Starting phenix.real_space_refine
on Tue Feb  3 15:05:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dbr_46725/02_2026/9dbr_46725.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dbr_46725/02_2026/9dbr_46725.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dbr_46725/02_2026/9dbr_46725.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dbr_46725/02_2026/9dbr_46725.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dbr_46725/02_2026/9dbr_46725.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dbr_46725/02_2026/9dbr_46725.cif"
  }
  resolution = 3.94
  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=   0.000 sd=   0.006
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       2      8.98       5
     S      14      5.16       5
     C    2709      2.51       5
     N     618      2.21       5
     O     694      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4037
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2006
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
    Chain: "B"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2006
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 25
          Unusual residues: {'  K': 2, 'P0T': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 0.73, per 1000 atoms: 0.18
  Number of scatterers: 4037
  At special positions: 0
  Unit cell: (95.824, 64.448, 86.496, 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       2     19.00
     S      14     16.00
     O     694      8.00
     N     618      7.00
     C    2709      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS B  93 " distance=2.03

  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: 0.22
  Conformation dependent library (CDL) restraints added in 94.9 milliseconds
  

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  924

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      79.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 91
      Proline residue:  A  71  - end of helix
    Processing helix  chain 'A' and resid 95 through 113
    Processing helix  chain 'A' and resid 128 through 142
    Processing helix  chain 'A' and resid 152 through 194
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 202 through 223
    Processing helix  chain 'A' and resid 223 through 234
    Processing helix  chain 'A' and resid 237 through 251
    Processing helix  chain 'A' and resid 269 through 297
      removed outlier: 3.512A  pdb=" N   ILE A 273 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 68
    Processing helix  chain 'B' and resid 69 through 91
      removed outlier: 3.566A  pdb=" N   GLU B  73 " --> pdb=" O   GLU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 113
    Processing helix  chain 'B' and resid 128 through 141
    Processing helix  chain 'B' and resid 152 through 193
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 202 through 223
    Processing helix  chain 'B' and resid 223 through 235
    Processing helix  chain 'B' and resid 237 through 250
    Processing helix  chain 'B' and resid 269 through 297

    326 hydrogen bonds defined for protein.
    978 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: 0.37

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 874
        1.33 -     1.45: 960
        1.45 -     1.57: 2286
        1.57 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 4142
  Sorted by residual:
  bond pdb=" N   VAL A 148 "
       pdb=" CA  VAL A 148 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.037 1.14e-02 7.69e+03 1.06e+01
  bond pdb=" N   GLU B  69 "
       pdb=" CA  GLU B  69 "
    ideal  model  delta    sigma   weight residual
    1.460  1.490 -0.030 1.14e-02 7.69e+03 6.85e+00
  bond pdb=" N   LEU B  68 "
       pdb=" CA  LEU B  68 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.32e-02 5.74e+03 6.82e+00
  bond pdb=" N   THR A 152 "
       pdb=" CA  THR A 152 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.23e-02 6.61e+03 6.48e+00
  bond pdb=" N   SER A 149 "
       pdb=" CA  SER A 149 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.25e-02 6.40e+03 6.20e+00
  ... (remaining 4137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 5367
        1.11 -     2.22: 199
        2.22 -     3.33: 41
        3.33 -     4.44: 13
        4.44 -     5.55: 11
  Bond angle restraints: 5631
  Sorted by residual:
  angle pdb=" N   ASN A 147 "
        pdb=" CA  ASN A 147 "
        pdb=" C   ASN A 147 "
      ideal   model   delta    sigma   weight residual
     111.82  107.87    3.95 1.16e+00 7.43e-01 1.16e+01
  angle pdb=" N   GLU B 263 "
        pdb=" CA  GLU B 263 "
        pdb=" C   GLU B 263 "
      ideal   model   delta    sigma   weight residual
     111.17  115.75   -4.58 1.41e+00 5.03e-01 1.05e+01
  angle pdb=" N   GLU B  69 "
        pdb=" CA  GLU B  69 "
        pdb=" C   GLU B  69 "
      ideal   model   delta    sigma   weight residual
     114.62  111.04    3.58 1.14e+00 7.69e-01 9.86e+00
  angle pdb=" N   HIS A 151 "
        pdb=" CA  HIS A 151 "
        pdb=" C   HIS A 151 "
      ideal   model   delta    sigma   weight residual
     112.90  109.09    3.81 1.31e+00 5.83e-01 8.47e+00
  angle pdb=" CA  THR A 152 "
        pdb=" C   THR A 152 "
        pdb=" O   THR A 152 "
      ideal   model   delta    sigma   weight residual
     121.19  118.09    3.10 1.10e+00 8.26e-01 7.92e+00
  ... (remaining 5626 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.69: 2287
       23.69 -    47.38: 61
       47.38 -    71.08: 5
       71.08 -    94.77: 7
       94.77 -   118.46: 2
  Dihedral angle restraints: 2362
    sinusoidal: 914
      harmonic: 1448
  Sorted by residual:
  dihedral pdb=" C04 P0T A 403 "
           pdb=" C03 P0T A 403 "
           pdb=" C05 P0T A 403 "
           pdb=" C06 P0T A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.60   56.86 -118.46     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" C06 P0T A 403 "
           pdb=" C03 P0T A 403 "
           pdb=" C05 P0T A 403 "
           pdb=" C10 P0T A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     186.18   67.81  118.37     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" C05 P0T A 403 "
           pdb=" C03 P0T A 403 "
           pdb=" C04 P0T A 403 "
           pdb=" C07 P0T A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
      41.58  -43.72   85.30     1      3.00e+01 1.11e-03 9.79e+00
  ... (remaining 2359 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 445
       0.034 -    0.068: 146
       0.068 -    0.102: 51
       0.102 -    0.136: 12
       0.136 -    0.170: 2
  Chirality restraints: 656
  Sorted by residual:
  chirality pdb=" CA  VAL A 148 "
            pdb=" N   VAL A 148 "
            pdb=" C   VAL A 148 "
            pdb=" CB  VAL A 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.19e-01
  chirality pdb=" CA  GLU B 263 "
            pdb=" N   GLU B 263 "
            pdb=" C   GLU B 263 "
            pdb=" CB  GLU B 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" C04 P0T A 403 "
            pdb=" C03 P0T A 403 "
            pdb=" C07 P0T A 403 "
            pdb=" C08 P0T A 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.34   -0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 653 not shown)

  Planarity restraints: 678
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  82 "    0.006 2.00e-02 2.50e+03   1.15e-02 1.33e+00
        pdb=" C   GLN A  82 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   GLN A  82 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLU A  83 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 115 "   -0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO B 116 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 116 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 116 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 271 "   -0.018 5.00e-02 4.00e+02   2.70e-02 1.16e+00
        pdb=" N   PRO B 272 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO B 272 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 272 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 675 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.79: 920
        2.79 -     3.38: 4815
        3.38 -     3.96: 7613
        3.96 -     4.55: 10309
        4.55 -     5.14: 14607
  Nonbonded interactions: 38264
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 137 "
            pdb=" OG1 THR A 141 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OE2 GLU A  73 "
            pdb=" OG  SER B 125 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   ALA B 112 "
            pdb=" NE2 HIS B 151 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" O   ALA B 227 "
            pdb=" OG  SER B 241 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   THR A 250 "
            pdb=" OG1 THR A 251 "
     model   vdw
     2.398 3.040
  ... (remaining 38259 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 43 through 297)
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.700
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
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      :  0.004   0.078   4143  Z= 0.218
  Angle     :  0.567   5.547   5633  Z= 0.341
  Chirality :  0.041   0.170    656
  Planarity :  0.003   0.028    678
  Dihedral  : 12.741 118.459   1435
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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 are not related in a simple way.
  whole:  2.80 (0.36), residues: 506
  helix:  2.72 (0.24), residues: 400
  sheet:  None (None), residues: 0
  loop : -1.82 (0.54), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 111 
 TYR   0.009   0.001   TYR A  57 
 PHE   0.010   0.001   PHE A 158 
 TRP   0.005   0.001   TRP A 127 
 HIS   0.002   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4142)
  covalent geometry    : angle       0.56669 ( 5631)
  SS BOND              : bond        0.00196 (    1)
  SS BOND              : angle       0.71142 (    2)
  hydrogen bonds       : bond        0.08093 (  326)
  hydrogen bonds       : angle       4.09181 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 HIS cc_start: 0.5820 (m-70) cc_final: 0.5008 (m90)
REVERT: A  195 MET cc_start: 0.0921 (mmm) cc_final: 0.0692 (ptm)
REVERT: B   44 TRP cc_start: 0.7543 (m-90) cc_final: 0.6920 (m-90)
REVERT: B  123 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7887 (mp0)
REVERT: B  165 LEU cc_start: 0.8598 (mp) cc_final: 0.8229 (tt)
REVERT: B  195 MET cc_start: 0.4871 (mmm) cc_final: 0.4472 (mtm)
REVERT: B  216 LEU cc_start: 0.8889 (tp) cc_final: 0.8615 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0605
  time to fit residues: 14.0806
Evaluate side-chains
  102 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 119 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.164094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.129010 restraints weight = 7397.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.133331 restraints weight = 4266.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.136299 restraints weight = 2950.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.138085 restraints weight = 2296.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.139531 restraints weight = 1962.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4143  Z= 0.221
  Angle     :  0.719   8.179   5633  Z= 0.373
  Chirality :  0.046   0.263    656
  Planarity :  0.004   0.028    678
  Dihedral  :  8.606  78.549    557
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 15.81 %
    Favored  : 77.91 %
  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 are not related in a simple way.
  whole:  2.76 (0.37), residues: 506
  helix:  2.66 (0.25), residues: 401
  sheet:  None (None), residues: 0
  loop : -1.73 (0.56), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  79 
 TYR   0.029   0.002   TYR B 243 
 PHE   0.014   0.001   PHE B 214 
 TRP   0.009   0.001   TRP A 127 
 HIS   0.004   0.002   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 4142)
  covalent geometry    : angle       0.71878 ( 5631)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.49312 (    2)
  hydrogen bonds       : bond        0.05276 (  326)
  hydrogen bonds       : angle       4.03385 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8587 (pttp)
REVERT: A  131 SER cc_start: 0.8027 (t) cc_final: 0.7606 (p)
REVERT: A  132 SER cc_start: 0.8999 (m) cc_final: 0.8451 (p)
REVERT: A  222 PHE cc_start: 0.9074 (m-80) cc_final: 0.8801 (m-10)
REVERT: B   44 TRP cc_start: 0.7589 (m-90) cc_final: 0.6614 (p90)
REVERT: B   68 LEU cc_start: 0.8304 (tp) cc_final: 0.8019 (tt)
REVERT: B  195 MET cc_start: 0.4667 (mmm) cc_final: 0.4402 (mtp)
REVERT: B  213 LEU cc_start: 0.8115 (mt) cc_final: 0.7837 (tt)
  outliers start: 27
  outliers final: 21
  residues processed: 129
  average time/residue: 0.0509
  time to fit residues: 8.7741
Evaluate side-chains
  117 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  189 ILE
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  110 ILE
Chi-restraints excluded: chain B residue  139 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  288 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0010
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.164754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.129481 restraints weight = 7389.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.133931 restraints weight = 4259.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.136895 restraints weight = 2943.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.138812 restraints weight = 2299.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.140215 restraints weight = 1957.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4143  Z= 0.132
  Angle     :  0.595   7.448   5633  Z= 0.303
  Chirality :  0.042   0.165    656
  Planarity :  0.003   0.032    678
  Dihedral  :  7.773  79.477    557
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 18.84 %
    Favored  : 76.28 %
  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 are not related in a simple way.
  whole:  3.12 (0.38), residues: 506
  helix:  2.92 (0.25), residues: 402
  sheet:  None (None), residues: 0
  loop : -1.62 (0.58), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 111 
 TYR   0.021   0.002   TYR B 243 
 PHE   0.015   0.001   PHE B 214 
 TRP   0.008   0.001   TRP A 277 
 HIS   0.003   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4142)
  covalent geometry    : angle       0.59497 ( 5631)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.33971 (    2)
  hydrogen bonds       : bond        0.04416 (  326)
  hydrogen bonds       : angle       3.64650 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8476 (pttp)
REVERT: A  131 SER cc_start: 0.8012 (t) cc_final: 0.7609 (p)
REVERT: A  132 SER cc_start: 0.8934 (m) cc_final: 0.8367 (p)
REVERT: A  222 PHE cc_start: 0.9048 (m-80) cc_final: 0.8730 (m-10)
REVERT: A  278 ILE cc_start: 0.9089 (mt) cc_final: 0.8850 (mm)
REVERT: B   44 TRP cc_start: 0.7467 (m-90) cc_final: 0.6537 (p90)
REVERT: B   68 LEU cc_start: 0.8383 (tp) cc_final: 0.8099 (tt)
REVERT: B  165 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8511 (tt)
REVERT: B  195 MET cc_start: 0.4751 (mmm) cc_final: 0.4487 (mtp)
REVERT: B  214 PHE cc_start: 0.6775 (t80) cc_final: 0.6568 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 118
  average time/residue: 0.0508
  time to fit residues: 7.9583
Evaluate side-chains
  114 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  288 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 32 optimal weight:    0.0270
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0670
   chunk 31 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.2954

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

Flipped N/Q/H residues before XYZ refinement:
B 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.166307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132067 restraints weight = 7345.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.136478 restraints weight = 4279.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.139475 restraints weight = 2958.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.141062 restraints weight = 2300.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.142623 restraints weight = 1976.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4143  Z= 0.124
  Angle     :  0.574   9.341   5633  Z= 0.291
  Chirality :  0.041   0.149    656
  Planarity :  0.003   0.032    678
  Dihedral  :  6.959  73.542    557
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 21.63 %
    Favored  : 73.49 %
  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 are not related in a simple way.
  whole:  3.26 (0.38), residues: 506
  helix:  3.01 (0.25), residues: 402
  sheet:  None (None), residues: 0
  loop : -1.56 (0.61), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 111 
 TYR   0.020   0.002   TYR B 243 
 PHE   0.008   0.001   PHE B 214 
 TRP   0.008   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4142)
  covalent geometry    : angle       0.57421 ( 5631)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       0.48620 (    2)
  hydrogen bonds       : bond        0.04103 (  326)
  hydrogen bonds       : angle       3.53835 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8685 (t80) cc_final: 0.7937 (t80)
REVERT: A  131 SER cc_start: 0.7932 (t) cc_final: 0.7509 (p)
REVERT: A  132 SER cc_start: 0.8860 (m) cc_final: 0.8282 (p)
REVERT: A  222 PHE cc_start: 0.8999 (m-80) cc_final: 0.8705 (m-10)
REVERT: B   44 TRP cc_start: 0.7430 (m-90) cc_final: 0.6521 (p90)
REVERT: B   68 LEU cc_start: 0.8268 (tp) cc_final: 0.8035 (tt)
REVERT: B   70 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7829 (mt0)
REVERT: B  216 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8495 (mp)
REVERT: B  257 PHE cc_start: 0.8975 (m-80) cc_final: 0.8418 (m-80)
REVERT: B  284 TYR cc_start: 0.8259 (t80) cc_final: 0.8046 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 126
  average time/residue: 0.0464
  time to fit residues: 7.8945
Evaluate side-chains
  115 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  249 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.162177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.128024 restraints weight = 7414.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132355 restraints weight = 4275.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.135242 restraints weight = 2925.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.137141 restraints weight = 2270.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138303 restraints weight = 1923.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
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   0.063   4143  Z= 0.148
  Angle     :  0.615   7.495   5633  Z= 0.319
  Chirality :  0.042   0.157    656
  Planarity :  0.003   0.033    678
  Dihedral  :  6.358  71.938    557
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 22.56 %
    Favored  : 72.09 %
  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 are not related in a simple way.
  whole:  3.16 (0.38), residues: 506
  helix:  2.89 (0.25), residues: 403
  sheet:  None (None), residues: 0
  loop : -1.38 (0.61), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 111 
 TYR   0.027   0.002   TYR A  57 
 PHE   0.027   0.001   PHE B 214 
 TRP   0.007   0.001   TRP A 277 
 HIS   0.002   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4142)
  covalent geometry    : angle       0.61485 ( 5631)
  SS BOND              : bond        0.00182 (    1)
  SS BOND              : angle       0.29358 (    2)
  hydrogen bonds       : bond        0.04441 (  326)
  hydrogen bonds       : angle       3.66186 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8630 (t80) cc_final: 0.8324 (t80)
REVERT: A  131 SER cc_start: 0.7966 (t) cc_final: 0.7533 (p)
REVERT: A  132 SER cc_start: 0.8967 (m) cc_final: 0.8345 (p)
REVERT: B   44 TRP cc_start: 0.7548 (m-90) cc_final: 0.6575 (p90)
REVERT: B   68 LEU cc_start: 0.8415 (tp) cc_final: 0.8142 (tt)
REVERT: B  216 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8487 (mp)
REVERT: B  257 PHE cc_start: 0.8991 (m-80) cc_final: 0.8434 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 118
  average time/residue: 0.0521
  time to fit residues: 8.2025
Evaluate side-chains
  119 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  288 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0980
   chunk 41 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.162470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.127779 restraints weight = 7521.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.132117 restraints weight = 4353.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.134993 restraints weight = 3000.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.136936 restraints weight = 2343.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.137895 restraints weight = 1985.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.4816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4143  Z= 0.136
  Angle     :  0.598   8.900   5633  Z= 0.303
  Chirality :  0.041   0.155    656
  Planarity :  0.003   0.035    678
  Dihedral  :  5.862  70.772    557
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.96 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 22.79 %
    Favored  : 70.70 %
  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 are not related in a simple way.
  whole:  3.22 (0.38), residues: 506
  helix:  2.93 (0.25), residues: 403
  sheet:  None (None), residues: 0
  loop : -1.40 (0.63), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 111 
 TYR   0.022   0.002   TYR A  57 
 PHE   0.017   0.001   PHE B 214 
 TRP   0.007   0.001   TRP A 277 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4142)
  covalent geometry    : angle       0.59845 ( 5631)
  SS BOND              : bond        0.00174 (    1)
  SS BOND              : angle       0.25418 (    2)
  hydrogen bonds       : bond        0.04192 (  326)
  hydrogen bonds       : angle       3.57708 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 TYR cc_start: 0.8594 (t80) cc_final: 0.8319 (t80)
REVERT: A   77 LYS cc_start: 0.8814 (pttp) cc_final: 0.8514 (pttp)
REVERT: A  131 SER cc_start: 0.7937 (t) cc_final: 0.7503 (p)
REVERT: A  132 SER cc_start: 0.8937 (m) cc_final: 0.8305 (p)
REVERT: B   44 TRP cc_start: 0.7558 (m-90) cc_final: 0.6633 (p90)
REVERT: B   68 LEU cc_start: 0.8438 (tp) cc_final: 0.8189 (tt)
REVERT: B  216 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8479 (mp)
REVERT: B  257 PHE cc_start: 0.8928 (m-80) cc_final: 0.8437 (m-80)
  outliers start: 28
  outliers final: 21
  residues processed: 117
  average time/residue: 0.0482
  time to fit residues: 7.7336
Evaluate side-chains
  120 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   98 GLU
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  291 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    0.0370
   chunk 44 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 7 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 10 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   overall best weight:    0.3658

-------------------------------------------------------------------------------
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 = 0.163199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.128504 restraints weight = 7547.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.132818 restraints weight = 4371.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.135726 restraints weight = 3012.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.137653 restraints weight = 2344.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.138818 restraints weight = 1985.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.4988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4143  Z= 0.126
  Angle     :  0.594   9.459   5633  Z= 0.301
  Chirality :  0.041   0.175    656
  Planarity :  0.003   0.034    678
  Dihedral  :  5.623  70.139    557
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.57 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 24.19 %
    Favored  : 70.47 %
  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 are not related in a simple way.
  whole:  3.29 (0.38), residues: 506
  helix:  2.97 (0.25), residues: 403
  sheet:  None (None), residues: 0
  loop : -1.32 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 111 
 TYR   0.020   0.002   TYR A  57 
 PHE   0.026   0.001   PHE B 214 
 TRP   0.008   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4142)
  covalent geometry    : angle       0.59453 ( 5631)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       0.40568 (    2)
  hydrogen bonds       : bond        0.03994 (  326)
  hydrogen bonds       : angle       3.52573 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8577 (t80) cc_final: 0.8345 (t80)
REVERT: A  131 SER cc_start: 0.7971 (t) cc_final: 0.7548 (p)
REVERT: A  132 SER cc_start: 0.8895 (m) cc_final: 0.8266 (p)
REVERT: B   44 TRP cc_start: 0.7530 (m-90) cc_final: 0.6620 (p90)
REVERT: B  216 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8490 (mp)
REVERT: B  256 ASP cc_start: 0.8138 (p0) cc_final: 0.7929 (p0)
REVERT: B  257 PHE cc_start: 0.8950 (m-80) cc_final: 0.8416 (m-80)
  outliers start: 23
  outliers final: 20
  residues processed: 120
  average time/residue: 0.0520
  time to fit residues: 8.3291
Evaluate side-chains
  120 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  291 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 44 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0570
   chunk 28 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.3958 r_free = 0.3958 target = 0.162054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.127990 restraints weight = 7382.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132225 restraints weight = 4256.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.135045 restraints weight = 2943.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136905 restraints weight = 2296.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.137853 restraints weight = 1951.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.5191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4143  Z= 0.129
  Angle     :  0.626   9.857   5633  Z= 0.311
  Chirality :  0.042   0.157    656
  Planarity :  0.003   0.034    678
  Dihedral  :  5.587  72.795    557
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.57 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 24.65 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.29 (0.38), residues: 506
  helix:  2.99 (0.25), residues: 403
  sheet:  None (None), residues: 0
  loop : -1.40 (0.63), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 111 
 TYR   0.022   0.002   TYR A  57 
 PHE   0.024   0.001   PHE B 214 
 TRP   0.007   0.001   TRP A 277 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4142)
  covalent geometry    : angle       0.62650 ( 5631)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       0.27379 (    2)
  hydrogen bonds       : bond        0.04050 (  326)
  hydrogen bonds       : angle       3.45696 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8608 (t80) cc_final: 0.8393 (t80)
REVERT: A  131 SER cc_start: 0.7981 (t) cc_final: 0.7542 (p)
REVERT: A  132 SER cc_start: 0.8922 (m) cc_final: 0.8315 (p)
REVERT: B   44 TRP cc_start: 0.7518 (m-90) cc_final: 0.6591 (p90)
REVERT: B   70 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8054 (mt0)
REVERT: B  216 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8500 (mp)
REVERT: B  256 ASP cc_start: 0.8224 (p0) cc_final: 0.7941 (p0)
REVERT: B  257 PHE cc_start: 0.9014 (m-80) cc_final: 0.8354 (m-80)
  outliers start: 24
  outliers final: 20
  residues processed: 119
  average time/residue: 0.0524
  time to fit residues: 8.3304
Evaluate side-chains
  124 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  291 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.1980
   chunk 20 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 9 optimal weight:    0.1980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.161538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126467 restraints weight = 7540.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.130855 restraints weight = 4311.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.133760 restraints weight = 2957.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.135618 restraints weight = 2301.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.136712 restraints weight = 1955.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.5324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4143  Z= 0.124
  Angle     :  0.633  10.574   5633  Z= 0.308
  Chirality :  0.041   0.152    656
  Planarity :  0.003   0.034    678
  Dihedral  :  5.541  73.555    557
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.77 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 25.58 %
    Favored  : 69.53 %
  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 are not related in a simple way.
  whole:  3.35 (0.38), residues: 506
  helix:  3.03 (0.25), residues: 403
  sheet:  None (None), residues: 0
  loop : -1.37 (0.64), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 111 
 TYR   0.020   0.002   TYR A  57 
 PHE   0.024   0.001   PHE B 185 
 TRP   0.007   0.001   TRP A 277 
 HIS   0.002   0.000   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4142)
  covalent geometry    : angle       0.63340 ( 5631)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       0.23405 (    2)
  hydrogen bonds       : bond        0.03923 (  326)
  hydrogen bonds       : angle       3.44829 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8592 (t80) cc_final: 0.8331 (t80)
REVERT: A  131 SER cc_start: 0.7970 (t) cc_final: 0.7522 (p)
REVERT: A  132 SER cc_start: 0.8931 (m) cc_final: 0.8306 (p)
REVERT: B   44 TRP cc_start: 0.7509 (m-90) cc_final: 0.6561 (p90)
REVERT: B   70 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8071 (mt0)
REVERT: B  158 PHE cc_start: 0.8122 (t80) cc_final: 0.7888 (t80)
REVERT: B  216 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8526 (mp)
REVERT: B  256 ASP cc_start: 0.8216 (p0) cc_final: 0.7967 (p0)
REVERT: B  257 PHE cc_start: 0.9010 (m-80) cc_final: 0.8380 (m-80)
REVERT: B  266 TYR cc_start: 0.7206 (m-80) cc_final: 0.6981 (m-80)
  outliers start: 21
  outliers final: 18
  residues processed: 117
  average time/residue: 0.0503
  time to fit residues: 7.8226
Evaluate side-chains
  122 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 TYR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  291 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0010
   chunk 10 optimal weight:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.4986

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.160699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.125912 restraints weight = 7315.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.130219 restraints weight = 4267.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.133094 restraints weight = 2957.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.134794 restraints weight = 2308.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.136064 restraints weight = 1976.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4143  Z= 0.138
  Angle     :  0.665  10.681   5633  Z= 0.324
  Chirality :  0.042   0.153    656
  Planarity :  0.004   0.033    678
  Dihedral  :  5.514  74.680    557
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.96 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 26.74 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.32 (0.38), residues: 506
  helix:  3.01 (0.25), residues: 403
  sheet:  None (None), residues: 0
  loop : -1.40 (0.63), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 111 
 TYR   0.021   0.002   TYR A  57 
 PHE   0.038   0.001   PHE B 214 
 TRP   0.007   0.001   TRP A 277 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4142)
  covalent geometry    : angle       0.66506 ( 5631)
  SS BOND              : bond        0.00231 (    1)
  SS BOND              : angle       0.24052 (    2)
  hydrogen bonds       : bond        0.04014 (  326)
  hydrogen bonds       : angle       3.47767 (  978)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A   57 TYR cc_start: 0.8623 (t80) cc_final: 0.8367 (t80)
REVERT: A  131 SER cc_start: 0.7992 (t) cc_final: 0.7536 (p)
REVERT: A  132 SER cc_start: 0.8944 (m) cc_final: 0.8303 (p)
REVERT: B   44 TRP cc_start: 0.7512 (m-90) cc_final: 0.6574 (p90)
REVERT: B  158 PHE cc_start: 0.8135 (t80) cc_final: 0.7913 (t80)
REVERT: B  257 PHE cc_start: 0.8999 (m-80) cc_final: 0.8400 (m-80)
REVERT: B  266 TYR cc_start: 0.7288 (m-80) cc_final: 0.7081 (m-80)
  outliers start: 19
  outliers final: 18
  residues processed: 120
  average time/residue: 0.0573
  time to fit residues: 9.0260
Evaluate side-chains
  122 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  159 CYS
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  265 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  232 HIS
Chi-restraints excluded: chain B residue  237 SER
Chi-restraints excluded: chain B residue  241 SER
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  291 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0870
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.160225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.125315 restraints weight = 7531.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.129492 restraints weight = 4348.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.132392 restraints weight = 3019.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.134160 restraints weight = 2354.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.135334 restraints weight = 2003.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.5728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4143  Z= 0.137
  Angle     :  0.661  10.521   5633  Z= 0.325
  Chirality :  0.043   0.166    656
  Planarity :  0.004   0.033    678
  Dihedral  :  5.587  76.917    557
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 26.74 %
    Favored  : 68.37 %
  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 are not related in a simple way.
  whole:  3.32 (0.38), residues: 506
  helix:  3.00 (0.25), residues: 402
  sheet:  None (None), residues: 0
  loop : -1.29 (0.64), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 111 
 TYR   0.021   0.002   TYR A  57 
 PHE   0.036   0.001   PHE B 185 
 TRP   0.007   0.001   TRP A 277 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4142)
  covalent geometry    : angle       0.66063 ( 5631)
  SS BOND              : bond        0.00193 (    1)
  SS BOND              : angle       0.23289 (    2)
  hydrogen bonds       : bond        0.04023 (  326)
  hydrogen bonds       : angle       3.53082 (  978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 886.90 seconds
wall clock time: 15 minutes 58.08 seconds (958.08 seconds total)