MET cc_start: 0.8499 (ttp) cc_final: 0.8074 (mmm)
REVERT: B   36 ARG cc_start: 0.8360 (tpp80) cc_final: 0.7668 (mtp180)
REVERT: B   44 GLU cc_start: 0.8148 (tp30) cc_final: 0.7769 (tp30)
REVERT: B   60 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7877 (tpp80)
REVERT: B  180 GLN cc_start: 0.7659 (mm110) cc_final: 0.6938 (tt0)
  outliers start: 10
  outliers final: 3
  residues processed: 109
  average time/residue: 0.1042
  time to fit residues: 13.3762
Evaluate side-chains
  101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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  134 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0670
   chunk 26 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0270
   chunk 40 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.170455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.119004 restraints weight = 4550.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.28
r_work: 0.3150 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4156  Z= 0.160
  Angle     :  0.530   6.819   5644  Z= 0.276
  Chirality :  0.037   0.108    650
  Planarity :  0.003   0.017    664
  Dihedral  :  4.951  34.166    952
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 11.27 %
    Favored  : 85.54 %
  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:  5.04 (0.38), residues: 476
  helix:  3.78 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.96 (0.84), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 131 
 TYR   0.023   0.002   TYR A  85 
 PHE   0.010   0.001   PHE B  16 
 TRP   0.003   0.001   TRP B  78 
 HIS   0.001   0.000   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 4156)
  covalent geometry    : angle       0.52954 ( 5644)
  hydrogen bonds       : bond        0.04576 (  333)
  hydrogen bonds       : angle       3.49103 (  981)

*********************** 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
  113 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7838 (mp)
REVERT: A   35 MET cc_start: 0.8497 (ttp) cc_final: 0.7989 (mmt)
REVERT: A   36 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7509 (mtp180)
REVERT: A   44 GLU cc_start: 0.8225 (tp30) cc_final: 0.7875 (tp30)
REVERT: A   60 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8106 (tpp80)
REVERT: A  180 GLN cc_start: 0.7741 (mm110) cc_final: 0.7035 (tt0)
REVERT: A  243 VAL cc_start: 0.7940 (t) cc_final: 0.7729 (t)
REVERT: B   19 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7849 (mp)
REVERT: B   31 SER cc_start: 0.8382 (p) cc_final: 0.8129 (m)
REVERT: B   35 MET cc_start: 0.8490 (ttp) cc_final: 0.8129 (mmt)
REVERT: B   36 ARG cc_start: 0.8382 (tpp80) cc_final: 0.7625 (mtp180)
REVERT: B   44 GLU cc_start: 0.8230 (tp30) cc_final: 0.7858 (tp30)
REVERT: B  180 GLN cc_start: 0.7748 (mm110) cc_final: 0.7041 (tt0)
REVERT: B  243 VAL cc_start: 0.7957 (t) cc_final: 0.7739 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 110
  average time/residue: 0.1066
  time to fit residues: 13.6931
Evaluate side-chains
  86 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
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  134 THR
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 23 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3773 r_free = 0.3773 target = 0.161674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.115739 restraints weight = 4505.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.22
r_work: 0.3065 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3951

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= 0.131
  Angle     :  0.497   5.633   5644  Z= 0.263
  Chirality :  0.035   0.113    650
  Planarity :  0.002   0.016    664
  Dihedral  :  4.774  36.683    952
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 13.48 %
    Favored  : 83.33 %
  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:  4.93 (0.38), residues: 476
  helix:  3.72 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.82 (0.81), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  73 
 TYR   0.013   0.001   TYR B  85 
 PHE   0.008   0.001   PHE B 109 
 TRP   0.002   0.001   TRP B  78 
 HIS   0.001   0.000   HIS B  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4156)
  covalent geometry    : angle       0.49652 ( 5644)
  hydrogen bonds       : bond        0.04269 (  333)
  hydrogen bonds       : angle       3.53431 (  981)

*********************** 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
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7518 (mp)
REVERT: A   31 SER cc_start: 0.8394 (p) cc_final: 0.8024 (m)
REVERT: A   35 MET cc_start: 0.8571 (ttp) cc_final: 0.7966 (mmt)
REVERT: A   44 GLU cc_start: 0.8183 (tp30) cc_final: 0.7842 (tp30)
REVERT: A   45 GLU cc_start: 0.7467 (pt0) cc_final: 0.7038 (pp20)
REVERT: A   60 ARG cc_start: 0.8403 (tpp80) cc_final: 0.8137 (tpp80)
REVERT: A  180 GLN cc_start: 0.7489 (mm110) cc_final: 0.6953 (tt0)
REVERT: A  243 VAL cc_start: 0.7702 (t) cc_final: 0.7483 (t)
REVERT: B   31 SER cc_start: 0.8383 (p) cc_final: 0.8050 (m)
REVERT: B   35 MET cc_start: 0.8510 (ttp) cc_final: 0.7997 (mmt)
REVERT: B   36 ARG cc_start: 0.8273 (tpp80) cc_final: 0.7538 (mtp180)
REVERT: B   40 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8151 (ttmm)
REVERT: B   44 GLU cc_start: 0.8145 (tp30) cc_final: 0.7735 (tp30)
REVERT: B   57 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7861 (pm20)
REVERT: B   64 LEU cc_start: 0.8830 (mp) cc_final: 0.8544 (mm)
REVERT: B  180 GLN cc_start: 0.7497 (mm110) cc_final: 0.6960 (tt0)
REVERT: B  243 VAL cc_start: 0.7681 (t) cc_final: 0.7463 (t)
  outliers start: 13
  outliers final: 9
  residues processed: 101
  average time/residue: 0.1067
  time to fit residues: 12.6118
Evaluate side-chains
  84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   88 ILE
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   32 ASP
Chi-restraints excluded: chain B residue   57 GLU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 7 optimal weight:    0.3980
   chunk 36 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3756 r_free = 0.3756 target = 0.160266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.115194 restraints weight = 4516.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.20
r_work: 0.3053 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.4178

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= 0.134
  Angle     :  0.539   6.663   5644  Z= 0.272
  Chirality :  0.036   0.110    650
  Planarity :  0.002   0.016    664
  Dihedral  :  4.746  39.841    952
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.42 %
    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 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:  4.88 (0.38), residues: 476
  helix:  3.69 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.77 (0.79), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  36 
 TYR   0.013   0.001   TYR B  85 
 PHE   0.008   0.001   PHE A  16 
 TRP   0.002   0.001   TRP B 184 
 HIS   0.001   0.000   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4156)
  covalent geometry    : angle       0.53939 ( 5644)
  hydrogen bonds       : bond        0.04309 (  333)
  hydrogen bonds       : angle       3.51226 (  981)

*********************** 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
  99 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7481 (mp)
REVERT: A   31 SER cc_start: 0.8403 (p) cc_final: 0.7942 (m)
REVERT: A   35 MET cc_start: 0.8578 (ttp) cc_final: 0.7820 (mmt)
REVERT: A   44 GLU cc_start: 0.8181 (tp30) cc_final: 0.7871 (tp30)
REVERT: A   45 GLU cc_start: 0.7320 (pt0) cc_final: 0.6928 (pp20)
REVERT: A   60 ARG cc_start: 0.8420 (tpp80) cc_final: 0.8148 (tpp80)
REVERT: A  180 GLN cc_start: 0.7516 (mm110) cc_final: 0.6990 (tt0)
REVERT: A  243 VAL cc_start: 0.7718 (t) cc_final: 0.7497 (t)
REVERT: B   31 SER cc_start: 0.8395 (p) cc_final: 0.7941 (m)
REVERT: B   35 MET cc_start: 0.8522 (ttp) cc_final: 0.8006 (mmm)
REVERT: B   36 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7579 (mtp180)
REVERT: B   44 GLU cc_start: 0.8154 (tp30) cc_final: 0.7749 (tp30)
REVERT: B  180 GLN cc_start: 0.7530 (mm110) cc_final: 0.7007 (tt0)
REVERT: B  243 VAL cc_start: 0.7723 (t) cc_final: 0.7500 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1112
  time to fit residues: 12.7348
Evaluate side-chains
  90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   88 ILE
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   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 18 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 39 optimal weight:    0.2980
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3773 r_free = 0.3773 target = 0.161582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.114472 restraints weight = 4647.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.30
r_work: 0.3071 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.4324

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= 0.130
  Angle     :  0.520   6.044   5644  Z= 0.267
  Chirality :  0.036   0.112    650
  Planarity :  0.002   0.017    664
  Dihedral  :  4.692  41.469    952
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.93 %
    Favored  : 81.13 %
  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:  4.88 (0.38), residues: 476
  helix:  3.70 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.72 (0.79), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  73 
 TYR   0.014   0.001   TYR B 138 
 PHE   0.009   0.001   PHE B 109 
 TRP   0.003   0.001   TRP B 184 
 HIS   0.001   0.000   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4156)
  covalent geometry    : angle       0.51982 ( 5644)
  hydrogen bonds       : bond        0.04294 (  333)
  hydrogen bonds       : angle       3.51273 (  981)

*********************** 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
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7472 (mp)
REVERT: A   31 SER cc_start: 0.8443 (p) cc_final: 0.7869 (m)
REVERT: A   35 MET cc_start: 0.8595 (ttp) cc_final: 0.7881 (mmm)
REVERT: A   44 GLU cc_start: 0.8176 (tp30) cc_final: 0.7888 (tp30)
REVERT: A   45 GLU cc_start: 0.7348 (pt0) cc_final: 0.6996 (pp20)
REVERT: A  180 GLN cc_start: 0.7451 (mm110) cc_final: 0.6963 (tt0)
REVERT: A  243 VAL cc_start: 0.7723 (t) cc_final: 0.7513 (t)
REVERT: B   19 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7463 (mp)
REVERT: B   31 SER cc_start: 0.8420 (p) cc_final: 0.7880 (m)
REVERT: B   35 MET cc_start: 0.8501 (ttp) cc_final: 0.7984 (mmm)
REVERT: B   36 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7581 (mtp180)
REVERT: B   44 GLU cc_start: 0.8202 (tp30) cc_final: 0.7853 (tp30)
REVERT: B  180 GLN cc_start: 0.7463 (mm110) cc_final: 0.6997 (tt0)
REVERT: B  243 VAL cc_start: 0.7774 (t) cc_final: 0.7563 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 98
  average time/residue: 0.1116
  time to fit residues: 12.7386
Evaluate side-chains
  102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
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   88 ILE
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 35 optimal weight:    0.3980
   chunk 41 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.162117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.115096 restraints weight = 4640.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.28
r_work: 0.3070 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4423

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= 0.131
  Angle     :  0.539   7.309   5644  Z= 0.273
  Chirality :  0.036   0.111    650
  Planarity :  0.002   0.018    664
  Dihedral  :  4.703  42.805    952
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.40 %
    Favored  : 79.66 %
  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:  4.87 (0.38), residues: 476
  helix:  3.70 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.62 (0.80), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  73 
 TYR   0.012   0.001   TYR B 138 
 PHE   0.009   0.001   PHE B 109 
 TRP   0.003   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4156)
  covalent geometry    : angle       0.53933 ( 5644)
  hydrogen bonds       : bond        0.04311 (  333)
  hydrogen bonds       : angle       3.49633 (  981)

*********************** 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
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7511 (mp)
REVERT: A   31 SER cc_start: 0.8485 (p) cc_final: 0.8026 (m)
REVERT: A   35 MET cc_start: 0.8609 (ttp) cc_final: 0.7857 (mmt)
REVERT: A   44 GLU cc_start: 0.8111 (tp30) cc_final: 0.7840 (tp30)
REVERT: A   45 GLU cc_start: 0.7349 (pt0) cc_final: 0.6911 (pp20)
REVERT: A  180 GLN cc_start: 0.7449 (mm110) cc_final: 0.6967 (tt0)
REVERT: A  243 VAL cc_start: 0.7757 (t) cc_final: 0.7530 (t)
REVERT: B   19 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7459 (mp)
REVERT: B   31 SER cc_start: 0.8454 (p) cc_final: 0.8035 (m)
REVERT: B   35 MET cc_start: 0.8548 (ttp) cc_final: 0.7942 (mmt)
REVERT: B   36 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7597 (mtp180)
REVERT: B   44 GLU cc_start: 0.8218 (tp30) cc_final: 0.7853 (tp30)
REVERT: B  180 GLN cc_start: 0.7465 (mm110) cc_final: 0.6992 (tt0)
REVERT: B  243 VAL cc_start: 0.7779 (t) cc_final: 0.7563 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 103
  average time/residue: 0.1061
  time to fit residues: 12.7855
Evaluate side-chains
  102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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   88 ILE
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 4 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0470
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.7078

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.161513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.114341 restraints weight = 4552.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.26
r_work: 0.3010 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4156  Z= 0.135
  Angle     :  0.543   7.426   5644  Z= 0.277
  Chirality :  0.036   0.111    650
  Planarity :  0.002   0.018    664
  Dihedral  :  4.727  43.761    952
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.40 %
    Favored  : 79.66 %
  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:  4.82 (0.38), residues: 476
  helix:  3.68 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.58 (0.79), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  73 
 TYR   0.011   0.001   TYR B 138 
 PHE   0.009   0.001   PHE B 109 
 TRP   0.003   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4156)
  covalent geometry    : angle       0.54265 ( 5644)
  hydrogen bonds       : bond        0.04423 (  333)
  hydrogen bonds       : angle       3.52577 (  981)

*********************** 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
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7487 (mp)
REVERT: A   31 SER cc_start: 0.8503 (p) cc_final: 0.8047 (m)
REVERT: A   35 MET cc_start: 0.8626 (ttp) cc_final: 0.7866 (mmt)
REVERT: A   44 GLU cc_start: 0.8095 (tp30) cc_final: 0.7832 (tp30)
REVERT: A   45 GLU cc_start: 0.7460 (pt0) cc_final: 0.7018 (pp20)
REVERT: A  180 GLN cc_start: 0.7453 (mm110) cc_final: 0.6960 (tt0)
REVERT: A  243 VAL cc_start: 0.7612 (t) cc_final: 0.7373 (t)
REVERT: B   19 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7462 (mp)
REVERT: B   31 SER cc_start: 0.8460 (p) cc_final: 0.8028 (m)
REVERT: B   35 MET cc_start: 0.8563 (ttp) cc_final: 0.7972 (mmt)
REVERT: B   36 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7590 (mtp180)
REVERT: B   44 GLU cc_start: 0.8210 (tp30) cc_final: 0.7872 (tp30)
REVERT: B  180 GLN cc_start: 0.7468 (mm110) cc_final: 0.6979 (tt0)
REVERT: B  243 VAL cc_start: 0.7671 (t) cc_final: 0.7446 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 101
  average time/residue: 0.0923
  time to fit residues: 11.0141
Evaluate side-chains
  102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
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   88 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 27 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 = 0.3760 r_free = 0.3760 target = 0.160606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.113042 restraints weight = 4644.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.30
r_work: 0.2995 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.4666

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= 0.143
  Angle     :  0.549   6.159   5644  Z= 0.281
  Chirality :  0.036   0.107    650
  Planarity :  0.002   0.024    664
  Dihedral  :  4.787  44.238    952
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.91 %
    Favored  : 79.66 %
  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:  4.74 (0.38), residues: 476
  helix:  3.63 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.49 (0.79), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  73 
 TYR   0.012   0.001   TYR B 138 
 PHE   0.009   0.001   PHE A 109 
 TRP   0.002   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4156)
  covalent geometry    : angle       0.54869 ( 5644)
  hydrogen bonds       : bond        0.04589 (  333)
  hydrogen bonds       : angle       3.55274 (  981)

*********************** 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
  107 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7504 (mp)
REVERT: A   31 SER cc_start: 0.8421 (p) cc_final: 0.7971 (m)
REVERT: A   35 MET cc_start: 0.8629 (ttp) cc_final: 0.7954 (mmt)
REVERT: A   44 GLU cc_start: 0.8108 (tp30) cc_final: 0.7748 (tp30)
REVERT: A  128 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7444 (mp)
REVERT: A  180 GLN cc_start: 0.7491 (mm110) cc_final: 0.6991 (tt0)
REVERT: A  243 VAL cc_start: 0.7638 (t) cc_final: 0.7397 (t)
REVERT: B   19 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7484 (mp)
REVERT: B   31 SER cc_start: 0.8456 (p) cc_final: 0.8050 (m)
REVERT: B   35 MET cc_start: 0.8594 (ttp) cc_final: 0.7942 (mmt)
REVERT: B   36 ARG cc_start: 0.8214 (tpp80) cc_final: 0.7578 (mtp180)
REVERT: B   44 GLU cc_start: 0.8198 (tp30) cc_final: 0.7855 (tp30)
REVERT: B  128 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7417 (mp)
REVERT: B  180 GLN cc_start: 0.7487 (mm110) cc_final: 0.6997 (tt0)
REVERT: B  243 VAL cc_start: 0.7687 (t) cc_final: 0.7463 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1072
  time to fit residues: 13.2444
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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   88 ILE
Chi-restraints excluded: chain A residue  128 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   32 ASP
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  128 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 7 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.160597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.113237 restraints weight = 4566.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.28
r_work: 0.2998 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.4705

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= 0.138
  Angle     :  0.551   6.107   5644  Z= 0.281
  Chirality :  0.036   0.108    650
  Planarity :  0.002   0.022    664
  Dihedral  :  4.800  45.101    952
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 17.65 %
    Favored  : 79.41 %
  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:  4.76 (0.38), residues: 476
  helix:  3.64 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.52 (0.79), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  73 
 TYR   0.011   0.001   TYR A  18 
 PHE   0.009   0.001   PHE B 109 
 TRP   0.003   0.001   TRP A 184 
 HIS   0.000   0.000   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4156)
  covalent geometry    : angle       0.55110 ( 5644)
  hydrogen bonds       : bond        0.04502 (  333)
  hydrogen bonds       : angle       3.53524 (  981)

********************** 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
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7492 (mp)
REVERT: A   31 SER cc_start: 0.8431 (p) cc_final: 0.7991 (m)
REVERT: A   35 MET cc_start: 0.8630 (ttp) cc_final: 0.7871 (mmt)
REVERT: A   44 GLU cc_start: 0.8097 (tp30) cc_final: 0.7799 (tp30)
REVERT: A   58 ASP cc_start: 0.8507 (m-30) cc_final: 0.8263 (m-30)
REVERT: A  180 GLN cc_start: 0.7457 (mm110) cc_final: 0.6920 (tt0)
REVERT: A  243 VAL cc_start: 0.7628 (t) cc_final: 0.7378 (t)
REVERT: B   19 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7480 (mp)
REVERT: B   31 SER cc_start: 0.8461 (p) cc_final: 0.8058 (m)
REVERT: B   35 MET cc_start: 0.8598 (ttp) cc_final: 0.7944 (mmt)
REVERT: B   36 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7568 (mtp180)
REVERT: B   44 GLU cc_start: 0.8200 (tp30) cc_final: 0.7854 (tp30)
REVERT: B   58 ASP cc_start: 0.8368 (m-30) cc_final: 0.8163 (m-30)
REVERT: B  180 GLN cc_start: 0.7505 (mm110) cc_final: 0.7036 (tt0)
REVERT: B  243 VAL cc_start: 0.7671 (t) cc_final: 0.7463 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 103
  average time/residue: 0.1034
  time to fit residues: 12.4869
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  : 0.169 
-------------------------------------------------------------------------------
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   88 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0570
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.159350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.112659 restraints weight = 4576.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.25
r_work: 0.3033 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.4752

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= 0.132
  Angle     :  0.547   5.966   5644  Z= 0.277
  Chirality :  0.036   0.110    650
  Planarity :  0.002   0.021    664
  Dihedral  :  4.820  45.735    952
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.16 %
    Favored  : 79.41 %
  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:  4.80 (0.38), residues: 476
  helix:  3.67 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.53 (0.79), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  73 
 TYR   0.011   0.001   TYR A  18 
 PHE   0.010   0.001   PHE A 109 
 TRP   0.004   0.001   TRP A 184 
 HIS   0.000   0.000   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4156)
  covalent geometry    : angle       0.54691 ( 5644)
  hydrogen bonds       : bond        0.04389 (  333)
  hydrogen bonds       : angle       3.51626 (  981)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1052.28 seconds
wall clock time: 18 minutes 45.74 seconds (1125.74 seconds total)