Starting phenix.real_space_refine
on Mon Jun  9 10:45:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s9d_24933/06_2025/7s9d_24933.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s9d_24933/06_2025/7s9d_24933.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s9d_24933/06_2025/7s9d_24933.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s9d_24933/06_2025/7s9d_24933.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s9d_24933/06_2025/7s9d_24933.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s9d_24933/06_2025/7s9d_24933.cif"
  }
  resolution = 4.6
  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=   0.003
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      50      5.16       5
     C    6860      2.51       5
     N    1682      2.21       5
     O    1870      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10462
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 677, 5231
          Classifications: {'peptide': 677}
          Link IDs: {'PTRANS': 33, 'TRANS': 643}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.91, per 1000 atoms: 0.95
  Number of scatterers: 10462
  At special positions: 0
  Unit cell: (115.867, 111.615, 112.678, 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      50     16.00
     O    1870      8.00
     N    1682      7.00
     C    6860      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: 2.95
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2500

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 2 sheets defined
      61.9% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 32
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 77 through 105
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 108 through 126
      removed outlier: 4.176A  pdb=" N   GLY A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 137 through 151
      removed outlier: 3.612A  pdb=" N   SER A 141 " --> pdb=" O   PHE A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 196
    Processing helix  chain 'A' and resid 199 through 205
      removed outlier: 4.124A  pdb=" N   LEU A 205 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 228
      removed outlier: 3.718A  pdb=" N   VAL A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
      removed outlier: 3.541A  pdb=" N   ASN A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 282
      removed outlier: 3.867A  pdb=" N   PHE A 282 " --> pdb=" O   PHE A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 306
      removed outlier: 3.790A  pdb=" N   VAL A 297 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 363
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 398 through 406
    Processing helix  chain 'A' and resid 411 through 428
    Processing helix  chain 'A' and resid 429 through 433
      removed outlier: 3.563A  pdb=" N   PHE A 432 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 453
    Processing helix  chain 'A' and resid 457 through 465
    Processing helix  chain 'A' and resid 465 through 482
      removed outlier: 3.759A  pdb=" N   LEU A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 503
    Processing helix  chain 'A' and resid 549 through 561
    Processing helix  chain 'A' and resid 563 through 581
      removed outlier: 3.514A  pdb=" N   LYS A 580 " --> pdb=" O   LYS A 576 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU A 581 " --> pdb=" O   LYS A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 681 through 690
    Processing helix  chain 'A' and resid 698 through 700
      No H-bonds generated for 'chain 'A' and resid 698 through 700'
    Processing helix  chain 'A' and resid 705 through 721
    Processing helix  chain 'B' and resid 25 through 32
    Processing helix  chain 'B' and resid 53 through 65
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 77 through 105
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 4.177A  pdb=" N   GLY B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 137 through 151
      removed outlier: 3.611A  pdb=" N   SER B 141 " --> pdb=" O   PHE B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 196
    Processing helix  chain 'B' and resid 199 through 205
      removed outlier: 4.125A  pdb=" N   LEU B 205 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 228
      removed outlier: 3.716A  pdb=" N   VAL B 210 " --> pdb=" O   THR B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
      removed outlier: 3.542A  pdb=" N   ASN B 253 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 282
      removed outlier: 3.868A  pdb=" N   PHE B 282 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 306
      removed outlier: 3.791A  pdb=" N   VAL B 297 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 363
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 398 through 406
    Processing helix  chain 'B' and resid 411 through 428
    Processing helix  chain 'B' and resid 429 through 433
      removed outlier: 3.564A  pdb=" N   PHE B 432 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 453
    Processing helix  chain 'B' and resid 457 through 465
    Processing helix  chain 'B' and resid 465 through 482
      removed outlier: 3.759A  pdb=" N   LEU B 469 " --> pdb=" O   SER B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 503
    Processing helix  chain 'B' and resid 549 through 561
    Processing helix  chain 'B' and resid 563 through 581
      removed outlier: 3.514A  pdb=" N   LYS B 580 " --> pdb=" O   LYS B 576 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU B 581 " --> pdb=" O   LYS B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 681 through 690
    Processing helix  chain 'B' and resid 698 through 700
      No H-bonds generated for 'chain 'B' and resid 698 through 700'
    Processing helix  chain 'B' and resid 705 through 721
    Processing sheet with id=AA1, first strand: chain 'A' and resid 535 through 539
      removed outlier: 6.230A  pdb=" N   ILE A 642 " --> pdb=" O   TYR A 675 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   ALA A 677 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   LEU A 644 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
      removed outlier: 8.435A  pdb=" N   PHE A 703 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   LEU A 676 " --> pdb=" O   PHE A 703 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 535 through 539
      removed outlier: 6.230A  pdb=" N   ILE B 642 " --> pdb=" O   TYR B 675 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   ALA B 677 " --> pdb=" O   ILE B 642 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU B 644 " --> pdb=" O   ALA B 677 " (cutoff:3.500A)
      removed outlier: 8.436A  pdb=" N   PHE B 703 " --> pdb=" O   VAL B 674 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LEU B 676 " --> pdb=" O   PHE B 703 " (cutoff:3.500A)

    602 hydrogen bonds defined for protein.
    1788 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: 3.12

  Time building geometry restraints manager: 3.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3240
        1.34 -     1.46: 2515
        1.46 -     1.58: 4861
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 10698
  Sorted by residual:
  bond pdb=" CA  SER B 400 "
       pdb=" CB  SER B 400 "
    ideal  model  delta    sigma   weight residual
    1.528  1.478  0.050 1.56e-02 4.11e+03 1.05e+01
  bond pdb=" CA  SER A 400 "
       pdb=" CB  SER A 400 "
    ideal  model  delta    sigma   weight residual
    1.528  1.478  0.050 1.56e-02 4.11e+03 1.04e+01
  bond pdb=" N   PHE A 137 "
       pdb=" CA  PHE A 137 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.19e-02 7.06e+03 7.05e+00
  bond pdb=" N   PHE B 137 "
       pdb=" CA  PHE B 137 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.19e-02 7.06e+03 6.96e+00
  bond pdb=" N   VAL A 139 "
       pdb=" CA  VAL A 139 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.24e-02 6.50e+03 5.42e+00
  ... (remaining 10693 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 14339
        2.94 -     5.88: 185
        5.88 -     8.82: 10
        8.82 -    11.76: 4
       11.76 -    14.70: 2
  Bond angle restraints: 14540
  Sorted by residual:
  angle pdb=" N   LEU B 397 "
        pdb=" CA  LEU B 397 "
        pdb=" C   LEU B 397 "
      ideal   model   delta    sigma   weight residual
     113.88  106.31    7.57 1.23e+00 6.61e-01 3.78e+01
  angle pdb=" N   LEU A 397 "
        pdb=" CA  LEU A 397 "
        pdb=" C   LEU A 397 "
      ideal   model   delta    sigma   weight residual
     113.88  106.33    7.55 1.23e+00 6.61e-01 3.77e+01
  angle pdb=" C   PHE A  23 "
        pdb=" N   SER A  24 "
        pdb=" CA  SER A  24 "
      ideal   model   delta    sigma   weight residual
     121.54  112.05    9.49 1.91e+00 2.74e-01 2.47e+01
  angle pdb=" C   PHE B  23 "
        pdb=" N   SER B  24 "
        pdb=" CA  SER B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  112.05    9.49 1.91e+00 2.74e-01 2.47e+01
  angle pdb=" CB  MET B 180 "
        pdb=" CG  MET B 180 "
        pdb=" SD  MET B 180 "
      ideal   model   delta    sigma   weight residual
     112.70   98.00   14.70 3.00e+00 1.11e-01 2.40e+01
  ... (remaining 14535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.57: 5572
       12.57 -    25.14: 582
       25.14 -    37.71: 148
       37.71 -    50.28: 30
       50.28 -    62.84: 6
  Dihedral angle restraints: 6338
    sinusoidal: 2432
      harmonic: 3906
  Sorted by residual:
  dihedral pdb=" CA  SER A  24 "
           pdb=" C   SER A  24 "
           pdb=" N   HIS A  25 "
           pdb=" CA  HIS A  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.95   28.05     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  SER B  24 "
           pdb=" C   SER B  24 "
           pdb=" N   HIS B  25 "
           pdb=" CA  HIS B  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.06   27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  TYR A 616 "
           pdb=" C   TYR A 616 "
           pdb=" N   PRO A 617 "
           pdb=" CA  PRO A 617 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 6335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1079
       0.039 -    0.077: 462
       0.077 -    0.115: 155
       0.115 -    0.154: 20
       0.154 -    0.192: 10
  Chirality restraints: 1726
  Sorted by residual:
  chirality pdb=" CA  LEU A 397 "
            pdb=" N   LEU A 397 "
            pdb=" C   LEU A 397 "
            pdb=" CB  LEU A 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.26e-01
  chirality pdb=" CA  LEU B 397 "
            pdb=" N   LEU B 397 "
            pdb=" C   LEU B 397 "
            pdb=" CB  LEU B 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.13e-01
  chirality pdb=" CG  LEU A  28 "
            pdb=" CB  LEU A  28 "
            pdb=" CD1 LEU A  28 "
            pdb=" CD2 LEU A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 1723 not shown)

  Planarity restraints: 1812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 136 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.39e+00
        pdb=" C   PRO A 136 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   PRO A 136 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A 137 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 136 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   PRO B 136 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PRO B 136 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE B 137 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 394 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.66e+00
        pdb=" C   SER A 394 "    0.028 2.00e-02 2.50e+03
        pdb=" O   SER A 394 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   CYS A 395 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1809 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 282
        2.66 -     3.22: 11872
        3.22 -     3.78: 17632
        3.78 -     4.34: 22681
        4.34 -     4.90: 34822
  Nonbonded interactions: 87289
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 227 "
            pdb=" OG1 THR A 234 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" NZ  LYS B 227 "
            pdb=" OG1 THR B 234 "
     model   vdw
     2.096 3.120
  nonbonded pdb=" O   THR A 234 "
            pdb=" NH1 ARG A 236 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" O   THR B 234 "
            pdb=" NH1 ARG B 236 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" O   PHE A 460 "
            pdb=" OG1 THR A 464 "
     model   vdw
     2.103 3.040
  ... (remaining 87284 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     29.560
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
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   0.051  10698  Z= 0.336
  Angle     :  0.888  14.704  14540  Z= 0.522
  Chirality :  0.047   0.192   1726
  Planarity :  0.005   0.039   1812
  Dihedral  : 11.266  62.844   3838
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 23.20
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 10.70 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.96 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.95 (0.23), residues: 1346
  helix:  0.66 (0.18), residues: 828
  sheet:  1.65 (0.83), residues: 38
  loop : -3.27 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP B 472 
 HIS   0.016   0.003   HIS A  25 
 PHE   0.016   0.002   PHE A 213 
 TYR   0.013   0.002   TYR B 118 
 ARG   0.007   0.001   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12419 (  602)
  hydrogen bonds       : angle       5.98100 ( 1788)
  covalent geometry    : bond        0.00639 (10698)
  covalent geometry    : angle       0.88785 (14540)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.560 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 32
  average time/residue: 0.1505
  time to fit residues: 7.0135
Evaluate side-chains
  26 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    7.9990
   chunk 101 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 105 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 63 optimal weight:    0.3980
   chunk 78 optimal weight:    0.0270
   chunk 121 optimal weight:    0.6980
   overall best weight:    1.5440
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 447 ASN
A 650 ASN
A 689 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.050869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.040049 restraints weight = 45633.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.040973 restraints weight = 27549.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.041759 restraints weight = 19646.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10698  Z= 0.136
  Angle     :  0.609   8.675  14540  Z= 0.312
  Chirality :  0.044   0.167   1726
  Planarity :  0.004   0.054   1812
  Dihedral  :  4.585  29.882   1448
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.17 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  6.26 %
    Favored  : 93.57 %
  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: -0.46 (0.23), residues: 1346
  helix:  1.08 (0.18), residues: 830
  sheet:  2.51 (0.79), residues: 36
  loop : -3.19 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 472 
 HIS   0.007   0.002   HIS A  25 
 PHE   0.013   0.001   PHE A  23 
 TYR   0.011   0.001   TYR B 123 
 ARG   0.010   0.001   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  602)
  hydrogen bonds       : angle       4.55909 ( 1788)
  covalent geometry    : bond        0.00297 (10698)
  covalent geometry    : angle       0.60894 (14540)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 MET cc_start: 0.8726 (tpt) cc_final: 0.8172 (tpp)
REVERT: A  575 MET cc_start: 0.9237 (mmt) cc_final: 0.8874 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1196
  time to fit residues: 6.9486
Evaluate side-chains
  26 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 117 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0670
   chunk 103 optimal weight:    4.9990
   chunk 73 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 108 optimal weight:   20.0000
   chunk 111 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7318
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.052204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.041279 restraints weight = 45286.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.042322 restraints weight = 27134.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.043044 restraints weight = 18968.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10698  Z= 0.118
  Angle     :  0.584   8.878  14540  Z= 0.292
  Chirality :  0.043   0.170   1726
  Planarity :  0.004   0.027   1812
  Dihedral  :  4.334  22.539   1448
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.69 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.23), residues: 1346
  helix:  1.25 (0.18), residues: 830
  sheet:  2.92 (0.81), residues: 36
  loop : -3.05 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 472 
 HIS   0.017   0.002   HIS B  25 
 PHE   0.017   0.001   PHE B 213 
 TYR   0.007   0.001   TYR A 486 
 ARG   0.005   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  602)
  hydrogen bonds       : angle       4.21390 ( 1788)
  covalent geometry    : bond        0.00255 (10698)
  covalent geometry    : angle       0.58429 (14540)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: B  126 PHE cc_start: 0.8970 (m-80) cc_final: 0.8728 (m-80)
REVERT: B  225 MET cc_start: 0.9125 (mmp) cc_final: 0.8899 (mmp)
REVERT: B  299 MET cc_start: 0.5844 (tpt) cc_final: 0.5516 (tpp)
REVERT: B  357 MET cc_start: 0.8763 (tpt) cc_final: 0.8102 (tpp)
REVERT: B  575 MET cc_start: 0.9264 (mmt) cc_final: 0.9045 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1163
  time to fit residues: 7.6270
Evaluate side-chains
  30 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 103 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 95 optimal weight:    6.9990
   chunk 120 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0770
   chunk 2 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    2.7542
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.051460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.040527 restraints weight = 45603.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.041557 restraints weight = 27604.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.042237 restraints weight = 19280.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10698  Z= 0.132
  Angle     :  0.551   6.311  14540  Z= 0.276
  Chirality :  0.041   0.154   1726
  Planarity :  0.003   0.023   1812
  Dihedral  :  4.052  17.163   1448
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.92 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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: -0.71 (0.22), residues: 1346
  helix:  0.83 (0.17), residues: 834
  sheet:  2.84 (0.83), residues: 36
  loop : -3.26 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 472 
 HIS   0.009   0.002   HIS A  25 
 PHE   0.008   0.001   PHE B 391 
 TYR   0.006   0.001   TYR B 546 
 ARG   0.004   0.000   ARG A 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03470 (  602)
  hydrogen bonds       : angle       4.12643 ( 1788)
  covalent geometry    : bond        0.00286 (10698)
  covalent geometry    : angle       0.55068 (14540)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.643 
Fit side-chains
REVERT: B   93 LEU cc_start: 0.9331 (mm) cc_final: 0.8861 (pp)
REVERT: B  126 PHE cc_start: 0.8954 (m-80) cc_final: 0.8713 (m-80)
REVERT: B  225 MET cc_start: 0.9107 (mmp) cc_final: 0.8878 (mmp)
REVERT: B  357 MET cc_start: 0.8982 (tpp) cc_final: 0.8351 (tpp)
REVERT: B  400 SER cc_start: 0.7971 (t) cc_final: 0.7530 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1222
  time to fit residues: 7.7151
Evaluate side-chains
  32 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 32 optimal weight:    0.1980
   chunk 58 optimal weight:    5.9990
   chunk 65 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 92 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0470
   chunk 16 optimal weight:    8.9990
   chunk 94 optimal weight:    0.0020
   chunk 26 optimal weight:    0.0980
   chunk 27 optimal weight:    0.0020
   overall best weight:    0.0694
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 HIS
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.053078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.042021 restraints weight = 43643.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.043108 restraints weight = 26086.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.043890 restraints weight = 18134.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10698  Z= 0.110
  Angle     :  0.563   6.377  14540  Z= 0.272
  Chirality :  0.042   0.168   1726
  Planarity :  0.003   0.025   1812
  Dihedral  :  3.979  17.090   1448
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.58 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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: -0.74 (0.22), residues: 1346
  helix:  0.74 (0.17), residues: 834
  sheet:  2.99 (0.80), residues: 36
  loop : -3.14 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B 472 
 HIS   0.006   0.001   HIS B  25 
 PHE   0.020   0.001   PHE B 213 
 TYR   0.006   0.001   TYR A 546 
 ARG   0.005   0.000   ARG B 716 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 (  602)
  hydrogen bonds       : angle       4.03612 ( 1788)
  covalent geometry    : bond        0.00239 (10698)
  covalent geometry    : angle       0.56278 (14540)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9301 (mm) cc_final: 0.8788 (pp)
REVERT: B  126 PHE cc_start: 0.8990 (m-80) cc_final: 0.8744 (m-80)
REVERT: B  225 MET cc_start: 0.9115 (mmp) cc_final: 0.8839 (mmp)
REVERT: B  299 MET cc_start: 0.5784 (tpt) cc_final: 0.5456 (tpp)
REVERT: B  357 MET cc_start: 0.8939 (tpp) cc_final: 0.8277 (tpp)
REVERT: B  652 MET cc_start: 0.8560 (tpt) cc_final: 0.8356 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1169
  time to fit residues: 7.5632
Evaluate side-chains
  30 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 124 optimal weight:   20.0000
   chunk 67 optimal weight:   10.0000
   chunk 123 optimal weight:    9.9990
   chunk 129 optimal weight:    0.0470
   chunk 34 optimal weight:    9.9990
   chunk 107 optimal weight:    0.8980
   chunk 87 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 115 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    3.9884
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.051284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.040402 restraints weight = 45980.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.041435 restraints weight = 27956.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.042106 restraints weight = 19580.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10698  Z= 0.165
  Angle     :  0.567   5.843  14540  Z= 0.288
  Chirality :  0.042   0.146   1726
  Planarity :  0.004   0.027   1812
  Dihedral  :  3.984  17.810   1448
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.92 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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: -0.71 (0.22), residues: 1346
  helix:  0.82 (0.18), residues: 834
  sheet:  2.45 (0.77), residues: 36
  loop : -3.22 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 472 
 HIS   0.008   0.002   HIS B 220 
 PHE   0.018   0.001   PHE B 213 
 TYR   0.011   0.001   TYR A 228 
 ARG   0.003   0.001   ARG B 716 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03357 (  602)
  hydrogen bonds       : angle       4.14464 ( 1788)
  covalent geometry    : bond        0.00349 (10698)
  covalent geometry    : angle       0.56730 (14540)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9343 (mm) cc_final: 0.8824 (pp)
REVERT: B  126 PHE cc_start: 0.8956 (m-80) cc_final: 0.8699 (m-80)
REVERT: B  225 MET cc_start: 0.9136 (mmp) cc_final: 0.8886 (mmp)
REVERT: B  357 MET cc_start: 0.8928 (tpp) cc_final: 0.8335 (tpp)
REVERT: B  575 MET cc_start: 0.9182 (mmt) cc_final: 0.8741 (mmm)
REVERT: B  652 MET cc_start: 0.8851 (tpt) cc_final: 0.8592 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1652
  time to fit residues: 10.4049
Evaluate side-chains
  28 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 99 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 120 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0370
   chunk 102 optimal weight:   10.0000
   chunk 125 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   overall best weight:    1.9864
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 HIS
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.051688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.040777 restraints weight = 44214.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.041826 restraints weight = 26614.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.042577 restraints weight = 18609.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10698  Z= 0.112
  Angle     :  0.542   5.812  14540  Z= 0.268
  Chirality :  0.042   0.153   1726
  Planarity :  0.003   0.023   1812
  Dihedral  :  3.921  17.241   1448
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.02 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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: -0.66 (0.23), residues: 1346
  helix:  0.87 (0.18), residues: 834
  sheet:  2.41 (0.78), residues: 36
  loop : -3.20 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 472 
 HIS   0.006   0.001   HIS A  25 
 PHE   0.009   0.001   PHE B 391 
 TYR   0.007   0.001   TYR B 228 
 ARG   0.002   0.000   ARG B 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03218 (  602)
  hydrogen bonds       : angle       4.04258 ( 1788)
  covalent geometry    : bond        0.00248 (10698)
  covalent geometry    : angle       0.54196 (14540)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9366 (mm) cc_final: 0.8828 (pp)
REVERT: B  126 PHE cc_start: 0.8964 (m-80) cc_final: 0.8690 (m-80)
REVERT: B  225 MET cc_start: 0.9031 (mmp) cc_final: 0.8806 (mmp)
REVERT: B  357 MET cc_start: 0.8924 (tpp) cc_final: 0.8324 (tpp)
REVERT: B  575 MET cc_start: 0.9227 (mmt) cc_final: 0.8842 (mmm)
REVERT: B  652 MET cc_start: 0.8823 (tpt) cc_final: 0.8525 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1828
  time to fit residues: 10.9688
Evaluate side-chains
  28 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 114 optimal weight:    0.0870
   chunk 113 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0040
   chunk 92 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    1.3174
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.052339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.041535 restraints weight = 45102.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.042586 restraints weight = 27339.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.043305 restraints weight = 19164.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10698  Z= 0.105
  Angle     :  0.545   6.251  14540  Z= 0.267
  Chirality :  0.042   0.159   1726
  Planarity :  0.003   0.026   1812
  Dihedral  :  3.866  17.622   1448
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.02 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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: -0.68 (0.22), residues: 1346
  helix:  0.82 (0.18), residues: 836
  sheet:  2.40 (0.82), residues: 36
  loop : -3.14 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 472 
 HIS   0.005   0.001   HIS B 220 
 PHE   0.018   0.001   PHE A 213 
 TYR   0.006   0.001   TYR B 546 
 ARG   0.002   0.000   ARG B 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03128 (  602)
  hydrogen bonds       : angle       4.07107 ( 1788)
  covalent geometry    : bond        0.00233 (10698)
  covalent geometry    : angle       0.54503 (14540)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9349 (mm) cc_final: 0.8806 (pp)
REVERT: B  126 PHE cc_start: 0.8992 (m-80) cc_final: 0.8721 (m-80)
REVERT: B  225 MET cc_start: 0.9002 (mmp) cc_final: 0.8770 (mmp)
REVERT: B  299 MET cc_start: 0.5997 (tpt) cc_final: 0.5574 (tpp)
REVERT: B  357 MET cc_start: 0.8896 (tpp) cc_final: 0.8304 (tpp)
REVERT: B  453 MET cc_start: 0.6872 (mtt) cc_final: 0.6494 (mtp)
REVERT: B  575 MET cc_start: 0.9225 (mmt) cc_final: 0.8824 (mmm)
REVERT: B  652 MET cc_start: 0.8789 (tpt) cc_final: 0.8471 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1751
  time to fit residues: 10.5747
Evaluate side-chains
  27 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0070
   chunk 103 optimal weight:    0.1980
   chunk 80 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.5998
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.053113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.042456 restraints weight = 45105.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.043481 restraints weight = 27160.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.044222 restraints weight = 19072.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10698  Z= 0.100
  Angle     :  0.555   6.583  14540  Z= 0.266
  Chirality :  0.042   0.161   1726
  Planarity :  0.003   0.025   1812
  Dihedral  :  3.802  17.372   1448
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.02 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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: -0.61 (0.23), residues: 1346
  helix:  0.83 (0.18), residues: 836
  sheet:  2.36 (0.84), residues: 36
  loop : -3.01 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 472 
 HIS   0.004   0.001   HIS A  25 
 PHE   0.010   0.001   PHE B  23 
 TYR   0.005   0.001   TYR A  17 
 ARG   0.002   0.000   ARG B 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03032 (  602)
  hydrogen bonds       : angle       3.96809 ( 1788)
  covalent geometry    : bond        0.00223 (10698)
  covalent geometry    : angle       0.55488 (14540)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 PHE cc_start: 0.8978 (m-80) cc_final: 0.8709 (m-80)
REVERT: A  225 MET cc_start: 0.9058 (mmp) cc_final: 0.8758 (mmp)
REVERT: A  299 MET cc_start: 0.6004 (tpt) cc_final: 0.5620 (tpp)
REVERT: A  357 MET cc_start: 0.8892 (tpp) cc_final: 0.8306 (tpp)
REVERT: A  453 MET cc_start: 0.6787 (mtt) cc_final: 0.6356 (mtp)
REVERT: A  652 MET cc_start: 0.8732 (tpt) cc_final: 0.8382 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1226
  time to fit residues: 7.8284
Evaluate side-chains
  29 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0040
   chunk 63 optimal weight:    0.0980
   chunk 2 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0370
   chunk 127 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0470
   chunk 21 optimal weight:    0.0270
   chunk 119 optimal weight:    0.3980
   chunk 103 optimal weight:   10.0000
   overall best weight:    0.0426
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.053979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.043246 restraints weight = 44894.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.044322 restraints weight = 27291.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.045076 restraints weight = 19147.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10698  Z= 0.104
  Angle     :  0.574   8.252  14540  Z= 0.274
  Chirality :  0.042   0.170   1726
  Planarity :  0.003   0.028   1812
  Dihedral  :  3.748  17.071   1448
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.43 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  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: -0.80 (0.22), residues: 1346
  helix:  0.60 (0.17), residues: 840
  sheet:  2.35 (0.87), residues: 36
  loop : -2.97 (0.25), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 472 
 HIS   0.012   0.001   HIS B 220 
 PHE   0.020   0.001   PHE A 213 
 TYR   0.008   0.001   TYR B 546 
 ARG   0.002   0.000   ARG B 399 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03041 (  602)
  hydrogen bonds       : angle       3.99348 ( 1788)
  covalent geometry    : bond        0.00226 (10698)
  covalent geometry    : angle       0.57406 (14540)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.745 
Fit side-chains
REVERT: B  126 PHE cc_start: 0.9013 (m-80) cc_final: 0.8709 (m-80)
REVERT: B  225 MET cc_start: 0.9067 (mmp) cc_final: 0.8698 (mmp)
REVERT: B  299 MET cc_start: 0.6088 (tpt) cc_final: 0.5730 (tpp)
REVERT: B  357 MET cc_start: 0.8881 (tpp) cc_final: 0.8200 (tpp)
REVERT: B  453 MET cc_start: 0.6904 (mtt) cc_final: 0.6526 (mtp)
REVERT: B  575 MET cc_start: 0.9220 (mmp) cc_final: 0.8879 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1972
  time to fit residues: 13.1507
Evaluate side-chains
  29 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 51 optimal weight:    0.0070
   chunk 16 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0040
   chunk 1 optimal weight:    7.9990
   chunk 127 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 124 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0040
   overall best weight:    1.2026
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.053680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.043198 restraints weight = 46300.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.044218 restraints weight = 28953.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.044964 restraints weight = 20606.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10698  Z= 0.107
  Angle     :  0.578   7.578  14540  Z= 0.280
  Chirality :  0.042   0.162   1726
  Planarity :  0.004   0.068   1812
  Dihedral  :  3.818  17.231   1448
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.88 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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: -0.68 (0.22), residues: 1346
  helix:  0.73 (0.18), residues: 840
  sheet:  2.48 (0.91), residues: 36
  loop : -2.98 (0.25), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 472 
 HIS   0.003   0.001   HIS B  25 
 PHE   0.008   0.001   PHE A 651 
 TYR   0.008   0.001   TYR B 501 
 ARG   0.011   0.001   ARG A 502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03003 (  602)
  hydrogen bonds       : angle       3.93408 ( 1788)
  covalent geometry    : bond        0.00241 (10698)
  covalent geometry    : angle       0.57812 (14540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2668.03 seconds
wall clock time: 48 minutes 56.33 seconds (2936.33 seconds total)