Starting phenix.real_space_refine
on Sun Apr 27 01:12:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1v_36805/04_2025/8k1v_36805.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1v_36805/04_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_36805/04_2025/8k1v_36805.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1v_36805/04_2025/8k1v_36805.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1v_36805/04_2025/8k1v_36805.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1v_36805/04_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-5669/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: 2.95, per 1000 atoms: 0.73
  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: 2.50
  Conformation dependent library (CDL) restraints added in 457.5 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: 0.35
  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: 1.09

  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:                  0.010
  Normalize map: mean=0, sd=1:             0.340
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.160
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.820
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.418 
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: 0.2219
  time to fit residues: 30.2940
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  : 0.414 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3970 r_free = 0.3970 target = 0.179189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.128310 restraints weight = 4574.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.31
r_work: 0.3239 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2667

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= 0.139
  Angle     :  0.485   5.610   5644  Z= 0.255
  Chirality :  0.037   0.128    650
  Planarity :  0.003   0.018    664
  Dihedral  :  5.403  31.743    952
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  8.82 %
    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:  5.51 (0.38), residues: 476
  helix:  4.10 (0.23), residues: 390
  sheet:  None (None), residues: 0
  loop :  1.12 (0.89), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 184 
 HIS   0.000   0.000   HIS B 188 
 PHE   0.009   0.001   PHE B 223 
 TYR   0.018   0.001   TYR B  85 
 ARG   0.003   0.001   ARG A  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03626 (  333)
  hydrogen bonds       : angle       3.48815 (  981)
  covalent geometry    : bond        0.00320 ( 4156)
  covalent geometry    : angle       0.48522 ( 5644)

*********************** 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
  109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A   35 MET cc_start: 0.8457 (ttp) cc_final: 0.7967 (mmm)
REVERT: A   36 ARG cc_start: 0.8291 (ttm-80) cc_final: 0.7461 (mtp180)
REVERT: A   42 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7874 (tppt)
REVERT: A   44 GLU cc_start: 0.8154 (tp30) cc_final: 0.7835 (tp30)
REVERT: A   60 ARG cc_start: 0.8204 (tpp80) cc_final: 0.7941 (tpp80)
REVERT: A  180 GLN cc_start: 0.7666 (mm110) cc_final: 0.6902 (tt0)
REVERT: B   35 MET cc_start: 0.8504 (ttp) cc_final: 0.8073 (mmm)
REVERT: B   36 ARG cc_start: 0.8370 (tpp80) cc_final: 0.7656 (mtp180)
REVERT: B   44 GLU cc_start: 0.8157 (tp30) cc_final: 0.7773 (tp30)
REVERT: B  180 GLN cc_start: 0.7642 (mm110) cc_final: 0.6904 (tt0)
  outliers start: 8
  outliers final: 3
  residues processed: 107
  average time/residue: 0.2243
  time to fit residues: 28.0550
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASP
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 17 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0470
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6478

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.175148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.123799 restraints weight = 4536.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.31
r_work: 0.3211 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3285

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= 0.126
  Angle     :  0.485   5.990   5644  Z= 0.252
  Chirality :  0.035   0.107    650
  Planarity :  0.002   0.014    664
  Dihedral  :  4.908  30.621    952
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  9.80 %
    Favored  : 87.75 %
  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:  5.26 (0.39), residues: 476
  helix:  3.90 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  1.15 (0.86), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  78 
 HIS   0.001   0.000   HIS B  72 
 PHE   0.007   0.001   PHE A  16 
 TYR   0.016   0.002   TYR A  85 
 ARG   0.005   0.001   ARG B  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03803 (  333)
  hydrogen bonds       : angle       3.39784 (  981)
  covalent geometry    : bond        0.00277 ( 4156)
  covalent geometry    : angle       0.48533 ( 5644)

*********************** 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
  112 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7715 (mp)
REVERT: A   35 MET cc_start: 0.8461 (ttp) cc_final: 0.8044 (mmt)
REVERT: A   36 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7491 (mtp180)
REVERT: A   42 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7430 (tppt)
REVERT: A   44 GLU cc_start: 0.8176 (tp30) cc_final: 0.7863 (tp30)
REVERT: A   45 GLU cc_start: 0.7414 (pt0) cc_final: 0.6951 (pp20)
REVERT: A   60 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8065 (tpp80)
REVERT: A  180 GLN cc_start: 0.7689 (mm110) cc_final: 0.6965 (tt0)
REVERT: A  243 VAL cc_start: 0.7865 (t) cc_final: 0.7654 (t)
REVERT: B   19 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7736 (mp)
REVERT: B   35 MET cc_start: 0.8467 (ttp) cc_final: 0.8115 (mmt)
REVERT: B   36 ARG cc_start: 0.8383 (tpp80) cc_final: 0.7693 (mtp180)
REVERT: B   44 GLU cc_start: 0.8174 (tp30) cc_final: 0.7760 (tp30)
REVERT: B   58 ASP cc_start: 0.8304 (m-30) cc_final: 0.8050 (t0)
REVERT: B  180 GLN cc_start: 0.7630 (mm110) cc_final: 0.6893 (tt0)
REVERT: B  243 VAL cc_start: 0.7870 (t) cc_final: 0.7644 (t)
  outliers start: 10
  outliers final: 4
  residues processed: 109
  average time/residue: 0.2219
  time to fit residues: 28.2795
Evaluate side-chains
  90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain B residue  134 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3776 r_free = 0.3776 target = 0.161727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.115085 restraints weight = 4549.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.24
r_work: 0.3109 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3744

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= 0.137
  Angle     :  0.494   5.509   5644  Z= 0.258
  Chirality :  0.036   0.106    650
  Planarity :  0.002   0.014    664
  Dihedral  :  4.746  35.514    952
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 14.22 %
    Favored  : 82.84 %
  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:  5.09 (0.38), residues: 476
  helix:  3.83 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.86 (0.82), 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  33 
 PHE   0.008   0.001   PHE A  16 
 TYR   0.018   0.002   TYR B  85 
 ARG   0.004   0.000   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04184 (  333)
  hydrogen bonds       : angle       3.42465 (  981)
  covalent geometry    : bond        0.00309 ( 4156)
  covalent geometry    : angle       0.49395 ( 5644)

*********************** 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: 12
    poor density    : 93
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7611 (mp)
REVERT: A   35 MET cc_start: 0.8578 (ttp) cc_final: 0.7987 (mmt)
REVERT: A   44 GLU cc_start: 0.8139 (tp30) cc_final: 0.7809 (tp30)
REVERT: A   60 ARG cc_start: 0.8417 (tpp80) cc_final: 0.8152 (tpp80)
REVERT: A  180 GLN cc_start: 0.7526 (mm110) cc_final: 0.6996 (tt0)
REVERT: A  243 VAL cc_start: 0.7695 (t) cc_final: 0.7482 (t)
REVERT: B   19 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7551 (mp)
REVERT: B   31 SER cc_start: 0.8376 (p) cc_final: 0.8059 (m)
REVERT: B   35 MET cc_start: 0.8507 (ttp) cc_final: 0.7996 (mmt)
REVERT: B   36 ARG cc_start: 0.8300 (tpp80) cc_final: 0.7579 (mtp180)
REVERT: B   40 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8158 (ttmm)
REVERT: B   44 GLU cc_start: 0.8148 (tp30) cc_final: 0.7744 (tp30)
REVERT: B   58 ASP cc_start: 0.8299 (m-30) cc_final: 0.7984 (t0)
REVERT: B   73 ARG cc_start: 0.8331 (tpp80) cc_final: 0.8076 (mmt90)
REVERT: B  180 GLN cc_start: 0.7507 (mm110) cc_final: 0.6990 (tt0)
REVERT: B  243 VAL cc_start: 0.7687 (t) cc_final: 0.7474 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 101
  average time/residue: 0.2403
  time to fit residues: 28.3180
Evaluate side-chains
  92 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 41 optimal weight:    0.3980
   chunk 38 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.162829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.117544 restraints weight = 4610.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.22
r_work: 0.3097 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3987

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     :  0.510   6.002   5644  Z= 0.266
  Chirality :  0.035   0.110    650
  Planarity :  0.002   0.014    664
  Dihedral  :  4.708  38.632    952
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.01
  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 (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:  5.00 (0.38), residues: 476
  helix:  3.78 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.77 (0.81), 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   0.000   ARG B  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04179 (  333)
  hydrogen bonds       : angle       3.45823 (  981)
  covalent geometry    : bond        0.00292 ( 4156)
  covalent geometry    : angle       0.51029 ( 5644)

*********************** 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
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7555 (mp)
REVERT: A   31 SER cc_start: 0.8407 (p) cc_final: 0.8055 (m)
REVERT: A   35 MET cc_start: 0.8605 (ttp) cc_final: 0.7858 (mmt)
REVERT: A   44 GLU cc_start: 0.8188 (tp30) cc_final: 0.7811 (tp30)
REVERT: A   45 GLU cc_start: 0.7435 (pt0) cc_final: 0.6979 (pp20)
REVERT: A   60 ARG cc_start: 0.8405 (tpp80) cc_final: 0.8143 (tpp80)
REVERT: A  180 GLN cc_start: 0.7480 (mm110) cc_final: 0.6977 (tt0)
REVERT: A  243 VAL cc_start: 0.7730 (t) cc_final: 0.7511 (t)
REVERT: B   19 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7557 (mp)
REVERT: B   31 SER cc_start: 0.8384 (p) cc_final: 0.8069 (m)
REVERT: B   35 MET cc_start: 0.8506 (ttp) cc_final: 0.7986 (mmt)
REVERT: B   36 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7575 (mtp180)
REVERT: B   44 GLU cc_start: 0.8146 (tp30) cc_final: 0.7747 (tp30)
REVERT: B  180 GLN cc_start: 0.7494 (mm110) cc_final: 0.6992 (tt0)
REVERT: B  243 VAL cc_start: 0.7712 (t) cc_final: 0.7489 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 100
  average time/residue: 0.2447
  time to fit residues: 28.9762
Evaluate side-chains
  95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
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  136 VAL
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:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0870
   chunk 5 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 41 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.3777 r_free = 0.3777 target = 0.162412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.118324 restraints weight = 4556.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.19
r_work: 0.3123 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4059

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= 0.119
  Angle     :  0.505   6.354   5644  Z= 0.257
  Chirality :  0.035   0.108    650
  Planarity :  0.002   0.017    664
  Dihedral  :  4.602  40.464    952
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.16 %
    Favored  : 80.15 %
  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:  3.81 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.83 (0.82), residues: 86

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  333)
  hydrogen bonds       : angle       3.39879 (  981)
  covalent geometry    : bond        0.00254 ( 4156)
  covalent geometry    : angle       0.50501 ( 5644)

*********************** 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
  104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7488 (mp)
REVERT: A   31 SER cc_start: 0.8397 (p) cc_final: 0.8070 (p)
REVERT: A   35 MET cc_start: 0.8577 (ttp) cc_final: 0.7809 (mmt)
REVERT: A   44 GLU cc_start: 0.8087 (tp30) cc_final: 0.7803 (tp30)
REVERT: A  180 GLN cc_start: 0.7342 (mm110) cc_final: 0.6847 (tt0)
REVERT: A  243 VAL cc_start: 0.7704 (t) cc_final: 0.7501 (t)
REVERT: B   19 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7616 (mp)
REVERT: B   31 SER cc_start: 0.8401 (p) cc_final: 0.8063 (m)
REVERT: B   35 MET cc_start: 0.8506 (ttp) cc_final: 0.7978 (mmt)
REVERT: B   36 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7583 (mtp180)
REVERT: B   44 GLU cc_start: 0.8145 (tp30) cc_final: 0.7765 (tp30)
REVERT: B  180 GLN cc_start: 0.7392 (mm110) cc_final: 0.6941 (tt0)
REVERT: B  243 VAL cc_start: 0.7697 (t) cc_final: 0.7486 (t)
  outliers start: 11
  outliers final: 9
  residues processed: 101
  average time/residue: 0.2201
  time to fit residues: 26.1840
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  : 0.429 
-------------------------------------------------------------------------------
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  136 VAL
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:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.159971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.115512 restraints weight = 4589.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.17
r_work: 0.3103 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.4265

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= 0.128
  Angle     :  0.530   6.369   5644  Z= 0.269
  Chirality :  0.035   0.111    650
  Planarity :  0.003   0.037    664
  Dihedral  :  4.631  41.699    952
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.14 %
    Favored  : 78.92 %
  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:  5.03 (0.38), residues: 476
  helix:  3.80 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.79 (0.81), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 184 
 HIS   0.000   0.000   HIS A  98 
 PHE   0.008   0.001   PHE B 109 
 TYR   0.012   0.001   TYR A 138 
 ARG   0.006   0.001   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04160 (  333)
  hydrogen bonds       : angle       3.43454 (  981)
  covalent geometry    : bond        0.00283 ( 4156)
  covalent geometry    : angle       0.52980 ( 5644)

*********************** 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
  107 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7524 (mp)
REVERT: A   31 SER cc_start: 0.8432 (p) cc_final: 0.8129 (p)
REVERT: A   35 MET cc_start: 0.8579 (ttp) cc_final: 0.7836 (mmt)
REVERT: A   44 GLU cc_start: 0.8086 (tp30) cc_final: 0.7808 (tp30)
REVERT: A  180 GLN cc_start: 0.7432 (mm110) cc_final: 0.6956 (tt0)
REVERT: A  243 VAL cc_start: 0.7744 (t) cc_final: 0.7505 (t)
REVERT: B   19 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7577 (mp)
REVERT: B   31 SER cc_start: 0.8418 (p) cc_final: 0.8080 (m)
REVERT: B   35 MET cc_start: 0.8512 (ttp) cc_final: 0.7989 (mmt)
REVERT: B   36 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7604 (mtp180)
REVERT: B   44 GLU cc_start: 0.8198 (tp30) cc_final: 0.7854 (tp30)
REVERT: B   60 ARG cc_start: 0.8321 (tpp80) cc_final: 0.8086 (tpp80)
REVERT: B  180 GLN cc_start: 0.7469 (mm110) cc_final: 0.7001 (tt0)
REVERT: B  243 VAL cc_start: 0.7758 (t) cc_final: 0.7544 (t)
  outliers start: 12
  outliers final: 10
  residues processed: 104
  average time/residue: 0.2306
  time to fit residues: 27.9813
Evaluate side-chains
  106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
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  136 VAL
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:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 27 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3781 r_free = 0.3781 target = 0.162470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.115195 restraints weight = 4489.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.24
r_work: 0.3084 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.4343

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= 0.129
  Angle     :  0.541   7.496   5644  Z= 0.273
  Chirality :  0.035   0.110    650
  Planarity :  0.003   0.034    664
  Dihedral  :  4.626  43.053    952
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.14 %
    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:  4.99 (0.38), residues: 476
  helix:  3.78 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.72 (0.80), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 184 
 HIS   0.000   0.000   HIS B  72 
 PHE   0.008   0.001   PHE B 109 
 TYR   0.012   0.001   TYR A 138 
 ARG   0.007   0.001   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04191 (  333)
  hydrogen bonds       : angle       3.44816 (  981)
  covalent geometry    : bond        0.00287 ( 4156)
  covalent geometry    : angle       0.54130 ( 5644)

*********************** 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
  109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7527 (mp)
REVERT: A   31 SER cc_start: 0.8466 (p) cc_final: 0.8169 (p)
REVERT: A   35 MET cc_start: 0.8603 (ttp) cc_final: 0.7850 (mmt)
REVERT: A   44 GLU cc_start: 0.8094 (tp30) cc_final: 0.7790 (tp30)
REVERT: A  180 GLN cc_start: 0.7437 (mm110) cc_final: 0.6963 (tt0)
REVERT: A  243 VAL cc_start: 0.7702 (t) cc_final: 0.7458 (t)
REVERT: B   19 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7594 (mp)
REVERT: B   31 SER cc_start: 0.8408 (p) cc_final: 0.7870 (m)
REVERT: B   35 MET cc_start: 0.8537 (ttp) cc_final: 0.7974 (mmm)
REVERT: B   36 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7597 (mtp180)
REVERT: B   44 GLU cc_start: 0.8212 (tp30) cc_final: 0.7866 (tp30)
REVERT: B  180 GLN cc_start: 0.7444 (mm110) cc_final: 0.6978 (tt0)
REVERT: B  243 VAL cc_start: 0.7720 (t) cc_final: 0.7498 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 106
  average time/residue: 0.2292
  time to fit residues: 28.3976
Evaluate side-chains
  109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
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  136 VAL
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  136 VAL
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:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0050
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5794

-------------------------------------------------------------------------------
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 = 0.3790 r_free = 0.3790 target = 0.163365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.115947 restraints weight = 4553.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.26
r_work: 0.3086 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
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   0.041   4156  Z= 0.128
  Angle     :  0.546   7.603   5644  Z= 0.277
  Chirality :  0.035   0.106    650
  Planarity :  0.003   0.031    664
  Dihedral  :  4.619  43.993    952
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.65 %
    Favored  : 79.17 %
  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:  4.97 (0.38), residues: 476
  helix:  3.76 (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   0.003   0.001   TRP A 184 
 HIS   0.000   0.000   HIS A  72 
 PHE   0.009   0.001   PHE B 109 
 TYR   0.012   0.001   TYR B 138 
 ARG   0.007   0.001   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  333)
  hydrogen bonds       : angle       3.47316 (  981)
  covalent geometry    : bond        0.00284 ( 4156)
  covalent geometry    : angle       0.54637 ( 5644)

*********************** 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
  109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   19 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7506 (mp)
REVERT: A   31 SER cc_start: 0.8504 (p) cc_final: 0.8205 (p)
REVERT: A   35 MET cc_start: 0.8605 (ttp) cc_final: 0.7854 (mmt)
REVERT: A   44 GLU cc_start: 0.8085 (tp30) cc_final: 0.7806 (tp30)
REVERT: A  180 GLN cc_start: 0.7392 (mm110) cc_final: 0.6881 (tt0)
REVERT: A  243 VAL cc_start: 0.7701 (t) cc_final: 0.7469 (t)
REVERT: B   19 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7586 (mp)
REVERT: B   31 SER cc_start: 0.8413 (p) cc_final: 0.7874 (m)
REVERT: B   35 MET cc_start: 0.8549 (ttp) cc_final: 0.7982 (mmm)
REVERT: B   36 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7609 (mtp180)
REVERT: B   44 GLU cc_start: 0.8214 (tp30) cc_final: 0.7864 (tp30)
REVERT: B  180 GLN cc_start: 0.7429 (mm110) cc_final: 0.6974 (tt0)
REVERT: B  243 VAL cc_start: 0.7688 (t) cc_final: 0.7470 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 106
  average time/residue: 0.2330
  time to fit residues: 28.8784
Evaluate side-chains
  108 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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  136 VAL
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  136 VAL
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:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 11 optimal weight:    0.3980
   chunk 5 optimal weight:    8.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.162241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.114551 restraints weight = 4562.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.28
r_work: 0.3018 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.4556

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= 0.137
  Angle     :  0.556   6.875   5644  Z= 0.286
  Chirality :  0.036   0.108    650
  Planarity :  0.003   0.032    664
  Dihedral  :  4.711  44.485    952
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.14 %
    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:  4.91 (0.38), residues: 476
  helix:  3.73 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.66 (0.80), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 184 
 HIS   0.001   0.000   HIS B  72 
 PHE   0.008   0.001   PHE B 109 
 TYR   0.013   0.001   TYR A 138 
 ARG   0.008   0.001   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04429 (  333)
  hydrogen bonds       : angle       3.50320 (  981)
  covalent geometry    : bond        0.00309 ( 4156)
  covalent geometry    : angle       0.55612 ( 5644)

********************** 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
  109 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A   31 SER cc_start: 0.8424 (p) cc_final: 0.8102 (p)
REVERT: A   35 MET cc_start: 0.8619 (ttp) cc_final: 0.7851 (mmt)
REVERT: A   44 GLU cc_start: 0.8140 (tp30) cc_final: 0.7858 (tp30)
REVERT: A  180 GLN cc_start: 0.7424 (mm110) cc_final: 0.6877 (tt0)
REVERT: A  243 VAL cc_start: 0.7603 (t) cc_final: 0.7359 (t)
REVERT: B   19 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7565 (mp)
REVERT: B   31 SER cc_start: 0.8429 (p) cc_final: 0.8008 (m)
REVERT: B   35 MET cc_start: 0.8564 (ttp) cc_final: 0.7969 (mmt)
REVERT: B   36 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7559 (mtp180)
REVERT: B   44 GLU cc_start: 0.8212 (tp30) cc_final: 0.7859 (tp30)
REVERT: B  180 GLN cc_start: 0.7449 (mm110) cc_final: 0.6980 (tt0)
REVERT: B  243 VAL cc_start: 0.7679 (t) cc_final: 0.7448 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 106
  average time/residue: 0.2319
  time to fit residues: 28.6677
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  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  136 VAL
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 20 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3758 r_free = 0.3758 target = 0.160327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.114446 restraints weight = 4562.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.22
r_work: 0.3026 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.4700

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= 0.145
  Angle     :  0.583   8.660   5644  Z= 0.292
  Chirality :  0.036   0.112    650
  Planarity :  0.003   0.030    664
  Dihedral  :  4.801  44.766    952
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.50
  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:  4.89 (0.38), residues: 476
  helix:  3.73 (0.24), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.59 (0.79), 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  72 
 PHE   0.012   0.001   PHE A  16 
 TYR   0.012   0.001   TYR B 113 
 ARG   0.007   0.001   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04556 (  333)
  hydrogen bonds       : angle       3.51063 (  981)
  covalent geometry    : bond        0.00333 ( 4156)
  covalent geometry    : angle       0.58324 ( 5644)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2118.73 seconds
wall clock time: 37 minutes 12.01 seconds (2232.01 seconds total)