Starting phenix.real_space_refine
on Tue Mar  3 13:43:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wh8_32497/03_2026/7wh8_32497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wh8_32497/03_2026/7wh8_32497.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wh8_32497/03_2026/7wh8_32497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wh8_32497/03_2026/7wh8_32497.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wh8_32497/03_2026/7wh8_32497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wh8_32497/03_2026/7wh8_32497.cif"
  }
  resolution = 3.11
  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=   0.002
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      23      5.16       5
     C    3462      2.51       5
     N     924      2.21       5
     O    1070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5479
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1646
          Classifications: {'peptide': 224}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211}
    Chain: "A"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1643
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201}
    Chain: "C"
      Number of atoms: 2190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2190
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 16, 'TRANS': 260}
  Time building chain proxies: 1.30, per 1000 atoms: 0.24
  Number of scatterers: 5479
  At special positions: 0
  Unit cell: (74.6572, 83.4404, 161.391, 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      23     16.00
     O    1070      8.00
     N     924      7.00
     C    3462      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 148 " - pdb=" SG  CYS B 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 134 " - pdb=" SG  CYS A 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 356.5 milliseconds
  

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1314

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 16 sheets defined
      6.0% alpha, 35.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 4.024A  pdb=" N   THR B  91 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 166
      No H-bonds generated for 'chain 'B' and resid 164 through 166'
    Processing helix  chain 'A' and resid 79 through 83
      removed outlier: 4.139A  pdb=" N   PHE A  83 " --> pdb=" O   PRO A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 364 through 370
      removed outlier: 4.351A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 387
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.984A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.762A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.761A  pdb=" N   GLY B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.967A  pdb=" N   VAL B 110 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 73
    Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 132
      removed outlier: 3.531A  pdb=" N   LYS B 151 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 188 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   TYR B 184 " --> pdb=" O   ASP B 152 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 132
      removed outlier: 3.531A  pdb=" N   LYS B 151 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 188 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   TYR B 184 " --> pdb=" O   ASP B 152 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 158 through 162
      removed outlier: 3.534A  pdb=" N   SER B 161 " --> pdb=" O   ASN B 205 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   TYR B 202 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS B 217 " --> pdb=" O   CYS B 204 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL B 215 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 4 through 7
      removed outlier: 3.689A  pdb=" N   CYS A  23 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   PHE A  71 " --> pdb=" O   CYS A  23 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP A  70 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 53 through 54
      removed outlier: 6.495A  pdb=" N   TRP A  35 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   TYR A  49 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LEU A  33 " --> pdb=" O   TYR A  49 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 118
      removed outlier: 6.018A  pdb=" N   TYR A 173 " --> pdb=" O   ASN A 138 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 154 through 155
      removed outlier: 4.437A  pdb=" N   TRP A 148 " --> pdb=" O   GLN A 155 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 328
      removed outlier: 4.104A  pdb=" N   VAL C 539 " --> pdb=" O   GLY C 550 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY C 550 " --> pdb=" O   VAL C 539 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY C 548 " --> pdb=" O   PHE C 541 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   THR C 553 " --> pdb=" O   ASP C 586 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ALA C 575 " --> pdb=" O   GLY C 566 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 354 through 357
      removed outlier: 3.536A  pdb=" N   SER C 399 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.055A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 474

    181 hydrogen bonds defined for protein.
    441 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.89

  Time building geometry restraints manager: 0.61 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: 1766
        1.34 -     1.46: 1286
        1.46 -     1.58: 2530
        1.58 -     1.70: 0
        1.70 -     1.82: 26
  Bond restraints: 5608
  Sorted by residual:
  bond pdb=" N   LEU B 101 "
       pdb=" CA  LEU B 101 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.81e+00
  bond pdb=" CA  LEU B 101 "
       pdb=" C   LEU B 101 "
    ideal  model  delta    sigma   weight residual
    1.523  1.554 -0.031 1.34e-02 5.57e+03 5.33e+00
  bond pdb=" C   VAL A  29 "
       pdb=" O   VAL A  29 "
    ideal  model  delta    sigma   weight residual
    1.238  1.221  0.016 1.06e-02 8.90e+03 2.32e+00
  bond pdb=" N   TYR A  32 "
       pdb=" CA  TYR A  32 "
    ideal  model  delta    sigma   weight residual
    1.462  1.445  0.016 1.26e-02 6.30e+03 1.70e+00
  bond pdb=" C   GLN C 493 "
       pdb=" O   GLN C 493 "
    ideal  model  delta    sigma   weight residual
    1.234  1.219  0.015 1.22e-02 6.72e+03 1.51e+00
  ... (remaining 5603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 7487
        2.31 -     4.62: 126
        4.62 -     6.93: 10
        6.93 -     9.24: 1
        9.24 -    11.55: 1
  Bond angle restraints: 7625
  Sorted by residual:
  angle pdb=" N   LEU B 101 "
        pdb=" CA  LEU B 101 "
        pdb=" C   LEU B 101 "
      ideal   model   delta    sigma   weight residual
     110.80  122.35  -11.55 2.13e+00 2.20e-01 2.94e+01
  angle pdb=" N   PHE B 103 "
        pdb=" CA  PHE B 103 "
        pdb=" C   PHE B 103 "
      ideal   model   delta    sigma   weight residual
     113.20  119.10   -5.90 1.21e+00 6.83e-01 2.38e+01
  angle pdb=" N   ASN A  93 "
        pdb=" CA  ASN A  93 "
        pdb=" C   ASN A  93 "
      ideal   model   delta    sigma   weight residual
     108.79  113.62   -4.83 1.53e+00 4.27e-01 9.96e+00
  angle pdb=" N   VAL B 119 "
        pdb=" CA  VAL B 119 "
        pdb=" C   VAL B 119 "
      ideal   model   delta    sigma   weight residual
     107.28  112.05   -4.77 1.59e+00 3.96e-01 9.01e+00
  angle pdb=" N   TYR B 106 "
        pdb=" CA  TYR B 106 "
        pdb=" C   TYR B 106 "
      ideal   model   delta    sigma   weight residual
     111.02  114.57   -3.55 1.22e+00 6.72e-01 8.48e+00
  ... (remaining 7620 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 2995
       17.35 -    34.69: 278
       34.69 -    52.04: 63
       52.04 -    69.39: 11
       69.39 -    86.74: 8
  Dihedral angle restraints: 3355
    sinusoidal: 1298
      harmonic: 2057
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.74  -72.74     1      1.00e+01 1.00e-02 6.75e+01
  dihedral pdb=" CB  CYS B 148 "
           pdb=" SG  CYS B 148 "
           pdb=" SG  CYS B 204 "
           pdb=" CB  CYS B 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.22  -64.22     1      1.00e+01 1.00e-02 5.43e+01
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -33.22  -52.78     1      1.00e+01 1.00e-02 3.79e+01
  ... (remaining 3352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 784
       0.092 -    0.184: 62
       0.184 -    0.276: 1
       0.276 -    0.368: 0
       0.368 -    0.461: 2
  Chirality restraints: 849
  Sorted by residual:
  chirality pdb=" CA  PHE B 103 "
            pdb=" N   PHE B 103 "
            pdb=" C   PHE B 103 "
            pdb=" CB  PHE B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CA  LEU B 101 "
            pdb=" N   LEU B 101 "
            pdb=" C   LEU B 101 "
            pdb=" CB  LEU B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.27e+00
  chirality pdb=" CA  ASN A  93 "
            pdb=" N   ASN A  93 "
            pdb=" C   ASN A  93 "
            pdb=" CB  ASN A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 846 not shown)

  Planarity restraints: 990
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 220 "   -0.059 5.00e-02 4.00e+02   8.81e-02 1.24e+01
        pdb=" N   PRO B 221 "    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO B 221 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 221 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 209 "   -0.046 5.00e-02 4.00e+02   6.95e-02 7.73e+00
        pdb=" N   PRO B 210 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 210 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 210 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 100 "   -0.013 2.00e-02 2.50e+03   2.53e-02 6.38e+00
        pdb=" C   GLY B 100 "    0.044 2.00e-02 2.50e+03
        pdb=" O   GLY B 100 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU B 101 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 987 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 890
        2.77 -     3.30: 4954
        3.30 -     3.83: 8526
        3.83 -     4.37: 9987
        4.37 -     4.90: 18117
  Nonbonded interactions: 42474
  Sorted by model distance:
  nonbonded pdb=" O   SER A  28 "
            pdb=" OG  SER A  28 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" CB  LEU B 132 "
            pdb=" O   GLY B 147 "
     model   vdw
     2.236 2.752
  nonbonded pdb=" O   ILE A 106 "
            pdb=" OH  TYR A 140 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   LEU A  13 "
            pdb=" N   LYS A 107 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   SER B 223 "
            pdb=" OG  SER B 223 "
     model   vdw
     2.299 3.040
  ... (remaining 42469 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.240
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.040
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5617  Z= 0.189
  Angle     :  0.711  11.555   7643  Z= 0.399
  Chirality :  0.051   0.461    849
  Planarity :  0.005   0.088    990
  Dihedral  : 14.335  86.735   2014
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.60 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  1.63 %
    Favored  : 95.75 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.32), residues: 709
  helix: -2.17 (0.88), residues: 35
  sheet: -1.35 (0.36), residues: 228
  loop : -1.42 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 142 
 TYR   0.014   0.001   TYR C 495 
 PHE   0.014   0.001   PHE C 377 
 TRP   0.010   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 5608)
  covalent geometry    : angle       0.70896 ( 7625)
  SS BOND              : bond        0.00638 (    9)
  SS BOND              : angle       1.34996 (   18)
  hydrogen bonds       : bond        0.29344 (  161)
  hydrogen bonds       : angle      11.82974 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.210 
Fit side-chains
REVERT: B   81 MET cc_start: 0.8857 (tmm) cc_final: 0.8456 (tmm)
REVERT: B  104 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8563 (pp)
REVERT: A   96 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8803 (mt)
REVERT: A  171 SER cc_start: 0.8597 (m) cc_final: 0.8307 (p)
REVERT: C  525 CYS cc_start: 0.5553 (p) cc_final: 0.5065 (p)
REVERT: C  554 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6312 (mm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0758
  time to fit residues: 9.7791
Evaluate side-chains
  81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  103 PHE
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  205 ASN
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain C residue  500 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN
B 207 ASN
A 147 GLN
C 370 ASN
C 493 GLN
C 501 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.155596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.128052 restraints weight = 7208.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.11
r_work: 0.3379 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5617  Z= 0.181
  Angle     :  0.673   7.692   7643  Z= 0.347
  Chirality :  0.047   0.152    849
  Planarity :  0.005   0.059    990
  Dihedral  :  6.507  57.850    792
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.31 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.32), residues: 709
  helix: -2.34 (0.84), residues: 35
  sheet: -0.99 (0.32), residues: 264
  loop : -1.26 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 567 
 TYR   0.012   0.002   TYR C 421 
 PHE   0.017   0.002   PHE B 103 
 TRP   0.014   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 5608)
  covalent geometry    : angle       0.67042 ( 7625)
  SS BOND              : bond        0.00658 (    9)
  SS BOND              : angle       1.29763 (   18)
  hydrogen bonds       : bond        0.04575 (  161)
  hydrogen bonds       : angle       7.30083 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B   81 MET cc_start: 0.9174 (tmm) cc_final: 0.8693 (tmm)
REVERT: B  211 SER cc_start: 0.8575 (t) cc_final: 0.8339 (p)
REVERT: A   27 GLN cc_start: 0.8246 (tt0) cc_final: 0.8033 (tt0)
REVERT: A  177 SER cc_start: 0.8949 (m) cc_final: 0.8571 (t)
REVERT: C  554 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6083 (mm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0689
  time to fit residues: 7.3833
Evaluate side-chains
  73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain C residue  320 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 2 optimal weight:    0.1980
   chunk 50 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0270
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0980
   overall best weight:    0.3238

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.157379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.127532 restraints weight = 7096.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.16
r_work: 0.3397 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5617  Z= 0.135
  Angle     :  0.610   9.387   7643  Z= 0.310
  Chirality :  0.045   0.145    849
  Planarity :  0.004   0.049    990
  Dihedral  :  5.618  59.141    776
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.42 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.32), residues: 709
  helix: -2.48 (0.78), residues: 35
  sheet: -0.65 (0.34), residues: 247
  loop : -1.27 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 567 
 TYR   0.010   0.001   TYR B  95 
 PHE   0.013   0.001   PHE B 103 
 TRP   0.011   0.001   TRP A  94 
 HIS   0.001   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5608)
  covalent geometry    : angle       0.60850 ( 7625)
  SS BOND              : bond        0.00613 (    9)
  SS BOND              : angle       1.03750 (   18)
  hydrogen bonds       : bond        0.03839 (  161)
  hydrogen bonds       : angle       6.55286 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.205 
Fit side-chains
REVERT: B   81 MET cc_start: 0.9133 (tmm) cc_final: 0.8742 (tmm)
REVERT: B  113 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8524 (pm20)
REVERT: A  181 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7977 (pp)
REVERT: C  320 VAL cc_start: 0.4366 (OUTLIER) cc_final: 0.4058 (t)
REVERT: C  554 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6238 (mm-30)
  outliers start: 12
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0728
  time to fit residues: 7.5772
Evaluate side-chains
  73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0050
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 68 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.152413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.123287 restraints weight = 7103.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.15
r_work: 0.3339 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5617  Z= 0.195
  Angle     :  0.663   7.477   7643  Z= 0.336
  Chirality :  0.047   0.149    849
  Planarity :  0.005   0.045    990
  Dihedral  :  5.725  55.334    776
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 11.76 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.32), residues: 709
  helix: -2.61 (0.77), residues: 35
  sheet: -0.58 (0.32), residues: 274
  loop : -1.24 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 567 
 TYR   0.013   0.002   TYR B  95 
 PHE   0.020   0.002   PHE B 103 
 TRP   0.011   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 5608)
  covalent geometry    : angle       0.66040 ( 7625)
  SS BOND              : bond        0.00682 (    9)
  SS BOND              : angle       1.39351 (   18)
  hydrogen bonds       : bond        0.03873 (  161)
  hydrogen bonds       : angle       6.35605 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.229 
Fit side-chains
REVERT: B   10 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8058 (mt-10)
REVERT: B   81 MET cc_start: 0.9169 (tmm) cc_final: 0.8673 (tmm)
REVERT: B  113 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8691 (pt0)
REVERT: C  498 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7762 (mm110)
REVERT: C  554 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6312 (mm-30)
REVERT: C  592 PHE cc_start: 0.3616 (p90) cc_final: 0.2864 (p90)
  outliers start: 19
  outliers final: 12
  residues processed: 75
  average time/residue: 0.0658
  time to fit residues: 6.8704
Evaluate side-chains
  73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  539 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0170
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.150691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.121493 restraints weight = 7211.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.21
r_work: 0.3306 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5617  Z= 0.205
  Angle     :  0.676  10.744   7643  Z= 0.340
  Chirality :  0.047   0.146    849
  Planarity :  0.005   0.042    990
  Dihedral  :  5.704  50.765    775
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 11.76 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.32), residues: 709
  helix: -2.54 (0.78), residues: 35
  sheet: -0.51 (0.32), residues: 274
  loop : -1.22 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.013   0.002   TYR B  95 
 PHE   0.018   0.002   PHE B 103 
 TRP   0.012   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 5608)
  covalent geometry    : angle       0.67370 ( 7625)
  SS BOND              : bond        0.00643 (    9)
  SS BOND              : angle       1.32343 (   18)
  hydrogen bonds       : bond        0.03852 (  161)
  hydrogen bonds       : angle       6.26961 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.253 
Fit side-chains
REVERT: B   10 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8007 (mt-10)
REVERT: B   81 MET cc_start: 0.9169 (tmm) cc_final: 0.8696 (tmm)
REVERT: B  113 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8735 (pt0)
REVERT: A   33 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8792 (tp)
REVERT: C  592 PHE cc_start: 0.3541 (p90) cc_final: 0.2834 (p90)
  outliers start: 21
  outliers final: 13
  residues processed: 80
  average time/residue: 0.0631
  time to fit residues: 6.9904
Evaluate side-chains
  76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain C residue  421 TYR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  539 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0870
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.150839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.121852 restraints weight = 7109.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.19
r_work: 0.3314 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5617  Z= 0.191
  Angle     :  0.669   9.444   7643  Z= 0.334
  Chirality :  0.047   0.143    849
  Planarity :  0.004   0.040    990
  Dihedral  :  5.653  46.677    775
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.58 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.32), residues: 709
  helix: -2.58 (0.78), residues: 35
  sheet: -0.42 (0.33), residues: 272
  loop : -1.20 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.012   0.002   TYR B  95 
 PHE   0.017   0.002   PHE B 103 
 TRP   0.011   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 5608)
  covalent geometry    : angle       0.66450 ( 7625)
  SS BOND              : bond        0.00623 (    9)
  SS BOND              : angle       1.71751 (   18)
  hydrogen bonds       : bond        0.03706 (  161)
  hydrogen bonds       : angle       6.15916 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.199 
Fit side-chains
REVERT: B   81 MET cc_start: 0.9150 (tmm) cc_final: 0.8689 (tmm)
REVERT: B  113 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8756 (pt0)
REVERT: A   33 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8793 (tp)
REVERT: C  390 LEU cc_start: 0.7342 (mt) cc_final: 0.7141 (mt)
REVERT: C  554 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6712 (pt0)
  outliers start: 19
  outliers final: 14
  residues processed: 74
  average time/residue: 0.0668
  time to fit residues: 6.7873
Evaluate side-chains
  73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain C residue  421 TYR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  539 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0030
   chunk 33 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0670
   chunk 10 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.3728

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN
A 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.153497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.124269 restraints weight = 7184.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.20
r_work: 0.3343 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5617  Z= 0.141
  Angle     :  0.613   8.022   7643  Z= 0.307
  Chirality :  0.045   0.143    849
  Planarity :  0.004   0.039    990
  Dihedral  :  5.237  40.644    775
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.91 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.32), residues: 709
  helix: -2.63 (0.76), residues: 35
  sheet: -0.34 (0.33), residues: 261
  loop : -1.16 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.010   0.001   TYR B  95 
 PHE   0.012   0.001   PHE B 103 
 TRP   0.009   0.001   TRP A  94 
 HIS   0.002   0.000   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5608)
  covalent geometry    : angle       0.60961 ( 7625)
  SS BOND              : bond        0.00537 (    9)
  SS BOND              : angle       1.37135 (   18)
  hydrogen bonds       : bond        0.03383 (  161)
  hydrogen bonds       : angle       5.94989 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.211 
Fit side-chains
REVERT: B   81 MET cc_start: 0.9137 (tmm) cc_final: 0.8750 (tmm)
REVERT: B  113 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8623 (pt0)
REVERT: A   33 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8813 (tp)
REVERT: C  418 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8390 (tt)
REVERT: C  554 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6710 (pt0)
  outliers start: 19
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0690
  time to fit residues: 7.0375
Evaluate side-chains
  73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  421 TYR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  539 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   chunk 45 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0270
   chunk 2 optimal weight:    0.2980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN
** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.152840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.123856 restraints weight = 7064.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.16
r_work: 0.3339 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5617  Z= 0.148
  Angle     :  0.634  12.694   7643  Z= 0.313
  Chirality :  0.045   0.143    849
  Planarity :  0.004   0.039    990
  Dihedral  :  5.147  40.633    774
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.05 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.32), residues: 709
  helix: -2.59 (0.78), residues: 35
  sheet: -0.31 (0.33), residues: 261
  loop : -1.12 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  18 
 TYR   0.011   0.001   TYR B  95 
 PHE   0.014   0.001   PHE B 103 
 TRP   0.010   0.001   TRP A  94 
 HIS   0.002   0.000   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 5608)
  covalent geometry    : angle       0.63133 ( 7625)
  SS BOND              : bond        0.00618 (    9)
  SS BOND              : angle       1.27138 (   18)
  hydrogen bonds       : bond        0.03397 (  161)
  hydrogen bonds       : angle       5.88831 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.229 
Fit side-chains
REVERT: B   81 MET cc_start: 0.9142 (tmm) cc_final: 0.8726 (tmm)
REVERT: B  113 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8651 (pt0)
REVERT: A   33 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8766 (tp)
REVERT: A   82 ASP cc_start: 0.8794 (m-30) cc_final: 0.8536 (m-30)
REVERT: A  143 GLU cc_start: 0.8342 (tp30) cc_final: 0.8101 (mp0)
REVERT: C  418 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8405 (tt)
REVERT: C  554 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6636 (pt0)
  outliers start: 17
  outliers final: 13
  residues processed: 72
  average time/residue: 0.0659
  time to fit residues: 6.5483
Evaluate side-chains
  71 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  421 TYR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  539 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 22 optimal weight:    0.0170
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.151313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.122128 restraints weight = 7148.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.22
r_work: 0.3313 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5617  Z= 0.182
  Angle     :  0.668  13.176   7643  Z= 0.330
  Chirality :  0.046   0.143    849
  Planarity :  0.004   0.038    990
  Dihedral  :  5.331  40.654    774
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.89 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.32), residues: 709
  helix: -2.53 (0.81), residues: 34
  sheet: -0.32 (0.33), residues: 261
  loop : -1.15 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  18 
 TYR   0.012   0.002   TYR B  95 
 PHE   0.017   0.002   PHE B 103 
 TRP   0.010   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 5608)
  covalent geometry    : angle       0.66508 ( 7625)
  SS BOND              : bond        0.00606 (    9)
  SS BOND              : angle       1.36957 (   18)
  hydrogen bonds       : bond        0.03547 (  161)
  hydrogen bonds       : angle       6.01091 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.246 
Fit side-chains
REVERT: B   81 MET cc_start: 0.9154 (tmm) cc_final: 0.8693 (tmm)
REVERT: B  113 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8749 (pt0)
REVERT: A   33 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8801 (tp)
REVERT: A  143 GLU cc_start: 0.8329 (tp30) cc_final: 0.8103 (mp0)
REVERT: C  418 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8334 (tt)
REVERT: C  554 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6653 (pt0)
  outliers start: 20
  outliers final: 14
  residues processed: 73
  average time/residue: 0.0656
  time to fit residues: 6.6545
Evaluate side-chains
  73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  421 TYR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  539 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 67 optimal weight:    0.0050
   chunk 8 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
B  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.123339 restraints weight = 7135.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.19
r_work: 0.3313 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5617  Z= 0.181
  Angle     :  0.664  13.129   7643  Z= 0.328
  Chirality :  0.046   0.141    849
  Planarity :  0.004   0.038    990
  Dihedral  :  5.333  41.297    774
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.54 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.32), residues: 709
  helix: -2.55 (0.81), residues: 34
  sheet: -0.27 (0.33), residues: 261
  loop : -1.16 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  18 
 TYR   0.012   0.001   TYR B  95 
 PHE   0.015   0.002   PHE B 103 
 TRP   0.009   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 5608)
  covalent geometry    : angle       0.66159 ( 7625)
  SS BOND              : bond        0.00613 (    9)
  SS BOND              : angle       1.32490 (   18)
  hydrogen bonds       : bond        0.03471 (  161)
  hydrogen bonds       : angle       5.98915 (  441)

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

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

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1418 Ramachandran restraints generated.
    709 Oldfield, 0 Emsley, 709 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.194 
Fit side-chains
REVERT: B   81 MET cc_start: 0.9159 (tmm) cc_final: 0.8722 (tmm)
REVERT: B  113 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8739 (pt0)
REVERT: A   33 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8808 (tp)
REVERT: A  143 GLU cc_start: 0.8319 (tp30) cc_final: 0.8105 (mp0)
REVERT: C  418 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8360 (tt)
REVERT: C  554 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6729 (pt0)
  outliers start: 17
  outliers final: 13
  residues processed: 71
  average time/residue: 0.0680
  time to fit residues: 6.6185
Evaluate side-chains
  72 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  113 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  421 TYR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  539 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0870
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 56 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0020
   overall best weight:    0.3566

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.124413 restraints weight = 7124.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.22
r_work: 0.3344 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5617  Z= 0.137
  Angle     :  0.615  12.503   7643  Z= 0.304
  Chirality :  0.045   0.142    849
  Planarity :  0.004   0.037    990
  Dihedral  :  5.095  42.336    774
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.54 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.32), residues: 709
  helix: -2.52 (0.81), residues: 34
  sheet: -0.19 (0.34), residues: 261
  loop : -1.10 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  18 
 TYR   0.010   0.001   TYR C 453 
 PHE   0.011   0.001   PHE B 103 
 TRP   0.009   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5608)
  covalent geometry    : angle       0.61361 ( 7625)
  SS BOND              : bond        0.00579 (    9)
  SS BOND              : angle       1.10895 (   18)
  hydrogen bonds       : bond        0.03222 (  161)
  hydrogen bonds       : angle       5.82262 (  441)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1734.60 seconds
wall clock time: 30 minutes 18.73 seconds (1818.73 seconds total)