Starting phenix.real_space_refine
on Fri Aug 22 14:49:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5ms1_3562/08_2025/5ms1_3562.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5ms1_3562/08_2025/5ms1_3562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5ms1_3562/08_2025/5ms1_3562.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5ms1_3562/08_2025/5ms1_3562.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5ms1_3562/08_2025/5ms1_3562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5ms1_3562/08_2025/5ms1_3562.map"
  }
  resolution = 4.25
  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=   0.001 sd=   0.028
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      30      5.16       5
     C    2774      2.51       5
     N     732      2.21       5
     O     814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4350
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1501
          Classifications: {'peptide': 189}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 170}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2849
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 14, 'TRANS': 352}
  Time building chain proxies: 1.13, per 1000 atoms: 0.26
  Number of scatterers: 4350
  At special positions: 0
  Unit cell: (89.1, 85.8, 91.3, 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      30     16.00
     O     814      8.00
     N     732      7.00
     C    2774      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: 0.27
  Conformation dependent library (CDL) restraints added in 156.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1034

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 9 sheets defined
      12.9% alpha, 46.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 61
    Processing helix  chain 'A' and resid 82 through 86
    Processing helix  chain 'A' and resid 137 through 141
    Processing helix  chain 'B' and resid 4 through 8
    Processing helix  chain 'B' and resid 48 through 52
    Processing helix  chain 'B' and resid 58 through 63
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 137 through 145
    Processing helix  chain 'B' and resid 230 through 237
    Processing helix  chain 'B' and resid 277 through 281
    Processing helix  chain 'B' and resid 300 through 304
    Processing helix  chain 'B' and resid 317 through 321
      removed outlier: 3.522A  pdb=" N   ASP B 321 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51
      removed outlier: 6.226A  pdb=" N   MET A 163 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51
      removed outlier: 6.226A  pdb=" N   MET A 163 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ALA A  63 " --> pdb=" O   ASN A 174 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASN A 174 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41
      removed outlier: 3.734A  pdb=" N   ARG A 106 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181
    Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32
      removed outlier: 6.017A  pdb=" N   LYS B  24 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ILE B 172 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46
      removed outlier: 5.691A  pdb=" N   VAL B  41 " --> pdb=" O   CYS B 152 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   CYS B 152 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   CYS B  87 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASP B 111 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202
      removed outlier: 7.015A  pdb=" N   CYS B 187 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   CYS B 355 " --> pdb=" O   CYS B 187 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ASN B 189 " --> pdb=" O   ASP B 353 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LYS B 347 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   MET B 197 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 9.575A  pdb=" N   GLY B 345 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   LYS B 199 " --> pdb=" O   ASN B 343 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   ASN B 343 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   THR B 251 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LEU B 348 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   GLU B 249 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   PHE B 354 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ARG B 243 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY B 356 " --> pdb=" O   TYR B 241 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 241 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202
      removed outlier: 7.015A  pdb=" N   CYS B 187 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   CYS B 355 " --> pdb=" O   CYS B 187 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ASN B 189 " --> pdb=" O   ASP B 353 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LYS B 347 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   MET B 197 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 9.575A  pdb=" N   GLY B 345 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   LYS B 199 " --> pdb=" O   ASN B 343 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   ASN B 343 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   THR B 251 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LEU B 348 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   GLU B 249 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   PHE B 354 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ARG B 243 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY B 356 " --> pdb=" O   TYR B 241 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 241 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214

    179 hydrogen bonds defined for protein.
    447 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: 0.60

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1009
        1.32 -     1.45: 1181
        1.45 -     1.57: 2226
        1.57 -     1.69: 0
        1.69 -     1.82: 47
  Bond restraints: 4463
  Sorted by residual:
  bond pdb=" N   PRO B 282 "
       pdb=" CA  PRO B 282 "
    ideal  model  delta    sigma   weight residual
    1.467  1.415  0.052 1.21e-02 6.83e+03 1.83e+01
  bond pdb=" N   PRO A 181 "
       pdb=" CA  PRO A 181 "
    ideal  model  delta    sigma   weight residual
    1.466  1.418  0.048 1.19e-02 7.06e+03 1.59e+01
  bond pdb=" N   PRO A  41 "
       pdb=" CA  PRO A  41 "
    ideal  model  delta    sigma   weight residual
    1.466  1.420  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" N   PRO A  13 "
       pdb=" CA  PRO A  13 "
    ideal  model  delta    sigma   weight residual
    1.467  1.421  0.046 1.21e-02 6.83e+03 1.44e+01
  bond pdb=" N   PRO B 214 "
       pdb=" CA  PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.467  1.423  0.044 1.21e-02 6.83e+03 1.34e+01
  ... (remaining 4458 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 4935
        1.69 -     3.37: 873
        3.37 -     5.06: 177
        5.06 -     6.74: 69
        6.74 -     8.43: 20
  Bond angle restraints: 6074
  Sorted by residual:
  angle pdb=" CA  ARG A  77 "
        pdb=" C   ARG A  77 "
        pdb=" O   ARG A  77 "
      ideal   model   delta    sigma   weight residual
     120.71  113.89    6.82 1.06e+00 8.90e-01 4.15e+01
  angle pdb=" C   PRO A  20 "
        pdb=" N   PRO A  21 "
        pdb=" CA  PRO A  21 "
      ideal   model   delta    sigma   weight residual
     120.03  126.37   -6.34 9.90e-01 1.02e+00 4.10e+01
  angle pdb=" C   GLY A 126 "
        pdb=" N   PRO A 127 "
        pdb=" CA  PRO A 127 "
      ideal   model   delta    sigma   weight residual
     119.64  125.65   -6.01 1.01e+00 9.80e-01 3.54e+01
  angle pdb=" C   PRO A  54 "
        pdb=" N   PRO A  55 "
        pdb=" CA  PRO A  55 "
      ideal   model   delta    sigma   weight residual
     119.32  125.73   -6.41 1.14e+00 7.69e-01 3.17e+01
  angle pdb=" C   THR A  19 "
        pdb=" N   PRO A  20 "
        pdb=" CA  PRO A  20 "
      ideal   model   delta    sigma   weight residual
     119.66  123.52   -3.86 7.30e-01 1.88e+00 2.79e+01
  ... (remaining 6069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 2555
       16.74 -    33.48: 41
       33.48 -    50.22: 15
       50.22 -    66.96: 9
       66.96 -    83.70: 4
  Dihedral angle restraints: 2624
    sinusoidal: 1022
      harmonic: 1602
  Sorted by residual:
  dihedral pdb=" CA  ARG A  77 "
           pdb=" C   ARG A  77 "
           pdb=" N   GLY A  78 "
           pdb=" CA  GLY A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   37.92  -37.92     0      5.00e+00 4.00e-02 5.75e+01
  dihedral pdb=" CG  ARG A 154 "
           pdb=" CD  ARG A 154 "
           pdb=" NE  ARG A 154 "
           pdb=" CZ  ARG A 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -130.34   40.34     2      1.50e+01 4.44e-03 8.94e+00
  dihedral pdb=" CA  ASP A 166 "
           pdb=" CB  ASP A 166 "
           pdb=" CG  ASP A 166 "
           pdb=" OD1 ASP A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.90   50.90     1      2.00e+01 2.50e-03 8.86e+00
  ... (remaining 2621 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 410
       0.058 -    0.117: 199
       0.117 -    0.175: 51
       0.175 -    0.234: 12
       0.234 -    0.292: 1
  Chirality restraints: 673
  Sorted by residual:
  chirality pdb=" CA  MET B 231 "
            pdb=" N   MET B 231 "
            pdb=" C   MET B 231 "
            pdb=" CB  MET B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CA  SER B 309 "
            pdb=" N   SER B 309 "
            pdb=" C   SER B 309 "
            pdb=" CB  SER B 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  LEU B 184 "
            pdb=" N   LEU B 184 "
            pdb=" C   LEU B 184 "
            pdb=" CB  LEU B 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.74e-01
  ... (remaining 670 not shown)

  Planarity restraints: 782
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  77 "    0.059 2.00e-02 2.50e+03   1.20e-01 1.43e+02
        pdb=" C   ARG A  77 "   -0.207 2.00e-02 2.50e+03
        pdb=" O   ARG A  77 "    0.077 2.00e-02 2.50e+03
        pdb=" N   GLY A  78 "    0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  47 "   -0.036 2.00e-02 2.50e+03   1.74e-02 7.60e+00
        pdb=" CG  TRP A  47 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  47 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  47 "    0.018 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  47 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  47 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  47 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  47 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  47 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 130 "    0.036 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO B 131 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 131 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 131 "    0.031 5.00e-02 4.00e+02
  ... (remaining 779 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 1966
        2.91 -     3.41: 3911
        3.41 -     3.91: 7317
        3.91 -     4.40: 8459
        4.40 -     4.90: 13903
  Nonbonded interactions: 35556
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 279 "
            pdb=" OE1 GLU B 279 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" OG  SER B 366 "
            pdb=" N   ARG B 367 "
     model   vdw
     2.438 3.120
  nonbonded pdb=" O   SER A 183 "
            pdb=" OG1 THR A 184 "
     model   vdw
     2.439 3.040
  nonbonded pdb=" N   GLU A 101 "
            pdb=" OE1 GLU A 101 "
     model   vdw
     2.442 3.120
  nonbonded pdb=" OG1 THR B 224 "
            pdb=" N   GLN B 225 "
     model   vdw
     2.474 3.120
  ... (remaining 35551 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 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:             7.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.060
  Find NCS groups from input model:        0.010
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
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      :  0.014   0.058   4463  Z= 0.874
  Angle     :  1.510   8.431   6074  Z= 1.007
  Chirality :  0.071   0.292    673
  Planarity :  0.008   0.120    782
  Dihedral  :  9.301  83.699   1590
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  :  5.45 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.34), residues: 550
  helix: -3.05 (0.45), residues: 53
  sheet:  1.15 (0.36), residues: 192
  loop : -1.24 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 367 
 TYR   0.021   0.005   TYR B 278 
 PHE   0.026   0.004   PHE B 125 
 TRP   0.036   0.006   TRP A  47 
 HIS   0.004   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01393 ( 4463)
  covalent geometry    : angle       1.51007 ( 6074)
  hydrogen bonds       : bond        0.16741 (  155)
  hydrogen bonds       : angle       7.71303 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   20 PRO cc_start: 0.9118 (Cg_exo) cc_final: 0.8803 (Cg_endo)
REVERT: A   39 ILE cc_start: 0.8932 (mt) cc_final: 0.8721 (mt)
REVERT: A   49 THR cc_start: 0.9359 (p) cc_final: 0.9003 (t)
REVERT: A   75 ASN cc_start: 0.7730 (m-40) cc_final: 0.7431 (m-40)
REVERT: A   82 LYS cc_start: 0.8103 (mttt) cc_final: 0.7096 (mmmt)
REVERT: A  113 PRO cc_start: 0.8812 (Cg_exo) cc_final: 0.8540 (Cg_endo)
REVERT: A  195 ARG cc_start: 0.5271 (mtm-85) cc_final: 0.5049 (mtt180)
REVERT: B   31 LEU cc_start: 0.8037 (tp) cc_final: 0.7695 (tt)
REVERT: B   87 CYS cc_start: 0.8880 (t) cc_final: 0.8182 (t)
REVERT: B  111 ASP cc_start: 0.8767 (m-30) cc_final: 0.8260 (m-30)
REVERT: B  116 ASN cc_start: 0.8548 (t0) cc_final: 0.8107 (t0)
REVERT: B  134 ASP cc_start: 0.7940 (p0) cc_final: 0.7696 (p0)
REVERT: B  152 CYS cc_start: 0.7941 (t) cc_final: 0.7079 (t)
REVERT: B  153 VAL cc_start: 0.8200 (t) cc_final: 0.7910 (t)
REVERT: B  259 LYS cc_start: 0.8547 (mttt) cc_final: 0.6947 (pttp)
REVERT: B  261 THR cc_start: 0.8227 (m) cc_final: 0.7930 (p)
REVERT: B  351 ILE cc_start: 0.7416 (mt) cc_final: 0.7107 (mt)
REVERT: B  353 ASP cc_start: 0.8361 (t0) cc_final: 0.8037 (t0)
REVERT: B  360 ASN cc_start: 0.9000 (t0) cc_final: 0.8683 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0748
  time to fit residues: 15.8267
Evaluate side-chains
  100 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 119 ASN
A 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.110267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.096438 restraints weight = 6385.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.098115 restraints weight = 4662.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.099255 restraints weight = 3669.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.100182 restraints weight = 3088.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.100675 restraints weight = 2720.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4463  Z= 0.133
  Angle     :  0.619   7.334   6074  Z= 0.334
  Chirality :  0.047   0.171    673
  Planarity :  0.005   0.044    782
  Dihedral  :  4.686  20.319    594
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.82 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.34), residues: 550
  helix: -1.60 (0.69), residues: 48
  sheet:  1.18 (0.38), residues: 183
  loop : -0.67 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  61 
 TYR   0.008   0.001   TYR B 278 
 PHE   0.016   0.002   PHE B 275 
 TRP   0.032   0.002   TRP A  47 
 HIS   0.001   0.000   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4463)
  covalent geometry    : angle       0.61912 ( 6074)
  hydrogen bonds       : bond        0.04208 (  155)
  hydrogen bonds       : angle       5.93624 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ILE cc_start: 0.9062 (mt) cc_final: 0.8859 (mt)
REVERT: A   49 THR cc_start: 0.9237 (p) cc_final: 0.8870 (t)
REVERT: A   82 LYS cc_start: 0.8183 (mttt) cc_final: 0.7468 (mmmt)
REVERT: B  102 THR cc_start: 0.8759 (p) cc_final: 0.8536 (p)
REVERT: B  111 ASP cc_start: 0.8708 (m-30) cc_final: 0.8442 (m-30)
REVERT: B  132 CYS cc_start: 0.9143 (p) cc_final: 0.8564 (p)
REVERT: B  239 TRP cc_start: 0.8921 (m-90) cc_final: 0.8389 (m100)
REVERT: B  259 LYS cc_start: 0.8230 (mttt) cc_final: 0.7204 (pttp)
REVERT: B  326 LEU cc_start: 0.9162 (tt) cc_final: 0.8797 (tt)
REVERT: B  351 ILE cc_start: 0.8069 (mt) cc_final: 0.7608 (mt)
REVERT: B  360 ASN cc_start: 0.8774 (t0) cc_final: 0.8513 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0453
  time to fit residues: 8.6523
Evaluate side-chains
  100 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0770
   chunk 38 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0270
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   overall best weight:    2.6200

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
B 287 GLN
B 302 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.103506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.095139 restraints weight = 6500.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.095945 restraints weight = 5155.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.096619 restraints weight = 4325.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.096764 restraints weight = 3765.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.096962 restraints weight = 3567.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4463  Z= 0.202
  Angle     :  0.661   6.888   6074  Z= 0.353
  Chirality :  0.047   0.155    673
  Planarity :  0.005   0.048    782
  Dihedral  :  4.696  16.920    594
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.27 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.35), residues: 550
  helix: -1.36 (0.69), residues: 47
  sheet:  0.87 (0.39), residues: 188
  loop : -0.65 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 106 
 TYR   0.023   0.002   TYR B 241 
 PHE   0.017   0.002   PHE B 202 
 TRP   0.011   0.002   TRP B 115 
 HIS   0.004   0.002   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 4463)
  covalent geometry    : angle       0.66071 ( 6074)
  hydrogen bonds       : bond        0.04486 (  155)
  hydrogen bonds       : angle       5.47795 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8274 (mttt) cc_final: 0.7752 (mmmt)
REVERT: B   92 ILE cc_start: 0.9715 (mm) cc_final: 0.9468 (mt)
REVERT: B  102 THR cc_start: 0.8679 (p) cc_final: 0.8417 (t)
REVERT: B  132 CYS cc_start: 0.9342 (p) cc_final: 0.8990 (p)
REVERT: B  137 SER cc_start: 0.9280 (p) cc_final: 0.9077 (p)
REVERT: B  152 CYS cc_start: 0.7073 (t) cc_final: 0.5428 (t)
REVERT: B  181 ILE cc_start: 0.9450 (mt) cc_final: 0.9230 (pt)
REVERT: B  259 LYS cc_start: 0.8346 (mttt) cc_final: 0.7481 (pttp)
REVERT: B  271 LEU cc_start: 0.8945 (tp) cc_final: 0.8641 (tt)
REVERT: B  279 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8132 (mm-30)
REVERT: B  360 ASN cc_start: 0.9321 (t0) cc_final: 0.8919 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0506
  time to fit residues: 7.7066
Evaluate side-chains
  89 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 10 optimal weight:    0.3980
   chunk 7 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0470
   chunk 2 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    3.6884

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

Flipped N/Q/H residues before XYZ refinement:
B 128 ASN
B 302 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.101079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.089831 restraints weight = 6730.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.090983 restraints weight = 5215.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.091742 restraints weight = 4279.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.092475 restraints weight = 3728.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.092475 restraints weight = 3343.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   4463  Z= 0.243
  Angle     :  0.678   8.217   6074  Z= 0.358
  Chirality :  0.048   0.153    673
  Planarity :  0.005   0.042    782
  Dihedral  :  4.746  20.640    594
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.73 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.29 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.35), residues: 550
  helix: -1.63 (0.62), residues: 54
  sheet:  0.71 (0.39), residues: 188
  loop : -0.83 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 367 
 TYR   0.025   0.002   TYR B 278 
 PHE   0.024   0.003   PHE A 165 
 TRP   0.011   0.002   TRP B 170 
 HIS   0.004   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 4463)
  covalent geometry    : angle       0.67792 ( 6074)
  hydrogen bonds       : bond        0.04294 (  155)
  hydrogen bonds       : angle       5.45200 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8550 (mttt) cc_final: 0.8149 (mmmt)
REVERT: A  118 LEU cc_start: 0.9199 (tt) cc_final: 0.8996 (tt)
REVERT: A  166 ASP cc_start: 0.8676 (t70) cc_final: 0.8185 (t70)
REVERT: B  110 GLN cc_start: 0.8623 (tt0) cc_final: 0.8412 (tm-30)
REVERT: B  116 ASN cc_start: 0.9090 (t0) cc_final: 0.8812 (t0)
REVERT: B  132 CYS cc_start: 0.9220 (p) cc_final: 0.8890 (p)
REVERT: B  134 ASP cc_start: 0.7627 (p0) cc_final: 0.7352 (p0)
REVERT: B  152 CYS cc_start: 0.7454 (t) cc_final: 0.5899 (t)
REVERT: B  206 VAL cc_start: 0.8585 (m) cc_final: 0.8325 (p)
REVERT: B  259 LYS cc_start: 0.8679 (mttt) cc_final: 0.7567 (pttp)
REVERT: B  271 LEU cc_start: 0.9004 (tp) cc_final: 0.8617 (tt)
REVERT: B  298 VAL cc_start: 0.9347 (t) cc_final: 0.9123 (m)
REVERT: B  321 ASP cc_start: 0.9036 (t0) cc_final: 0.8818 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0530
  time to fit residues: 8.4093
Evaluate side-chains
  87 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
** B 130 ASN ** 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 = 0.3055 r_free = 0.3055 target = 0.105732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.093814 restraints weight = 6768.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.095009 restraints weight = 5184.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.095918 restraints weight = 4254.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.096686 restraints weight = 3674.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.096943 restraints weight = 3277.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.5806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4463  Z= 0.140
  Angle     :  0.583   5.451   6074  Z= 0.309
  Chirality :  0.046   0.147    673
  Planarity :  0.004   0.046    782
  Dihedral  :  4.462  18.794    594
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.09 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.35), residues: 550
  helix: -1.39 (0.66), residues: 53
  sheet:  0.87 (0.39), residues: 189
  loop : -0.81 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 367 
 TYR   0.031   0.002   TYR B 278 
 PHE   0.020   0.002   PHE B 123 
 TRP   0.013   0.001   TRP B 115 
 HIS   0.002   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4463)
  covalent geometry    : angle       0.58253 ( 6074)
  hydrogen bonds       : bond        0.03921 (  155)
  hydrogen bonds       : angle       5.34522 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8612 (mttt) cc_final: 0.8231 (mmmt)
REVERT: A  166 ASP cc_start: 0.8550 (t70) cc_final: 0.8204 (t70)
REVERT: B  132 CYS cc_start: 0.9268 (p) cc_final: 0.8819 (p)
REVERT: B  152 CYS cc_start: 0.7547 (t) cc_final: 0.5850 (t)
REVERT: B  206 VAL cc_start: 0.8626 (m) cc_final: 0.8333 (p)
REVERT: B  259 LYS cc_start: 0.8746 (mttt) cc_final: 0.7569 (pttp)
REVERT: B  271 LEU cc_start: 0.9085 (tp) cc_final: 0.8420 (tt)
REVERT: B  298 VAL cc_start: 0.9296 (t) cc_final: 0.9082 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0547
  time to fit residues: 7.1224
Evaluate side-chains
  79 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 49 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
** B 130 ASN ** 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 = 0.3060 r_free = 0.3060 target = 0.106264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.094478 restraints weight = 6931.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.095468 restraints weight = 5216.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.096585 restraints weight = 4358.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.097200 restraints weight = 3753.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.097406 restraints weight = 3351.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.6094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4463  Z= 0.154
  Angle     :  0.585   6.771   6074  Z= 0.304
  Chirality :  0.046   0.145    673
  Planarity :  0.004   0.050    782
  Dihedral  :  4.341  19.400    594
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.73 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.35), residues: 550
  helix: -1.17 (0.74), residues: 48
  sheet:  0.96 (0.39), residues: 187
  loop : -0.79 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  61 
 TYR   0.007   0.001   TYR B 278 
 PHE   0.017   0.002   PHE B  62 
 TRP   0.012   0.001   TRP B 115 
 HIS   0.002   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4463)
  covalent geometry    : angle       0.58509 ( 6074)
  hydrogen bonds       : bond        0.03724 (  155)
  hydrogen bonds       : angle       5.23590 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9018 (m100) cc_final: 0.8637 (m100)
REVERT: A   48 ASN cc_start: 0.8575 (t0) cc_final: 0.8238 (t0)
REVERT: A   57 MET cc_start: 0.8956 (mmm) cc_final: 0.8705 (mmt)
REVERT: A   82 LYS cc_start: 0.8672 (mttt) cc_final: 0.8328 (mmmt)
REVERT: A  128 ASN cc_start: 0.8914 (t0) cc_final: 0.8531 (t0)
REVERT: A  152 ASN cc_start: 0.9079 (t0) cc_final: 0.8740 (t0)
REVERT: A  166 ASP cc_start: 0.8559 (t70) cc_final: 0.8246 (t70)
REVERT: B  132 CYS cc_start: 0.9256 (p) cc_final: 0.8698 (p)
REVERT: B  134 ASP cc_start: 0.7546 (p0) cc_final: 0.7310 (p0)
REVERT: B  152 CYS cc_start: 0.7757 (t) cc_final: 0.6446 (t)
REVERT: B  206 VAL cc_start: 0.8694 (m) cc_final: 0.8425 (p)
REVERT: B  259 LYS cc_start: 0.8798 (mttt) cc_final: 0.7558 (pttp)
REVERT: B  271 LEU cc_start: 0.9078 (tp) cc_final: 0.8687 (tt)
REVERT: B  298 VAL cc_start: 0.9325 (t) cc_final: 0.9078 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0506
  time to fit residues: 7.5471
Evaluate side-chains
  83 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 46 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 19 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0070
   chunk 53 optimal weight:   10.0000
   overall best weight:    5.0006

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
** A 162 ASN ** 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 = 0.2967 r_free = 0.2967 target = 0.099742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.086774 restraints weight = 6942.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.088428 restraints weight = 4963.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.089556 restraints weight = 3869.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.090300 restraints weight = 3216.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.090633 restraints weight = 2825.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.6578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.063   4463  Z= 0.306
  Angle     :  0.715   7.212   6074  Z= 0.376
  Chirality :  0.049   0.152    673
  Planarity :  0.005   0.055    782
  Dihedral  :  4.899  20.380    594
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.35), residues: 550
  helix: -1.34 (0.69), residues: 53
  sheet:  0.79 (0.40), residues: 188
  loop : -1.01 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 106 
 TYR   0.027   0.002   TYR B 278 
 PHE   0.022   0.003   PHE B 202 
 TRP   0.021   0.002   TRP B 115 
 HIS   0.004   0.001   HIS A  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00705 ( 4463)
  covalent geometry    : angle       0.71514 ( 6074)
  hydrogen bonds       : bond        0.04643 (  155)
  hydrogen bonds       : angle       5.42718 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8855 (mttt) cc_final: 0.8348 (mmmt)
REVERT: B   36 MET cc_start: 0.8565 (ptt) cc_final: 0.8245 (ptt)
REVERT: B   82 ASP cc_start: 0.8609 (m-30) cc_final: 0.8342 (m-30)
REVERT: B   89 MET cc_start: 0.8707 (ttp) cc_final: 0.8428 (ptm)
REVERT: B  132 CYS cc_start: 0.9170 (p) cc_final: 0.8738 (p)
REVERT: B  152 CYS cc_start: 0.8072 (t) cc_final: 0.7470 (t)
REVERT: B  204 GLN cc_start: 0.8583 (mt0) cc_final: 0.8363 (mm110)
REVERT: B  206 VAL cc_start: 0.8916 (m) cc_final: 0.8544 (p)
REVERT: B  298 VAL cc_start: 0.9388 (t) cc_final: 0.9165 (m)
REVERT: B  321 ASP cc_start: 0.9107 (t70) cc_final: 0.8816 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0567
  time to fit residues: 7.4207
Evaluate side-chains
  74 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
A 162 ASN
B  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.103542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.090603 restraints weight = 6822.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.092242 restraints weight = 4772.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.093483 restraints weight = 3678.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.094256 restraints weight = 3027.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.094898 restraints weight = 2643.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.6757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4463  Z= 0.168
  Angle     :  0.620   8.496   6074  Z= 0.324
  Chirality :  0.046   0.147    673
  Planarity :  0.005   0.054    782
  Dihedral  :  4.643  19.147    594
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.35), residues: 550
  helix: -1.57 (0.67), residues: 54
  sheet:  0.74 (0.39), residues: 184
  loop : -1.02 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 315 
 TYR   0.007   0.001   TYR B 105 
 PHE   0.037   0.002   PHE A 108 
 TRP   0.015   0.001   TRP B 115 
 HIS   0.002   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 4463)
  covalent geometry    : angle       0.62011 ( 6074)
  hydrogen bonds       : bond        0.03947 (  155)
  hydrogen bonds       : angle       5.31237 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9036 (m100) cc_final: 0.8498 (m100)
REVERT: A   57 MET cc_start: 0.8953 (mmm) cc_final: 0.8479 (mmt)
REVERT: A   82 LYS cc_start: 0.8872 (mttt) cc_final: 0.8450 (mmmt)
REVERT: B   82 ASP cc_start: 0.8541 (m-30) cc_final: 0.8338 (m-30)
REVERT: B   89 MET cc_start: 0.8585 (ttp) cc_final: 0.8233 (ptm)
REVERT: B  132 CYS cc_start: 0.8968 (p) cc_final: 0.8632 (p)
REVERT: B  152 CYS cc_start: 0.7978 (t) cc_final: 0.7306 (t)
REVERT: B  204 GLN cc_start: 0.8599 (mt0) cc_final: 0.8384 (mm110)
REVERT: B  206 VAL cc_start: 0.8866 (m) cc_final: 0.8533 (p)
REVERT: B  217 ILE cc_start: 0.9391 (pt) cc_final: 0.9175 (pt)
REVERT: B  298 VAL cc_start: 0.9370 (t) cc_final: 0.9138 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0487
  time to fit residues: 6.3790
Evaluate side-chains
  74 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    0.1980
   chunk 14 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
B  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.106324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.093679 restraints weight = 6679.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.095328 restraints weight = 4676.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.096590 restraints weight = 3596.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.097256 restraints weight = 2967.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.097898 restraints weight = 2606.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.6899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4463  Z= 0.125
  Angle     :  0.593   9.353   6074  Z= 0.305
  Chirality :  0.045   0.149    673
  Planarity :  0.004   0.052    782
  Dihedral  :  4.431  17.979    594
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.36), residues: 550
  helix: -1.59 (0.66), residues: 54
  sheet:  0.62 (0.39), residues: 185
  loop : -0.94 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 315 
 TYR   0.024   0.001   TYR B 278 
 PHE   0.026   0.002   PHE A 108 
 TRP   0.012   0.001   TRP B 115 
 HIS   0.002   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4463)
  covalent geometry    : angle       0.59307 ( 6074)
  hydrogen bonds       : bond        0.03759 (  155)
  hydrogen bonds       : angle       5.21471 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A    8 SER cc_start: 0.7669 (t) cc_final: 0.7094 (m)
REVERT: A   47 TRP cc_start: 0.8949 (m100) cc_final: 0.8447 (m100)
REVERT: A   82 LYS cc_start: 0.8867 (mttt) cc_final: 0.8529 (mmmt)
REVERT: A   87 ASP cc_start: 0.7978 (p0) cc_final: 0.7681 (p0)
REVERT: A  122 PHE cc_start: 0.9140 (p90) cc_final: 0.8804 (p90)
REVERT: A  166 ASP cc_start: 0.8633 (t70) cc_final: 0.8234 (t70)
REVERT: B   89 MET cc_start: 0.8567 (ttp) cc_final: 0.8341 (ptm)
REVERT: B  132 CYS cc_start: 0.8933 (p) cc_final: 0.8717 (p)
REVERT: B  152 CYS cc_start: 0.7899 (t) cc_final: 0.6708 (t)
REVERT: B  204 GLN cc_start: 0.8573 (mt0) cc_final: 0.8365 (mm110)
REVERT: B  206 VAL cc_start: 0.8836 (m) cc_final: 0.8486 (p)
REVERT: B  298 VAL cc_start: 0.9350 (t) cc_final: 0.9117 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0480
  time to fit residues: 5.9818
Evaluate side-chains
  78 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 119 ASN
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.103281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.090903 restraints weight = 6761.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.092526 restraints weight = 4781.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.093697 restraints weight = 3692.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.094373 restraints weight = 3070.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.094993 restraints weight = 2701.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.7064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4463  Z= 0.200
  Angle     :  0.629   8.112   6074  Z= 0.325
  Chirality :  0.046   0.146    673
  Planarity :  0.005   0.054    782
  Dihedral  :  4.622  17.923    594
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.35), residues: 550
  helix: -1.58 (0.68), residues: 52
  sheet:  0.59 (0.39), residues: 185
  loop : -1.04 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 315 
 TYR   0.009   0.001   TYR B 278 
 PHE   0.024   0.002   PHE A 108 
 TRP   0.017   0.001   TRP B 115 
 HIS   0.002   0.001   HIS A  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 4463)
  covalent geometry    : angle       0.62870 ( 6074)
  hydrogen bonds       : bond        0.04016 (  155)
  hydrogen bonds       : angle       5.21547 (  447)

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A    8 SER cc_start: 0.7626 (t) cc_final: 0.7125 (m)
REVERT: A   47 TRP cc_start: 0.9017 (m100) cc_final: 0.8466 (m100)
REVERT: A   82 LYS cc_start: 0.8830 (mttt) cc_final: 0.8545 (mmmt)
REVERT: A  119 ASN cc_start: 0.8818 (m-40) cc_final: 0.8514 (m-40)
REVERT: B  152 CYS cc_start: 0.8014 (t) cc_final: 0.6814 (t)
REVERT: B  206 VAL cc_start: 0.8893 (m) cc_final: 0.8550 (p)
REVERT: B  236 ILE cc_start: 0.9550 (tt) cc_final: 0.9331 (tt)
REVERT: B  298 VAL cc_start: 0.9386 (t) cc_final: 0.9155 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.0505
  time to fit residues: 6.3402
Evaluate side-chains
  74 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.106280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.093599 restraints weight = 6679.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.095309 restraints weight = 4672.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.096558 restraints weight = 3590.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.097354 restraints weight = 2943.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.097856 restraints weight = 2564.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.7146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4463  Z= 0.140
  Angle     :  0.599   7.707   6074  Z= 0.310
  Chirality :  0.045   0.149    673
  Planarity :  0.005   0.052    782
  Dihedral  :  4.470  18.419    594
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.36), residues: 550
  helix: -1.65 (0.70), residues: 46
  sheet:  0.52 (0.39), residues: 186
  loop : -1.02 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 315 
 TYR   0.020   0.001   TYR B 278 
 PHE   0.022   0.002   PHE A 108 
 TRP   0.013   0.001   TRP A  86 
 HIS   0.002   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4463)
  covalent geometry    : angle       0.59869 ( 6074)
  hydrogen bonds       : bond        0.03779 (  155)
  hydrogen bonds       : angle       5.22980 (  447)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 835.66 seconds
wall clock time: 15 minutes 4.01 seconds (904.01 seconds total)