Starting phenix.real_space_refine
on Wed Feb 12 10:36:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug4_42213/02_2025/8ug4_42213.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug4_42213/02_2025/8ug4_42213.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ug4_42213/02_2025/8ug4_42213.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug4_42213/02_2025/8ug4_42213.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug4_42213/02_2025/8ug4_42213.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug4_42213/02_2025/8ug4_42213.cif"
  }
  resolution = 3.02
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5182      2.51       5
     N    1270      2.21       5
     O    1298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7802
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3901
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 486, 3891
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 8, 'TRANS': 477}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 486, 3891
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 8, 'TRANS': 477}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 3975
  Restraints were copied for chains:
    B
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AHIS A 567 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 567 " occ=0.50
    residue:
      pdb=" N  AHIS B 567 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 567 " occ=0.50
  Time building chain proxies: 8.77, per 1000 atoms: 1.12
  Number of scatterers: 7802
  At special positions: 0
  Unit cell: (100.43, 92.13, 90.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1298      8.00
     N    1270      7.00
     C    5182      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: 2.04
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      77.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 86
    Processing helix  chain 'A' and resid 93 through 119
    Processing helix  chain 'A' and resid 122 through 136
    Processing helix  chain 'A' and resid 158 through 186
    Processing helix  chain 'A' and resid 190 through 213
      removed outlier: 3.765A  pdb=" N   ILE A 194 " --> pdb=" O   LYS A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 268
      removed outlier: 3.890A  pdb=" N   ALA A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA A 253 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   HIS A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 314 through 340
      removed outlier: 3.632A  pdb=" N   PHE A 318 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 389
      removed outlier: 3.589A  pdb=" N   PHE A 389 " --> pdb=" O   MET A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 395 through 425
    Processing helix  chain 'A' and resid 436 through 467
      removed outlier: 4.273A  pdb=" N   GLU A 440 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 499
    Processing helix  chain 'A' and resid 504 through 510
    Processing helix  chain 'A' and resid 513 through 535
    Processing helix  chain 'A' and resid 544 through 549
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'B' and resid 57 through 86
    Processing helix  chain 'B' and resid 93 through 119
    Processing helix  chain 'B' and resid 122 through 136
    Processing helix  chain 'B' and resid 158 through 186
    Processing helix  chain 'B' and resid 190 through 213
      removed outlier: 3.765A  pdb=" N   ILE B 194 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 268
      removed outlier: 3.890A  pdb=" N   ALA B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS B 252 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA B 253 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   HIS B 254 " --> pdb=" O   GLU B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 312
    Processing helix  chain 'B' and resid 314 through 340
      removed outlier: 3.632A  pdb=" N   PHE B 318 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 389
      removed outlier: 3.589A  pdb=" N   PHE B 389 " --> pdb=" O   MET B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 395
    Processing helix  chain 'B' and resid 395 through 425
    Processing helix  chain 'B' and resid 436 through 467
      removed outlier: 4.272A  pdb=" N   GLU B 440 " --> pdb=" O   GLU B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 499
    Processing helix  chain 'B' and resid 504 through 510
    Processing helix  chain 'B' and resid 513 through 535
    Processing helix  chain 'B' and resid 544 through 549
    Processing helix  chain 'B' and resid 563 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429
    Processing sheet with id=AA2, first strand: chain 'B' and resid 428 through 429

    614 hydrogen bonds defined for protein.
    1820 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: 2.48

  Time building geometry restraints manager: 2.31 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: 1357
        1.33 -     1.45: 2158
        1.45 -     1.57: 4401
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 7998
  Sorted by residual:
  bond pdb=" CA  SER A 396 "
       pdb=" CB  SER A 396 "
    ideal  model  delta    sigma   weight residual
    1.531  1.481  0.049 1.59e-02 3.96e+03 9.65e+00
  bond pdb=" CA  SER B 396 "
       pdb=" CB  SER B 396 "
    ideal  model  delta    sigma   weight residual
    1.531  1.481  0.049 1.59e-02 3.96e+03 9.65e+00
  bond pdb=" N   ILE B 146 "
       pdb=" CA  ILE B 146 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.12e-02 7.97e+03 9.61e+00
  bond pdb=" N   ILE A 146 "
       pdb=" CA  ILE A 146 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.12e-02 7.97e+03 9.59e+00
  bond pdb=" N   VAL B 219 "
       pdb=" CA  VAL B 219 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.89e+00
  ... (remaining 7993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 10110
        1.35 -     2.70: 551
        2.70 -     4.05: 124
        4.05 -     5.40: 25
        5.40 -     6.75: 8
  Bond angle restraints: 10818
  Sorted by residual:
  angle pdb=" CA BHIS A 567 "
        pdb=" CB BHIS A 567 "
        pdb=" CG BHIS A 567 "
      ideal   model   delta    sigma   weight residual
     113.80  107.05    6.75 1.00e+00 1.00e+00 4.56e+01
  angle pdb=" CA BHIS B 567 "
        pdb=" CB BHIS B 567 "
        pdb=" CG BHIS B 567 "
      ideal   model   delta    sigma   weight residual
     113.80  107.06    6.74 1.00e+00 1.00e+00 4.54e+01
  angle pdb=" N   LEU B 400 "
        pdb=" CA  LEU B 400 "
        pdb=" C   LEU B 400 "
      ideal   model   delta    sigma   weight residual
     111.14  106.86    4.28 1.08e+00 8.57e-01 1.57e+01
  angle pdb=" N   VAL B 437 "
        pdb=" CA  VAL B 437 "
        pdb=" C   VAL B 437 "
      ideal   model   delta    sigma   weight residual
     112.76  107.75    5.01 1.27e+00 6.20e-01 1.55e+01
  angle pdb=" N   LEU A 400 "
        pdb=" CA  LEU A 400 "
        pdb=" C   LEU A 400 "
      ideal   model   delta    sigma   weight residual
     111.14  106.88    4.26 1.08e+00 8.57e-01 1.55e+01
  ... (remaining 10813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4105
       17.85 -    35.69: 435
       35.69 -    53.53: 66
       53.53 -    71.38: 12
       71.38 -    89.22: 8
  Dihedral angle restraints: 4626
    sinusoidal: 1784
      harmonic: 2842
  Sorted by residual:
  dihedral pdb=" CD  ARG A 133 "
           pdb=" NE  ARG A 133 "
           pdb=" CZ  ARG A 133 "
           pdb=" NH1 ARG A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   65.82  -65.82     1      1.00e+01 1.00e-02 5.67e+01
  dihedral pdb=" CD  ARG B 133 "
           pdb=" NE  ARG B 133 "
           pdb=" CZ  ARG B 133 "
           pdb=" NH1 ARG B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   65.78  -65.78     1      1.00e+01 1.00e-02 5.66e+01
  dihedral pdb=" N   LEU A 306 "
           pdb=" C   LEU A 306 "
           pdb=" CA  LEU A 306 "
           pdb=" CB  LEU A 306 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  113.75    9.05     0      2.50e+00 1.60e-01 1.31e+01
  ... (remaining 4623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1064
       0.066 -    0.132: 141
       0.132 -    0.198: 35
       0.198 -    0.264: 8
       0.264 -    0.331: 4
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  LEU A 306 "
            pdb=" N   LEU A 306 "
            pdb=" C   LEU A 306 "
            pdb=" CB  LEU A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CA  LEU B 306 "
            pdb=" N   LEU B 306 "
            pdb=" C   LEU B 306 "
            pdb=" CB  LEU B 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CA  LEU B 400 "
            pdb=" N   LEU B 400 "
            pdb=" C   LEU B 400 "
            pdb=" CB  LEU B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.27 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 1249 not shown)

  Planarity restraints: 1294
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 133 "   -1.003 9.50e-02 1.11e+02   4.49e-01 1.22e+02
        pdb=" NE  ARG A 133 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 133 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 133 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 133 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 133 "   -1.002 9.50e-02 1.11e+02   4.49e-01 1.22e+02
        pdb=" NE  ARG B 133 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 133 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 133 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 133 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA BHIS B 567 "   -0.024 2.00e-02 2.50e+03   4.85e-02 2.35e+01
        pdb=" C  BHIS B 567 "    0.084 2.00e-02 2.50e+03
        pdb=" O  BHIS B 567 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   SER B 568 "   -0.029 2.00e-02 2.50e+03
  ... (remaining 1291 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 875
        2.75 -     3.28: 8130
        3.28 -     3.82: 14096
        3.82 -     4.36: 15823
        4.36 -     4.90: 27639
  Nonbonded interactions: 66563
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 512 "
            pdb=" OH  TYR B 580 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   PRO A 512 "
            pdb=" OH  TYR A 580 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ILE A  99 "
            pdb=" OG  SER A 103 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ILE B  99 "
            pdb=" OG  SER B 103 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ASP A 314 "
            pdb=" OG1 THR A 317 "
     model   vdw
     2.350 3.040
  ... (remaining 66558 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.340
  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:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     26.520
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
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      :  0.006   0.049   7998  Z= 0.364
  Angle     :  0.726   6.749  10818  Z= 0.505
  Chirality :  0.055   0.331   1252
  Planarity :  0.018   0.449   1294
  Dihedral  : 14.721  89.224   2798
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.83 (0.27), residues: 962
  helix:  2.10 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -1.70 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 338 
 HIS   0.005   0.001   HIS B 578 
 PHE   0.018   0.001   PHE B 542 
 TYR   0.017   0.002   TYR B 101 
 ARG   0.002   0.000   ARG B 565 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.7867 (t80) cc_final: 0.7575 (t80)
REVERT: A  436 GLU cc_start: 0.6713 (tp30) cc_final: 0.6420 (tp30)
REVERT: B  181 PHE cc_start: 0.7825 (t80) cc_final: 0.7568 (t80)
REVERT: B  436 GLU cc_start: 0.6691 (tp30) cc_final: 0.6418 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2292
  time to fit residues: 37.2756
Evaluate side-chains
  101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 567 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.137966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.092828 restraints weight = 23080.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.90
r_work: 0.2879 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7998  Z= 0.237
  Angle     :  0.486   7.730  10818  Z= 0.273
  Chirality :  0.040   0.231   1252
  Planarity :  0.003   0.030   1294
  Dihedral  :  3.545  14.576   1058
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.53 %
    Favored  : 92.76 %
  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:  2.49 (0.26), residues: 962
  helix:  2.57 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.39 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.012   0.001   PHE A  63 
 TYR   0.018   0.002   TYR A 101 
 ARG   0.002   0.000   ARG A 133 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8164 (t80) cc_final: 0.7851 (t80)
REVERT: B  181 PHE cc_start: 0.8129 (t80) cc_final: 0.7824 (t80)
REVERT: B  430 ARG cc_start: 0.8357 (ptt90) cc_final: 0.7851 (ptt180)
  outliers start: 6
  outliers final: 4
  residues processed: 113
  average time/residue: 0.2031
  time to fit residues: 31.1660
Evaluate side-chains
  108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  432 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 67 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.139580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.095833 restraints weight = 17111.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.55
r_work: 0.2948 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7998  Z= 0.165
  Angle     :  0.442   6.652  10818  Z= 0.250
  Chirality :  0.038   0.178   1252
  Planarity :  0.003   0.032   1294
  Dihedral  :  3.371  12.938   1058
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.67 %
    Favored  : 90.26 %
  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:  2.82 (0.26), residues: 962
  helix:  2.79 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.21 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.002   0.001   HIS A 232 
 PHE   0.010   0.001   PHE A 542 
 TYR   0.015   0.001   TYR A 101 
 ARG   0.004   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8112 (t80) cc_final: 0.7863 (t80)
REVERT: A  366 SER cc_start: 0.7841 (m) cc_final: 0.7635 (p)
REVERT: A  430 ARG cc_start: 0.8338 (ptt90) cc_final: 0.7764 (ptt180)
REVERT: A  436 GLU cc_start: 0.6933 (tp30) cc_final: 0.6709 (tp30)
REVERT: B  181 PHE cc_start: 0.8134 (t80) cc_final: 0.7873 (t80)
REVERT: B  430 ARG cc_start: 0.8309 (ptt90) cc_final: 0.7841 (ptt180)
REVERT: B  436 GLU cc_start: 0.6913 (tp30) cc_final: 0.6709 (tp30)
  outliers start: 9
  outliers final: 4
  residues processed: 111
  average time/residue: 0.2022
  time to fit residues: 31.0437
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  432 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 64 optimal weight:    0.3980
   chunk 76 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.137622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.092917 restraints weight = 23913.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.92
r_work: 0.2908 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7998  Z= 0.193
  Angle     :  0.432   4.338  10818  Z= 0.247
  Chirality :  0.038   0.157   1252
  Planarity :  0.003   0.033   1294
  Dihedral  :  3.378  14.074   1058
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.14 %
    Favored  : 89.67 %
  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:  2.81 (0.26), residues: 962
  helix:  2.77 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.16 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.002   0.001   HIS B 209 
 PHE   0.011   0.001   PHE A  63 
 TYR   0.017   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8126 (t80) cc_final: 0.7883 (t80)
REVERT: A  430 ARG cc_start: 0.8434 (ptt90) cc_final: 0.7819 (ptt180)
REVERT: A  436 GLU cc_start: 0.6937 (tp30) cc_final: 0.6727 (tp30)
REVERT: B  181 PHE cc_start: 0.8136 (t80) cc_final: 0.7916 (t80)
REVERT: B  430 ARG cc_start: 0.8391 (ptt90) cc_final: 0.7876 (ptt180)
REVERT: B  436 GLU cc_start: 0.6989 (tp30) cc_final: 0.6780 (tp30)
  outliers start: 10
  outliers final: 4
  residues processed: 107
  average time/residue: 0.2421
  time to fit residues: 36.2404
Evaluate side-chains
  104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   chunk 78 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 81 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.135723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.095119 restraints weight = 25958.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 4.12
r_work: 0.2715 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7998  Z= 0.335
  Angle     :  0.507   4.906  10818  Z= 0.286
  Chirality :  0.041   0.151   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.648  15.306   1058
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  9.98 %
    Favored  : 88.72 %
  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:  2.32 (0.26), residues: 962
  helix:  2.37 (0.18), residues: 726
  sheet:  None (None), residues: 0
  loop : -1.21 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  89 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.014   0.002   PHE A  63 
 TYR   0.022   0.002   TYR A 453 
 ARG   0.003   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8202 (t80) cc_final: 0.7964 (t80)
REVERT: A  260 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6767 (mmmt)
REVERT: A  436 GLU cc_start: 0.7088 (tp30) cc_final: 0.6795 (tp30)
REVERT: B  181 PHE cc_start: 0.8203 (t80) cc_final: 0.7960 (t80)
REVERT: B  260 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6775 (mmmt)
REVERT: B  261 GLN cc_start: 0.7265 (mm-40) cc_final: 0.7015 (mm-40)
REVERT: B  436 GLU cc_start: 0.7083 (tp30) cc_final: 0.6799 (tp30)
  outliers start: 11
  outliers final: 8
  residues processed: 111
  average time/residue: 0.2186
  time to fit residues: 32.8371
Evaluate side-chains
  110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  539 SER
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 71 optimal weight:    0.0770
   chunk 77 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0030
   overall best weight:    0.4348

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

Flipped N/Q/H residues before XYZ refinement:
B 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.140069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.097269 restraints weight = 16824.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.52
r_work: 0.2971 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7998  Z= 0.130
  Angle     :  0.408   4.681  10818  Z= 0.232
  Chirality :  0.036   0.122   1252
  Planarity :  0.003   0.034   1294
  Dihedral  :  3.342  15.344   1058
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.86 %
    Favored  : 89.19 %
  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:  3.01 (0.26), residues: 962
  helix:  2.87 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.93 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 338 
 HIS   0.002   0.001   HIS A 232 
 PHE   0.009   0.001   PHE B 493 
 TYR   0.013   0.001   TYR B 101 
 ARG   0.004   0.000   ARG B 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8110 (t80) cc_final: 0.7902 (t80)
REVERT: A  430 ARG cc_start: 0.8342 (ptt90) cc_final: 0.7785 (ptt180)
REVERT: B  261 GLN cc_start: 0.7261 (mm-40) cc_final: 0.7029 (mm-40)
REVERT: B  430 ARG cc_start: 0.8269 (ptt90) cc_final: 0.7674 (ptt180)
  outliers start: 8
  outliers final: 3
  residues processed: 109
  average time/residue: 0.2068
  time to fit residues: 30.7932
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  266 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.137751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.092502 restraints weight = 23015.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 2.86
r_work: 0.2877 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7998  Z= 0.228
  Angle     :  0.447   4.643  10818  Z= 0.253
  Chirality :  0.038   0.134   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.474  16.252   1058
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  9.74 %
    Favored  : 89.19 %
  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:  2.80 (0.26), residues: 962
  helix:  2.72 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.99 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 239 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.011   0.001   PHE A  63 
 TYR   0.018   0.001   TYR B 101 
 ARG   0.004   0.000   ARG B 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 1.063 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8141 (t80) cc_final: 0.7933 (t80)
REVERT: B  260 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6806 (mmmt)
REVERT: B  430 ARG cc_start: 0.8421 (ptt90) cc_final: 0.7804 (ptt180)
  outliers start: 9
  outliers final: 5
  residues processed: 97
  average time/residue: 0.2183
  time to fit residues: 28.8096
Evaluate side-chains
  97 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  266 TYR
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 68 optimal weight:   10.0000
   chunk 71 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.139441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.099150 restraints weight = 27309.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 4.01
r_work: 0.2816 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7998  Z= 0.161
  Angle     :  0.420   5.204  10818  Z= 0.238
  Chirality :  0.037   0.123   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.381  16.581   1058
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.69 %
    Favored  : 88.48 %
  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:  2.96 (0.26), residues: 962
  helix:  2.84 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.96 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 338 
 HIS   0.002   0.001   HIS A 209 
 PHE   0.010   0.001   PHE A  63 
 TYR   0.015   0.001   TYR A 101 
 ARG   0.004   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8169 (t80) cc_final: 0.7944 (t80)
REVERT: B  260 LYS cc_start: 0.7058 (mmtt) cc_final: 0.6724 (mmmt)
REVERT: B  430 ARG cc_start: 0.8444 (ptt90) cc_final: 0.7808 (ptt180)
REVERT: B  554 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8477 (tt)
  outliers start: 7
  outliers final: 6
  residues processed: 98
  average time/residue: 0.2147
  time to fit residues: 28.6572
Evaluate side-chains
  103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  266 TYR
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 70 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
B 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.136395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.095591 restraints weight = 25646.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 4.25
r_work: 0.2654 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   7998  Z= 0.391
  Angle     :  0.528   4.967  10818  Z= 0.296
  Chirality :  0.042   0.159   1252
  Planarity :  0.004   0.035   1294
  Dihedral  :  3.765  17.317   1058
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.33 %
    Favored  : 88.24 %
  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:  2.14 (0.26), residues: 962
  helix:  2.18 (0.18), residues: 740
  sheet:  None (None), residues: 0
  loop : -1.29 (0.37), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B  89 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.014   0.002   PHE A  63 
 TYR   0.023   0.002   TYR A 453 
 ARG   0.005   0.001   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8153 (t80) cc_final: 0.7912 (t80)
REVERT: A  260 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6762 (mmmt)
REVERT: B  260 LYS cc_start: 0.7186 (mmtt) cc_final: 0.6816 (mmmt)
REVERT: B  261 GLN cc_start: 0.7249 (mm-40) cc_final: 0.7048 (mm-40)
REVERT: B  554 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8464 (tt)
  outliers start: 12
  outliers final: 5
  residues processed: 96
  average time/residue: 0.2252
  time to fit residues: 28.8786
Evaluate side-chains
  96 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  539 SER
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0370
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.9864

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

Flipped N/Q/H residues before XYZ refinement:
A 311 HIS
B 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.138001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.100586 restraints weight = 35545.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 5.07
r_work: 0.2736 rms_B_bonded: 5.01 restraints_weight: 2.0000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2665
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7998  Z= 0.180
  Angle     :  0.436   5.206  10818  Z= 0.247
  Chirality :  0.037   0.131   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.502  17.699   1058
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.52 %
    Favored  : 87.89 %
  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:  2.59 (0.26), residues: 962
  helix:  2.55 (0.18), residues: 736
  sheet:  None (None), residues: 0
  loop : -1.24 (0.37), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 338 
 HIS   0.002   0.001   HIS B 209 
 PHE   0.010   0.001   PHE B  63 
 TYR   0.016   0.001   TYR A 101 
 ARG   0.004   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8216 (t80) cc_final: 0.8003 (t80)
REVERT: A  260 LYS cc_start: 0.7095 (mmtt) cc_final: 0.6744 (mmmt)
REVERT: B  260 LYS cc_start: 0.7048 (mmtt) cc_final: 0.6835 (mmmt)
REVERT: B  430 ARG cc_start: 0.8521 (ptt90) cc_final: 0.7892 (ptt180)
REVERT: B  554 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8470 (tt)
  outliers start: 5
  outliers final: 2
  residues processed: 93
  average time/residue: 0.2291
  time to fit residues: 28.6630
Evaluate side-chains
  91 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  554 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 89 optimal weight:    0.0670
   chunk 61 optimal weight:    0.4980
   chunk 64 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 42 optimal weight:    0.1980
   chunk 63 optimal weight:    0.6980
   chunk 79 optimal weight:    0.3980
   chunk 36 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.3118

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

Flipped N/Q/H residues before XYZ refinement:
B 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.141448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.101356 restraints weight = 25913.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 3.91
r_work: 0.2912 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7998  Z= 0.126
  Angle     :  0.403   5.505  10818  Z= 0.227
  Chirality :  0.036   0.115   1252
  Planarity :  0.003   0.034   1294
  Dihedral  :  3.321  17.126   1058
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 11.16 %
    Favored  : 88.48 %
  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:  3.01 (0.27), residues: 962
  helix:  2.83 (0.18), residues: 738
  sheet:  None (None), residues: 0
  loop : -1.07 (0.38), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 338 
 HIS   0.001   0.000   HIS B 531 
 PHE   0.009   0.001   PHE A 389 
 TYR   0.013   0.001   TYR B 101 
 ARG   0.004   0.000   ARG A 430 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4177.05 seconds
wall clock time: 74 minutes 58.47 seconds (4498.47 seconds total)