Starting phenix.real_space_refine
on Wed Sep 17 07:07:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jdb_61387/09_2025/9jdb_61387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jdb_61387/09_2025/9jdb_61387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jdb_61387/09_2025/9jdb_61387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jdb_61387/09_2025/9jdb_61387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jdb_61387/09_2025/9jdb_61387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jdb_61387/09_2025/9jdb_61387.cif"
  }
  resolution = 2.64
  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=   0.056
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
     Fe      2      7.16       5
     S      32      5.16       5
     C    4214      2.51       5
     N    1122      2.21       5
     O    1222      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6592
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3253
          Classifications: {'peptide': 404}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 374}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3253
          Classifications: {'peptide': 404}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 374}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.85, per 1000 atoms: 0.28
  Number of scatterers: 6592
  At special positions: 0
  Unit cell: (101.15, 107.95, 66.3, 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)
     Fe      2     26.01
     S      32     16.00
     O    1222      8.00
     N    1122      7.00
     C    4214      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 299.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1536

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      44.6% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 44
      removed outlier: 3.632A  pdb=" N   ARG A  44 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 79
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 138 through 147
    Processing helix  chain 'A' and resid 156 through 167
      removed outlier: 4.086A  pdb=" N   TRP A 160 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 179 through 184
      removed outlier: 4.082A  pdb=" N   MET A 184 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 249
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 309 through 314
    Processing helix  chain 'A' and resid 333 through 351
      removed outlier: 3.645A  pdb=" N   PHE A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR A 343 " --> pdb=" O   ARG A 339 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
      removed outlier: 3.571A  pdb=" N   HIS A 349 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 392
    Processing helix  chain 'A' and resid 393 through 395
      No H-bonds generated for 'chain 'A' and resid 393 through 395'
    Processing helix  chain 'A' and resid 396 through 401
      removed outlier: 3.818A  pdb=" N   SER A 400 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 421
      Proline residue:  A 410  - end of helix
      Proline residue:  A 418  - end of helix
    Processing helix  chain 'A' and resid 422 through 438
      removed outlier: 3.806A  pdb=" N   GLN A 426 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 453
    Processing helix  chain 'A' and resid 456 through 468
    Processing helix  chain 'B' and resid 33 through 44
      removed outlier: 3.627A  pdb=" N   ARG B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 79
    Processing helix  chain 'B' and resid 135 through 137
      No H-bonds generated for 'chain 'B' and resid 135 through 137'
    Processing helix  chain 'B' and resid 138 through 147
    Processing helix  chain 'B' and resid 156 through 167
      removed outlier: 4.003A  pdb=" N   TRP B 160 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 178
    Processing helix  chain 'B' and resid 179 through 184
      removed outlier: 4.106A  pdb=" N   MET B 184 " --> pdb=" O   PHE B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 249
    Processing helix  chain 'B' and resid 266 through 270
    Processing helix  chain 'B' and resid 309 through 314
    Processing helix  chain 'B' and resid 333 through 351
      removed outlier: 3.644A  pdb=" N   PHE B 341 " --> pdb=" O   GLN B 337 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
      removed outlier: 3.569A  pdb=" N   HIS B 349 " --> pdb=" O   ASP B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 392
    Processing helix  chain 'B' and resid 393 through 395
      No H-bonds generated for 'chain 'B' and resid 393 through 395'
    Processing helix  chain 'B' and resid 396 through 401
      removed outlier: 3.869A  pdb=" N   SER B 400 " --> pdb=" O   SER B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 421
      removed outlier: 4.054A  pdb=" N   TYR B 407 " --> pdb=" O   ASN B 403 " (cutoff:3.500A)
      Proline residue:  B 410  - end of helix
      Proline residue:  B 418  - end of helix
    Processing helix  chain 'B' and resid 422 through 438
      removed outlier: 3.757A  pdb=" N   GLN B 426 " --> pdb=" O   GLY B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 453
    Processing helix  chain 'B' and resid 456 through 468
    Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 330
      removed outlier: 3.831A  pdb=" N   GLY A 299 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   VAL A 259 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   CYS A 297 " --> pdb=" O   VAL A 259 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   TYR A  60 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A  61 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 328 through 330
      removed outlier: 3.823A  pdb=" N   GLY B 299 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   VAL B 259 " --> pdb=" O   CYS B 297 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   CYS B 297 " --> pdb=" O   VAL B 259 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   TYR B  60 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    792 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.00 -     1.22: 1
        1.22 -     1.43: 2999
        1.43 -     1.65: 3732
        1.65 -     1.87: 52
        1.87 -     2.08: 8
  Bond restraints: 6792
  Sorted by residual:
  bond pdb=" CB  PRO A 418 "
       pdb=" CG  PRO A 418 "
    ideal  model  delta    sigma   weight residual
    1.492  1.003  0.489 5.00e-02 4.00e+02 9.57e+01
  bond pdb=" CG  PRO A 418 "
       pdb=" CD  PRO A 418 "
    ideal  model  delta    sigma   weight residual
    1.503  1.234  0.269 3.40e-02 8.65e+02 6.28e+01
  bond pdb=" CA  PRO A 418 "
       pdb=" CB  PRO A 418 "
    ideal  model  delta    sigma   weight residual
    1.533  1.584 -0.051 1.42e-02 4.96e+03 1.28e+01
  bond pdb=" N   PRO A 418 "
       pdb=" CA  PRO A 418 "
    ideal  model  delta    sigma   weight residual
    1.469  1.509 -0.041 1.28e-02 6.10e+03 1.01e+01
  bond pdb=" N   PRO A 418 "
       pdb=" CD  PRO A 418 "
    ideal  model  delta    sigma   weight residual
    1.473  1.507 -0.034 1.40e-02 5.10e+03 5.73e+00
  ... (remaining 6787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.76: 9259
       14.76 -    29.53: 4
       29.53 -    44.29: 0
       44.29 -    59.05: 0
       59.05 -    73.82: 1
  Bond angle restraints: 9264
  Sorted by residual:
  angle pdb=" CB  PRO A 418 "
        pdb=" CG  PRO A 418 "
        pdb=" CD  PRO A 418 "
      ideal   model   delta    sigma   weight residual
     106.10  179.92  -73.82 3.20e+00 9.77e-02 5.32e+02
  angle pdb=" N   PRO A 418 "
        pdb=" CD  PRO A 418 "
        pdb=" CG  PRO A 418 "
      ideal   model   delta    sigma   weight residual
     103.20   75.83   27.37 1.50e+00 4.44e-01 3.33e+02
  angle pdb=" CA  PRO A 418 "
        pdb=" CB  PRO A 418 "
        pdb=" CG  PRO A 418 "
      ideal   model   delta    sigma   weight residual
     104.50   75.80   28.70 1.90e+00 2.77e-01 2.28e+02
  angle pdb=" CA  PRO A 418 "
        pdb=" N   PRO A 418 "
        pdb=" CD  PRO A 418 "
      ideal   model   delta    sigma   weight residual
     112.00  105.67    6.33 1.40e+00 5.10e-01 2.04e+01
  angle pdb=" CA  LYS B 305 "
        pdb=" CB  LYS B 305 "
        pdb=" CG  LYS B 305 "
      ideal   model   delta    sigma   weight residual
     114.10  120.74   -6.64 2.00e+00 2.50e-01 1.10e+01
  ... (remaining 9259 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.98: 3671
       24.98 -    49.95: 286
       49.95 -    74.93: 49
       74.93 -    99.91: 8
       99.91 -   124.88: 2
  Dihedral angle restraints: 4016
    sinusoidal: 1656
      harmonic: 2360
  Sorted by residual:
  dihedral pdb=" N   PRO A 418 "
           pdb=" CG  PRO A 418 "
           pdb=" CD  PRO A 418 "
           pdb=" CB  PRO A 418 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -154.88  124.88     1      1.50e+01 4.44e-03 6.71e+01
  dihedral pdb=" CA  PRO A 418 "
           pdb=" CB  PRO A 418 "
           pdb=" CG  PRO A 418 "
           pdb=" CD  PRO A 418 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -38.00 -144.01  106.01     1      2.00e+01 2.50e-03 3.06e+01
  dihedral pdb=" CA  THR A  94 "
           pdb=" C   THR A  94 "
           pdb=" N   ALA A  95 "
           pdb=" CA  ALA A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.87  -23.13     0      5.00e+00 4.00e-02 2.14e+01
  ... (remaining 4013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 812
       0.059 -    0.118: 139
       0.118 -    0.177: 8
       0.177 -    0.236: 0
       0.236 -    0.295: 1
  Chirality restraints: 960
  Sorted by residual:
  chirality pdb=" CG  LEU A 466 "
            pdb=" CB  LEU A 466 "
            pdb=" CD1 LEU A 466 "
            pdb=" CD2 LEU A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" CA  ILE B 293 "
            pdb=" N   ILE B 293 "
            pdb=" C   ILE B 293 "
            pdb=" CB  ILE B 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CA  ILE A  47 "
            pdb=" N   ILE A  47 "
            pdb=" C   ILE A  47 "
            pdb=" CB  ILE A  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 957 not shown)

  Planarity restraints: 1204
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 417 "    0.032 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO A 418 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 418 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 418 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 416 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.20e+00
        pdb=" C   ALA A 416 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ALA A 416 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A 417 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 128 "    0.023 5.00e-02 4.00e+02   3.54e-02 2.01e+00
        pdb=" N   PRO B 129 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1201 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1355
        2.78 -     3.31: 5531
        3.31 -     3.84: 10961
        3.84 -     4.37: 13499
        4.37 -     4.90: 22956
  Nonbonded interactions: 54302
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 217 "
            pdb=" NZ  LYS B 300 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OD2 ASP A 217 "
            pdb=" NZ  LYS A 300 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" NE2 HIS A 172 "
            pdb=" OH  TYR A 286 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" NE2 HIS B 172 "
            pdb=" OH  TYR B 286 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" OG1 THR A  94 "
            pdb=" O   VAL A 107 "
     model   vdw
     2.322 3.040
  ... (remaining 54297 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: 0.01
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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.530
  Find NCS groups from input model:        0.100
  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:6.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
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      :  0.008   0.489   6794  Z= 0.209
  Angle     :  1.097  73.817   9264  Z= 0.452
  Chirality :  0.044   0.295    960
  Planarity :  0.005   0.046   1204
  Dihedral  : 18.082 124.882   2480
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 20.06 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.30), residues: 796
  helix:  1.09 (0.32), residues: 290
  sheet:  0.04 (0.44), residues: 140
  loop : -0.86 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 419 
 TYR   0.009   0.001   TYR B 209 
 PHE   0.007   0.001   PHE A 425 
 TRP   0.011   0.001   TRP B 161 
 HIS   0.004   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00737 ( 6792)
  covalent geometry    : angle       1.09730 ( 9264)
  hydrogen bonds       : bond        0.18977 (  286)
  hydrogen bonds       : angle       6.71112 (  792)
  Misc. bond           : bond        0.09515 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.234 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 74
  average time/residue: 0.8212
  time to fit residues: 63.0029
Evaluate side-chains
  72 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  238 SER
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  315 GLU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  315 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.137245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.118436 restraints weight = 7926.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.49
r_work: 0.3331 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.0726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   6794  Z= 0.113
  Angle     :  0.588  12.062   9264  Z= 0.267
  Chirality :  0.043   0.135    960
  Planarity :  0.004   0.034   1204
  Dihedral  :  6.762  68.014    902
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 19.77 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.30), residues: 796
  helix:  1.22 (0.32), residues: 296
  sheet:  0.21 (0.41), residues: 150
  loop : -0.94 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 445 
 TYR   0.005   0.001   TYR B 449 
 PHE   0.006   0.001   PHE B 178 
 TRP   0.010   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6792)
  covalent geometry    : angle       0.58827 ( 9264)
  hydrogen bonds       : bond        0.03813 (  286)
  hydrogen bonds       : angle       4.73681 (  792)
  Misc. bond           : bond        0.07821 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  305 LYS cc_start: 0.8071 (tmtt) cc_final: 0.7857 (tptp)
  outliers start: 9
  outliers final: 6
  residues processed: 85
  average time/residue: 0.8558
  time to fit residues: 75.4146
Evaluate side-chains
  78 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  427 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0010
   chunk 18 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.138635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.119815 restraints weight = 7906.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.48
r_work: 0.3345 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.0945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6794  Z= 0.100
  Angle     :  0.557  11.229   9264  Z= 0.250
  Chirality :  0.043   0.135    960
  Planarity :  0.004   0.035   1204
  Dihedral  :  6.244  67.637    889
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.21 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.30), residues: 796
  helix:  1.46 (0.32), residues: 296
  sheet:  0.42 (0.40), residues: 150
  loop : -0.88 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 445 
 TYR   0.005   0.001   TYR B 209 
 PHE   0.007   0.001   PHE A 178 
 TRP   0.009   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6792)
  covalent geometry    : angle       0.55670 ( 9264)
  hydrogen bonds       : bond        0.03300 (  286)
  hydrogen bonds       : angle       4.39670 (  792)
  Misc. bond           : bond        0.07632 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.191 
Fit side-chains
  outliers start: 16
  outliers final: 2
  residues processed: 93
  average time/residue: 0.8200
  time to fit residues: 79.0390
Evaluate side-chains
  72 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain B residue  114 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0170
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.138600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.119827 restraints weight = 7992.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.47
r_work: 0.3343 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6794  Z= 0.103
  Angle     :  0.563  11.808   9264  Z= 0.251
  Chirality :  0.043   0.135    960
  Planarity :  0.004   0.035   1204
  Dihedral  :  6.212  67.871    888
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.64 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.30), residues: 796
  helix:  1.52 (0.32), residues: 296
  sheet:  0.68 (0.40), residues: 150
  loop : -0.86 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  90 
 TYR   0.007   0.001   TYR A 310 
 PHE   0.007   0.001   PHE B 178 
 TRP   0.009   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6792)
  covalent geometry    : angle       0.56273 ( 9264)
  hydrogen bonds       : bond        0.03292 (  286)
  hydrogen bonds       : angle       4.26684 (  792)
  Misc. bond           : bond        0.07641 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.276 
Fit side-chains
REVERT: B  429 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7888 (tp)
  outliers start: 16
  outliers final: 3
  residues processed: 88
  average time/residue: 0.8272
  time to fit residues: 75.5521
Evaluate side-chains
  71 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  429 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0270
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 52 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0870
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.140907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.121922 restraints weight = 8020.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.52
r_work: 0.3379 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.069   6794  Z= 0.090
  Angle     :  0.525   9.164   9264  Z= 0.238
  Chirality :  0.042   0.134    960
  Planarity :  0.004   0.034   1204
  Dihedral  :  5.945  67.106    888
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.35 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.30), residues: 796
  helix:  1.68 (0.32), residues: 296
  sheet:  0.84 (0.40), residues: 150
  loop : -0.79 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 419 
 TYR   0.006   0.001   TYR B 449 
 PHE   0.005   0.001   PHE A 178 
 TRP   0.008   0.001   TRP A 161 
 HIS   0.002   0.000   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 6792)
  covalent geometry    : angle       0.52522 ( 9264)
  hydrogen bonds       : bond        0.02812 (  286)
  hydrogen bonds       : angle       4.07379 (  792)
  Misc. bond           : bond        0.06848 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  249 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7028 (mtm-85)
REVERT: B  429 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7889 (tp)
  outliers start: 15
  outliers final: 3
  residues processed: 81
  average time/residue: 0.8460
  time to fit residues: 71.0654
Evaluate side-chains
  73 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  249 ARG
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  429 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.136844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.117793 restraints weight = 8044.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.50
r_work: 0.3319 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   6794  Z= 0.143
  Angle     :  0.648  15.088   9264  Z= 0.282
  Chirality :  0.045   0.134    960
  Planarity :  0.004   0.035   1204
  Dihedral  :  6.621  69.352    888
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.63 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.30), residues: 796
  helix:  1.45 (0.31), residues: 296
  sheet:  0.93 (0.41), residues: 146
  loop : -0.89 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  90 
 TYR   0.008   0.001   TYR B 209 
 PHE   0.010   0.002   PHE B 178 
 TRP   0.009   0.001   TRP B 161 
 HIS   0.004   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6792)
  covalent geometry    : angle       0.64773 ( 9264)
  hydrogen bonds       : bond        0.04088 (  286)
  hydrogen bonds       : angle       4.42755 (  792)
  Misc. bond           : bond        0.07585 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8696 (ttt) cc_final: 0.8312 (ttt)
REVERT: A  249 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7189 (mtm-85)
REVERT: A  329 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7037 (mm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 78
  average time/residue: 0.8511
  time to fit residues: 68.9670
Evaluate side-chains
  74 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  249 ARG
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  214 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0980
   chunk 54 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.137997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.119075 restraints weight = 7902.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.48
r_work: 0.3336 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6794  Z= 0.114
  Angle     :  0.598  12.359   9264  Z= 0.264
  Chirality :  0.043   0.135    960
  Planarity :  0.004   0.036   1204
  Dihedral  :  6.325  67.538    888
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 20.20 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.30), residues: 796
  helix:  1.47 (0.31), residues: 296
  sheet:  0.78 (0.40), residues: 150
  loop : -0.87 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  90 
 TYR   0.006   0.001   TYR B 209 
 PHE   0.008   0.001   PHE B  91 
 TRP   0.009   0.001   TRP A 161 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6792)
  covalent geometry    : angle       0.59833 ( 9264)
  hydrogen bonds       : bond        0.03534 (  286)
  hydrogen bonds       : angle       4.30592 (  792)
  Misc. bond           : bond        0.07715 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  249 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7132 (mtm-85)
  outliers start: 8
  outliers final: 4
  residues processed: 78
  average time/residue: 0.7820
  time to fit residues: 63.4692
Evaluate side-chains
  77 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  249 ARG
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  214 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0270
   chunk 61 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.7244

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.116414 restraints weight = 7986.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.49
r_work: 0.3300 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.0841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   6794  Z= 0.166
  Angle     :  0.693  16.192   9264  Z= 0.300
  Chirality :  0.046   0.134    960
  Planarity :  0.005   0.037   1204
  Dihedral  :  6.954  72.324    888
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 20.20 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.29), residues: 796
  helix:  1.21 (0.31), residues: 296
  sheet:  0.80 (0.40), residues: 146
  loop : -1.01 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  90 
 TYR   0.008   0.002   TYR B 209 
 PHE   0.011   0.002   PHE B 178 
 TRP   0.010   0.001   TRP A 161 
 HIS   0.004   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 6792)
  covalent geometry    : angle       0.69291 ( 9264)
  hydrogen bonds       : bond        0.04549 (  286)
  hydrogen bonds       : angle       4.57197 (  792)
  Misc. bond           : bond        0.07858 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8620 (ttp) cc_final: 0.8310 (ttt)
REVERT: A  249 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7256 (mtm-85)
REVERT: A  329 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7217 (mm-30)
  outliers start: 9
  outliers final: 1
  residues processed: 74
  average time/residue: 0.8160
  time to fit residues: 62.6756
Evaluate side-chains
  71 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 ARG
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain B residue  114 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.137591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.118595 restraints weight = 8060.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.51
r_work: 0.3334 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   6794  Z= 0.112
  Angle     :  0.602  12.029   9264  Z= 0.267
  Chirality :  0.043   0.135    960
  Planarity :  0.004   0.036   1204
  Dihedral  :  6.350  67.597    888
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 21.05 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.30), residues: 796
  helix:  1.37 (0.31), residues: 296
  sheet:  0.73 (0.40), residues: 150
  loop : -0.93 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  90 
 TYR   0.006   0.001   TYR B 209 
 PHE   0.008   0.001   PHE B  91 
 TRP   0.008   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6792)
  covalent geometry    : angle       0.60195 ( 9264)
  hydrogen bonds       : bond        0.03528 (  286)
  hydrogen bonds       : angle       4.31710 (  792)
  Misc. bond           : bond        0.07910 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  249 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7150 (mtm-85)
  outliers start: 3
  outliers final: 2
  residues processed: 78
  average time/residue: 0.8061
  time to fit residues: 65.2009
Evaluate side-chains
  74 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  249 ARG
Chi-restraints excluded: chain B residue  114 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.137545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.118545 restraints weight = 7989.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.50
r_work: 0.3335 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   6794  Z= 0.118
  Angle     :  0.623  12.942   9264  Z= 0.274
  Chirality :  0.044   0.135    960
  Planarity :  0.004   0.046   1204
  Dihedral  :  6.440  67.654    888
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 20.48 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.30), residues: 796
  helix:  1.37 (0.31), residues: 296
  sheet:  0.69 (0.40), residues: 150
  loop : -0.95 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  55 
 TYR   0.007   0.001   TYR A 209 
 PHE   0.008   0.001   PHE B  91 
 TRP   0.009   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6792)
  covalent geometry    : angle       0.62349 ( 9264)
  hydrogen bonds       : bond        0.03641 (  286)
  hydrogen bonds       : angle       4.33284 (  792)
  Misc. bond           : bond        0.07904 (    2)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  249 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7151 (mtm-85)
REVERT: A  425 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.5583 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 77
  average time/residue: 0.8464
  time to fit residues: 67.6048
Evaluate side-chains
  74 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  249 ARG
Chi-restraints excluded: chain A residue  425 PHE
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  214 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0470
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 35 optimal weight:    0.2980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5880

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.139496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.120646 restraints weight = 7939.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.48
r_work: 0.3359 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   6794  Z= 0.100
  Angle     :  0.577  10.320   9264  Z= 0.257
  Chirality :  0.043   0.135    960
  Planarity :  0.004   0.041   1204
  Dihedral  :  6.140  67.534    888
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 20.76 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.30), residues: 796
  helix:  1.50 (0.31), residues: 296
  sheet:  0.76 (0.39), residues: 150
  loop : -0.88 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  55 
 TYR   0.007   0.001   TYR A 449 
 PHE   0.007   0.001   PHE A  91 
 TRP   0.008   0.001   TRP A 161 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6792)
  covalent geometry    : angle       0.57734 ( 9264)
  hydrogen bonds       : bond        0.03137 (  286)
  hydrogen bonds       : angle       4.14954 (  792)
  Misc. bond           : bond        0.07339 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2532.40 seconds
wall clock time: 43 minutes 55.04 seconds (2635.04 seconds total)