Starting phenix.real_space_refine
on Thu Mar  6 01:52:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5ms1_3562/03_2025/5ms1_3562.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5ms1_3562/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5ms1_3562/03_2025/5ms1_3562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5ms1_3562/03_2025/5ms1_3562.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5ms1_3562/03_2025/5ms1_3562.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5ms1_3562/03_2025/5ms1_3562.cif"
  }
  resolution = 4.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.61, per 1000 atoms: 1.06
  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: 0.93
  Conformation dependent library (CDL) restraints added in 486.8 milliseconds
  

  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: 0.58
  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: 1.31

  Time building geometry restraints manager: 1.14 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:             8.390
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.840
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.300
-------------------------------------------------------------------------------
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= 0.906
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (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
 TRP   0.036   0.006   TRP A  47 
 HIS   0.004   0.001   HIS A  50 
 PHE   0.026   0.004   PHE B 125 
 TYR   0.021   0.005   TYR B 278 
 ARG   0.004   0.001   ARG B 367 

*********************** 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  : 0.501 
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: 0.8720 (mt)
REVERT: A   49 THR cc_start: 0.9359 (p) cc_final: 0.9002 (t)
REVERT: A   75 ASN cc_start: 0.7730 (m-40) cc_final: 0.7429 (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: 0.1735
  time to fit residues: 36.5831
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  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3055 r_free = 0.3055 target = 0.106846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.094834 restraints weight = 6447.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.095933 restraints weight = 5025.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.096993 restraints weight = 4186.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4463  Z= 0.272
  Angle     :  0.638   7.336   6074  Z= 0.345
  Chirality :  0.047   0.160    673
  Planarity :  0.006   0.043    782
  Dihedral  :  4.796  19.951    594
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.64 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.34), residues: 550
  helix: -1.62 (0.69), residues: 48
  sheet:  0.99 (0.37), residues: 195
  loop : -0.77 (0.32), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A  47 
 HIS   0.002   0.001   HIS A  71 
 PHE   0.020   0.002   PHE B 275 
 TYR   0.012   0.002   TYR B 241 
 ARG   0.004   0.001   ARG A  61 

*********************** 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
  133 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8241 (mttt) cc_final: 0.7524 (mmmt)
REVERT: B   92 ILE cc_start: 0.9561 (mm) cc_final: 0.9359 (mp)
REVERT: B  102 THR cc_start: 0.8804 (p) cc_final: 0.8543 (t)
REVERT: B  130 ASN cc_start: 0.9025 (t0) cc_final: 0.8480 (t0)
REVERT: B  132 CYS cc_start: 0.9252 (p) cc_final: 0.8349 (p)
REVERT: B  137 SER cc_start: 0.9286 (p) cc_final: 0.9052 (p)
REVERT: B  181 ILE cc_start: 0.9351 (mt) cc_final: 0.9132 (pt)
REVERT: B  239 TRP cc_start: 0.9000 (m-90) cc_final: 0.8328 (m100)
REVERT: B  259 LYS cc_start: 0.8185 (mttt) cc_final: 0.7130 (pttp)
REVERT: B  271 LEU cc_start: 0.8912 (tp) cc_final: 0.8678 (tt)
REVERT: B  360 ASN cc_start: 0.8919 (t0) cc_final: 0.8626 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1232
  time to fit residues: 22.0842
Evaluate side-chains
  103 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 38 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
B 233 ASN
B 287 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.103976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.092380 restraints weight = 6676.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.093355 restraints weight = 5195.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.094295 restraints weight = 4328.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.4399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4463  Z= 0.284
  Angle     :  0.647   6.738   6074  Z= 0.345
  Chirality :  0.046   0.157    673
  Planarity :  0.005   0.045    782
  Dihedral  :  4.580  17.468    594
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.45 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.35), residues: 550
  helix: -1.29 (0.69), residues: 48
  sheet:  0.92 (0.39), residues: 188
  loop : -0.71 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 170 
 HIS   0.005   0.001   HIS B 331 
 PHE   0.015   0.002   PHE B 275 
 TYR   0.014   0.002   TYR B 241 
 ARG   0.008   0.001   ARG A 106 

*********************** 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  : 0.478 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8372 (mttt) cc_final: 0.7809 (mmmt)
REVERT: A  165 PHE cc_start: 0.9214 (m-10) cc_final: 0.8936 (m-10)
REVERT: B   92 ILE cc_start: 0.9647 (mm) cc_final: 0.9423 (mp)
REVERT: B  102 THR cc_start: 0.8803 (p) cc_final: 0.8577 (t)
REVERT: B  110 GLN cc_start: 0.8570 (tt0) cc_final: 0.8330 (tm-30)
REVERT: B  113 MET cc_start: 0.7168 (ptt) cc_final: 0.6925 (ptt)
REVERT: B  132 CYS cc_start: 0.9381 (p) cc_final: 0.8992 (p)
REVERT: B  152 CYS cc_start: 0.7125 (t) cc_final: 0.5349 (t)
REVERT: B  181 ILE cc_start: 0.9454 (mt) cc_final: 0.9241 (pt)
REVERT: B  239 TRP cc_start: 0.9116 (m-90) cc_final: 0.8315 (m100)
REVERT: B  259 LYS cc_start: 0.8373 (mttt) cc_final: 0.7384 (pttp)
REVERT: B  271 LEU cc_start: 0.8961 (tp) cc_final: 0.8629 (tt)
REVERT: B  351 ILE cc_start: 0.8765 (mt) cc_final: 0.8081 (mt)
REVERT: B  360 ASN cc_start: 0.9299 (t0) cc_final: 0.8978 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1215
  time to fit residues: 18.4785
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  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0870
   chunk 23 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.4166

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

Flipped N/Q/H residues before XYZ refinement:
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.103838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.092672 restraints weight = 6665.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.093901 restraints weight = 5052.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.094402 restraints weight = 4113.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4463  Z= 0.273
  Angle     :  0.608   6.803   6074  Z= 0.321
  Chirality :  0.046   0.150    673
  Planarity :  0.004   0.048    782
  Dihedral  :  4.453  19.393    594
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.91 %
    Favored  : 96.91 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.35), residues: 550
  helix: -1.42 (0.64), residues: 54
  sheet:  1.05 (0.39), residues: 196
  loop : -0.76 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 170 
 HIS   0.002   0.001   HIS A  71 
 PHE   0.014   0.002   PHE B 125 
 TYR   0.012   0.001   TYR B 278 
 ARG   0.006   0.001   ARG B 367 

*********************** 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
  116 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8528 (mttt) cc_final: 0.8146 (mmmt)
REVERT: A  119 ASN cc_start: 0.8647 (m110) cc_final: 0.8437 (m110)
REVERT: A  165 PHE cc_start: 0.9220 (m-10) cc_final: 0.8907 (m-10)
REVERT: B   86 CYS cc_start: 0.8710 (p) cc_final: 0.8504 (p)
REVERT: B  105 TYR cc_start: 0.8547 (t80) cc_final: 0.8335 (t80)
REVERT: B  116 ASN cc_start: 0.9119 (t0) cc_final: 0.8673 (t0)
REVERT: B  132 CYS cc_start: 0.9216 (p) cc_final: 0.8861 (p)
REVERT: B  134 ASP cc_start: 0.7525 (p0) cc_final: 0.7208 (p0)
REVERT: B  152 CYS cc_start: 0.7431 (t) cc_final: 0.5815 (t)
REVERT: B  206 VAL cc_start: 0.8428 (m) cc_final: 0.8121 (p)
REVERT: B  259 LYS cc_start: 0.8521 (mttt) cc_final: 0.7493 (pttp)
REVERT: B  271 LEU cc_start: 0.8998 (tp) cc_final: 0.8522 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1341
  time to fit residues: 20.5431
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  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 35 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    2.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
B  27 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.103577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.092018 restraints weight = 6862.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.093069 restraints weight = 5239.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.094013 restraints weight = 4349.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.5628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4463  Z= 0.275
  Angle     :  0.605   6.636   6074  Z= 0.317
  Chirality :  0.046   0.141    673
  Planarity :  0.005   0.051    782
  Dihedral  :  4.439  18.115    594
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.45 %
    Favored  : 96.36 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.35), residues: 550
  helix: -1.30 (0.69), residues: 48
  sheet:  0.97 (0.39), residues: 188
  loop : -0.77 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 115 
 HIS   0.002   0.001   HIS A  71 
 PHE   0.015   0.002   PHE B 275 
 TYR   0.010   0.002   TYR A  52 
 ARG   0.005   0.001   ARG B 367 

*********************** 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
  111 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8575 (mttt) cc_final: 0.8134 (mmmt)
REVERT: A   87 ASP cc_start: 0.7906 (p0) cc_final: 0.7418 (p0)
REVERT: A  155 GLN cc_start: 0.8886 (mt0) cc_final: 0.8390 (mt0)
REVERT: B  132 CYS cc_start: 0.9254 (p) cc_final: 0.8792 (p)
REVERT: B  134 ASP cc_start: 0.7558 (p0) cc_final: 0.7182 (p0)
REVERT: B  152 CYS cc_start: 0.7617 (t) cc_final: 0.5959 (t)
REVERT: B  206 VAL cc_start: 0.8608 (m) cc_final: 0.8319 (p)
REVERT: B  259 LYS cc_start: 0.8662 (mttt) cc_final: 0.7556 (pttp)
REVERT: B  271 LEU cc_start: 0.9044 (tp) cc_final: 0.8657 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1327
  time to fit residues: 19.3928
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  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 158 GLN
B  27 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.102556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.091365 restraints weight = 6777.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.091546 restraints weight = 5063.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.092916 restraints weight = 4703.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.6151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   4463  Z= 0.330
  Angle     :  0.631   6.718   6074  Z= 0.334
  Chirality :  0.046   0.148    673
  Planarity :  0.005   0.049    782
  Dihedral  :  4.550  18.556    594
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.27 %
    Favored  : 96.55 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.35), residues: 550
  helix: -1.40 (0.66), residues: 54
  sheet:  0.78 (0.38), residues: 189
  loop : -0.82 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 196 
 HIS   0.003   0.001   HIS B 331 
 PHE   0.016   0.002   PHE B 248 
 TYR   0.021   0.002   TYR B 278 
 ARG   0.003   0.001   ARG A  61 

*********************** 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
  100 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8744 (mttt) cc_final: 0.8342 (mmmt)
REVERT: A  119 ASN cc_start: 0.8746 (m-40) cc_final: 0.8439 (m110)
REVERT: B  132 CYS cc_start: 0.9284 (p) cc_final: 0.8850 (p)
REVERT: B  134 ASP cc_start: 0.7479 (p0) cc_final: 0.7143 (p0)
REVERT: B  152 CYS cc_start: 0.7781 (t) cc_final: 0.6176 (t)
REVERT: B  206 VAL cc_start: 0.8786 (m) cc_final: 0.8499 (p)
REVERT: B  238 MET cc_start: 0.8577 (tpp) cc_final: 0.8351 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1390
  time to fit residues: 18.3843
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  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 33 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3053 r_free = 0.3053 target = 0.106327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.094172 restraints weight = 6645.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.095401 restraints weight = 5043.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.096408 restraints weight = 4117.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.6251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4463  Z= 0.169
  Angle     :  0.567   7.696   6074  Z= 0.294
  Chirality :  0.045   0.143    673
  Planarity :  0.004   0.050    782
  Dihedral  :  4.326  16.463    594
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.35), residues: 550
  helix: -1.34 (0.71), residues: 48
  sheet:  0.80 (0.38), residues: 184
  loop : -0.79 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 115 
 HIS   0.002   0.000   HIS B 283 
 PHE   0.013   0.002   PHE B 125 
 TYR   0.005   0.001   TYR B 327 
 ARG   0.002   0.000   ARG B 195 

*********************** 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  : 0.486 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9036 (m100) cc_final: 0.8570 (m100)
REVERT: A   48 ASN cc_start: 0.8617 (t0) cc_final: 0.8275 (t0)
REVERT: A   57 MET cc_start: 0.8918 (mmm) cc_final: 0.8708 (mmt)
REVERT: A   82 LYS cc_start: 0.8740 (mttt) cc_final: 0.8376 (mmmt)
REVERT: B  132 CYS cc_start: 0.9297 (p) cc_final: 0.8878 (p)
REVERT: B  152 CYS cc_start: 0.7738 (t) cc_final: 0.6469 (t)
REVERT: B  206 VAL cc_start: 0.8732 (m) cc_final: 0.8476 (p)
REVERT: B  238 MET cc_start: 0.8428 (tpp) cc_final: 0.8172 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1439
  time to fit residues: 18.6031
Evaluate side-chains
  76 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 2 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 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 = 0.2994 r_free = 0.2994 target = 0.101671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.088596 restraints weight = 6742.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.090172 restraints weight = 4864.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.091053 restraints weight = 3815.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.6632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   4463  Z= 0.366
  Angle     :  0.646   7.777   6074  Z= 0.337
  Chirality :  0.047   0.144    673
  Planarity :  0.005   0.052    782
  Dihedral  :  4.575  17.717    594
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.35), residues: 550
  helix: -1.36 (0.71), residues: 48
  sheet:  0.65 (0.37), residues: 189
  loop : -0.89 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 170 
 HIS   0.003   0.001   HIS A  71 
 PHE   0.020   0.002   PHE B 202 
 TYR   0.026   0.002   TYR B 278 
 ARG   0.005   0.001   ARG A  61 

*********************** 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
  86 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.977 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9069 (m100) cc_final: 0.8443 (m100)
REVERT: A   82 LYS cc_start: 0.8832 (mttt) cc_final: 0.8399 (mmmt)
REVERT: A  119 ASN cc_start: 0.8864 (m110) cc_final: 0.8529 (m-40)
REVERT: B   36 MET cc_start: 0.8422 (ptt) cc_final: 0.8065 (ptt)
REVERT: B  132 CYS cc_start: 0.9190 (p) cc_final: 0.8759 (p)
REVERT: B  134 ASP cc_start: 0.7639 (p0) cc_final: 0.7347 (p0)
REVERT: B  152 CYS cc_start: 0.8108 (t) cc_final: 0.7507 (t)
REVERT: B  206 VAL cc_start: 0.8916 (m) cc_final: 0.8634 (p)
REVERT: B  238 MET cc_start: 0.8644 (tpp) cc_final: 0.8435 (tpp)
REVERT: B  279 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8100 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1780
  time to fit residues: 20.5710
Evaluate side-chains
  72 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 158 GLN
B 130 ASN

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 = 0.103442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.090147 restraints weight = 6820.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.091804 restraints weight = 4855.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.092836 restraints weight = 3785.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.6782

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= 0.237
  Angle     :  0.594   8.881   6074  Z= 0.307
  Chirality :  0.045   0.146    673
  Planarity :  0.005   0.051    782
  Dihedral  :  4.444  15.959    594
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.04 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.35), residues: 550
  helix: -1.79 (0.64), residues: 54
  sheet:  0.56 (0.38), residues: 183
  loop : -0.94 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 115 
 HIS   0.001   0.000   HIS A  71 
 PHE   0.014   0.002   PHE B 202 
 TYR   0.007   0.001   TYR B 241 
 ARG   0.010   0.001   ARG B 315 

*********************** 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: 1
    poor density    : 88
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9016 (m100) cc_final: 0.8448 (m100)
REVERT: A   48 ASN cc_start: 0.8710 (t0) cc_final: 0.8227 (t0)
REVERT: A   82 LYS cc_start: 0.8869 (mttt) cc_final: 0.8542 (mmmt)
REVERT: A  119 ASN cc_start: 0.8808 (m-40) cc_final: 0.8455 (m-40)
REVERT: B  115 TRP cc_start: 0.8738 (p-90) cc_final: 0.8208 (p-90)
REVERT: B  132 CYS cc_start: 0.9218 (p) cc_final: 0.8850 (p)
REVERT: B  152 CYS cc_start: 0.8077 (t) cc_final: 0.7432 (t)
REVERT: B  206 VAL cc_start: 0.8902 (m) cc_final: 0.8604 (p)
REVERT: B  236 ILE cc_start: 0.9602 (tt) cc_final: 0.9400 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1039
  time to fit residues: 12.9935
Evaluate side-chains
  76 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0010
   chunk 36 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   overall best weight:    1.1590

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 158 GLN
B 233 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.105443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.094062 restraints weight = 6535.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.095237 restraints weight = 5015.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.095951 restraints weight = 4103.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.6897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4463  Z= 0.187
  Angle     :  0.578   8.881   6074  Z= 0.297
  Chirality :  0.045   0.157    673
  Planarity :  0.005   0.051    782
  Dihedral  :  4.270  15.987    594
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.35), residues: 550
  helix: -1.71 (0.65), residues: 50
  sheet:  0.51 (0.38), residues: 183
  loop : -0.97 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 115 
 HIS   0.001   0.000   HIS B 331 
 PHE   0.012   0.001   PHE B 125 
 TYR   0.021   0.001   TYR B 278 
 ARG   0.010   0.001   ARG B 315 

********************** 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
  94 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 SER cc_start: 0.7717 (t) cc_final: 0.7158 (m)
REVERT: A   47 TRP cc_start: 0.8942 (m100) cc_final: 0.8481 (m100)
REVERT: A   48 ASN cc_start: 0.8655 (t0) cc_final: 0.8319 (t0)
REVERT: A   82 LYS cc_start: 0.8811 (mttt) cc_final: 0.8602 (mmmt)
REVERT: A  119 ASN cc_start: 0.8648 (m-40) cc_final: 0.8320 (m-40)
REVERT: B  130 ASN cc_start: 0.9734 (t0) cc_final: 0.9350 (t0)
REVERT: B  132 CYS cc_start: 0.9155 (p) cc_final: 0.8761 (p)
REVERT: B  152 CYS cc_start: 0.7908 (t) cc_final: 0.7048 (t)
REVERT: B  206 VAL cc_start: 0.8856 (m) cc_final: 0.8579 (p)
REVERT: B  233 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8260 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1159
  time to fit residues: 15.1573
Evaluate side-chains
  80 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0370
   overall best weight:    1.6066

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 158 GLN
B 233 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.105945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.094127 restraints weight = 6641.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.095230 restraints weight = 5062.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.096265 restraints weight = 4182.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.6947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4463  Z= 0.210
  Angle     :  0.600  12.598   6074  Z= 0.306
  Chirality :  0.046   0.169    673
  Planarity :  0.005   0.050    782
  Dihedral  :  4.231  15.899    594
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.35), residues: 550
  helix: -1.77 (0.68), residues: 45
  sheet:  0.44 (0.39), residues: 184
  loop : -0.95 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 115 
 HIS   0.001   0.000   HIS A  71 
 PHE   0.023   0.002   PHE A 108 
 TYR   0.009   0.001   TYR B 327 
 ARG   0.010   0.001   ARG B 315 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2575.82 seconds
wall clock time: 46 minutes 47.14 seconds (2807.14 seconds total)