Starting phenix.real_space_refine
on Tue Feb 11 06:21:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5ms1_3562/02_2025/5ms1_3562.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5ms1_3562/02_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_3562/02_2025/5ms1_3562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5ms1_3562/02_2025/5ms1_3562.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5ms1_3562/02_2025/5ms1_3562.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5ms1_3562/02_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-5592/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: 5.07, per 1000 atoms: 1.17
  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: 0.94
  Conformation dependent library (CDL) restraints added in 535.6 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: 0.55
  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: 1.23

  Time building geometry restraints manager: 1.12 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:             4.800
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.270
  Find NCS groups from input model:        0.050
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.140
-------------------------------------------------------------------------------
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  : 0.450 
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: 0.1686
  time to fit residues: 35.4537
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  : 0.502 
-------------------------------------------------------------------------------
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 = 58)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.094851 restraints weight = 6447.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.095977 restraints weight = 4996.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.096970 restraints weight = 4152.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
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  : 0.471 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8247 (mttt) cc_final: 0.7523 (mmmt)
REVERT: B   92 ILE cc_start: 0.9561 (mm) cc_final: 0.9357 (mp)
REVERT: B  102 THR cc_start: 0.8810 (p) cc_final: 0.8548 (t)
REVERT: B  130 ASN cc_start: 0.9024 (t0) cc_final: 0.8484 (t0)
REVERT: B  132 CYS cc_start: 0.9252 (p) cc_final: 0.8349 (p)
REVERT: B  137 SER cc_start: 0.9288 (p) cc_final: 0.9054 (p)
REVERT: B  181 ILE cc_start: 0.9351 (mt) cc_final: 0.9132 (pt)
REVERT: B  239 TRP cc_start: 0.9004 (m-90) cc_final: 0.8330 (m100)
REVERT: B  259 LYS cc_start: 0.8194 (mttt) cc_final: 0.7129 (pttp)
REVERT: B  271 LEU cc_start: 0.8912 (tp) cc_final: 0.8676 (tt)
REVERT: B  360 ASN cc_start: 0.8924 (t0) cc_final: 0.8627 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1212
  time to fit residues: 21.7248
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  : 0.529 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
B 128 ASN
** B 233 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 = 0.2979 r_free = 0.2979 target = 0.100903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.089592 restraints weight = 6800.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.090712 restraints weight = 5256.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.091323 restraints weight = 4354.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.4782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4463  Z= 0.365
  Angle     :  0.693   7.997   6074  Z= 0.369
  Chirality :  0.048   0.159    673
  Planarity :  0.005   0.047    782
  Dihedral  :  4.850  17.822    594
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.27 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.66 %
    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 (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: -0.40 (0.34), residues: 550
  helix: -1.25 (0.68), residues: 47
  sheet:  0.87 (0.39), residues: 188
  loop : -0.83 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 170 
 HIS   0.004   0.001   HIS B 331 
 PHE   0.019   0.002   PHE B 202 
 TYR   0.023   0.002   TYR B 278 
 ARG   0.011   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
  112 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8442 (mttt) cc_final: 0.8053 (mmmt)
REVERT: B   36 MET cc_start: 0.8137 (ptt) cc_final: 0.7929 (ptt)
REVERT: B  102 THR cc_start: 0.8808 (p) cc_final: 0.8585 (t)
REVERT: B  110 GLN cc_start: 0.8686 (tt0) cc_final: 0.8376 (tm-30)
REVERT: B  116 ASN cc_start: 0.9103 (t0) cc_final: 0.8697 (t0)
REVERT: B  132 CYS cc_start: 0.9342 (p) cc_final: 0.8947 (p)
REVERT: B  152 CYS cc_start: 0.7377 (t) cc_final: 0.5745 (t)
REVERT: B  206 VAL cc_start: 0.8343 (m) cc_final: 0.8038 (p)
REVERT: B  259 LYS cc_start: 0.8400 (mttt) cc_final: 0.7394 (pttp)
REVERT: B  271 LEU cc_start: 0.8984 (tp) cc_final: 0.8622 (tt)
REVERT: B  321 ASP cc_start: 0.9126 (t0) cc_final: 0.8799 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 112
  average time/residue: 0.1276
  time to fit residues: 19.1885
Evaluate side-chains
  83 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 17 optimal weight:    0.2980
   chunk 46 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0470
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.0080

-------------------------------------------------------------------------------
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  27 GLN
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 GLN
B 302 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.107370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.095873 restraints weight = 6610.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.096930 restraints weight = 5187.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.097929 restraints weight = 4268.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.5183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4463  Z= 0.186
  Angle     :  0.581   6.253   6074  Z= 0.309
  Chirality :  0.045   0.148    673
  Planarity :  0.004   0.044    782
  Dihedral  :  4.468  20.244    594
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.82 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    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: -0.42 (0.35), residues: 550
  helix: -1.58 (0.64), residues: 54
  sheet:  0.99 (0.39), residues: 190
  loop : -0.87 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 170 
 HIS   0.002   0.001   HIS A  50 
 PHE   0.023   0.002   PHE A 165 
 TYR   0.015   0.001   TYR B 278 
 ARG   0.003   0.000   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
  114 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8538 (mttt) cc_final: 0.8168 (mmmt)
REVERT: A  119 ASN cc_start: 0.8668 (m110) cc_final: 0.8390 (m110)
REVERT: A  166 ASP cc_start: 0.8455 (t70) cc_final: 0.7784 (t70)
REVERT: B  110 GLN cc_start: 0.8540 (tt0) cc_final: 0.8301 (tm-30)
REVERT: B  132 CYS cc_start: 0.9292 (p) cc_final: 0.8915 (p)
REVERT: B  152 CYS cc_start: 0.7385 (t) cc_final: 0.5750 (t)
REVERT: B  259 LYS cc_start: 0.8506 (mttt) cc_final: 0.7477 (pttp)
REVERT: B  271 LEU cc_start: 0.8974 (tp) cc_final: 0.8495 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1502
  time to fit residues: 21.8700
Evaluate side-chains
  90 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0270
   chunk 31 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    2.6046

-------------------------------------------------------------------------------
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  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 = 0.3025 r_free = 0.3025 target = 0.103725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.091255 restraints weight = 6848.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.092868 restraints weight = 4770.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.094047 restraints weight = 3668.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.5677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4463  Z= 0.271
  Angle     :  0.601   6.627   6074  Z= 0.316
  Chirality :  0.046   0.146    673
  Planarity :  0.005   0.046    782
  Dihedral  :  4.416  17.871    594
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.09 %
    Favored  : 96.73 %
  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 (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: -1.57 (0.69), residues: 48
  sheet:  1.03 (0.39), residues: 195
  loop : -0.78 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 170 
 HIS   0.004   0.001   HIS B 283 
 PHE   0.016   0.002   PHE B 275 
 TYR   0.010   0.001   TYR B 100 
 ARG   0.005   0.000   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
  112 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8633 (mttt) cc_final: 0.8129 (mmmt)
REVERT: A   87 ASP cc_start: 0.7926 (p0) cc_final: 0.7445 (p0)
REVERT: A  155 GLN cc_start: 0.8911 (mt0) cc_final: 0.8462 (mt0)
REVERT: A  166 ASP cc_start: 0.8607 (t70) cc_final: 0.8274 (t70)
REVERT: B   36 MET cc_start: 0.8327 (ptt) cc_final: 0.8123 (ptt)
REVERT: B   92 ILE cc_start: 0.9691 (mp) cc_final: 0.9381 (mt)
REVERT: B  110 GLN cc_start: 0.8591 (tt0) cc_final: 0.8242 (tm-30)
REVERT: B  132 CYS cc_start: 0.9270 (p) cc_final: 0.8895 (p)
REVERT: B  134 ASP cc_start: 0.7664 (p0) cc_final: 0.7336 (p0)
REVERT: B  152 CYS cc_start: 0.7674 (t) cc_final: 0.5977 (t)
REVERT: B  206 VAL cc_start: 0.8626 (m) cc_final: 0.8349 (p)
REVERT: B  271 LEU cc_start: 0.9016 (tp) cc_final: 0.8601 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1407
  time to fit residues: 20.8501
Evaluate side-chains
  92 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 7 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    3.2588

-------------------------------------------------------------------------------
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**
B 233 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.103438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.090734 restraints weight = 6783.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.092275 restraints weight = 4781.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.093270 restraints weight = 3730.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.6258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4463  Z= 0.321
  Angle     :  0.630   6.566   6074  Z= 0.331
  Chirality :  0.047   0.143    673
  Planarity :  0.005   0.050    782
  Dihedral  :  4.580  18.624    594
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.27 %
    Favored  : 96.55 %
  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: -0.52 (0.35), residues: 550
  helix: -1.71 (0.65), residues: 53
  sheet:  0.78 (0.39), residues: 191
  loop : -0.83 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 115 
 HIS   0.007   0.001   HIS B 283 
 PHE   0.016   0.002   PHE B 248 
 TYR   0.030   0.002   TYR B 278 
 ARG   0.004   0.001   ARG B 195 

*********************** 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
  101 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8764 (mttt) cc_final: 0.8330 (mmmt)
REVERT: A  119 ASN cc_start: 0.8882 (m110) cc_final: 0.8602 (m110)
REVERT: A  166 ASP cc_start: 0.8638 (t70) cc_final: 0.8308 (t70)
REVERT: B   82 ASP cc_start: 0.8574 (m-30) cc_final: 0.8329 (m-30)
REVERT: B  110 GLN cc_start: 0.8742 (tt0) cc_final: 0.8327 (tm-30)
REVERT: B  132 CYS cc_start: 0.9270 (p) cc_final: 0.8888 (p)
REVERT: B  134 ASP cc_start: 0.7620 (p0) cc_final: 0.7282 (p0)
REVERT: B  152 CYS cc_start: 0.7832 (t) cc_final: 0.6234 (t)
REVERT: B  206 VAL cc_start: 0.8783 (m) cc_final: 0.8500 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1272
  time to fit residues: 17.2856
Evaluate side-chains
  81 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 23 optimal weight:    5.9990
   chunk 24 optimal weight:    0.1980
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3073 r_free = 0.3073 target = 0.107219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.094410 restraints weight = 6812.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.096081 restraints weight = 4793.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.097225 restraints weight = 3692.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.6329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4463  Z= 0.159
  Angle     :  0.571   6.432   6074  Z= 0.294
  Chirality :  0.045   0.142    673
  Planarity :  0.004   0.051    782
  Dihedral  :  4.352  17.194    594
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  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: -0.45 (0.36), residues: 550
  helix: -1.79 (0.65), residues: 53
  sheet:  0.91 (0.39), residues: 189
  loop : -0.80 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 115 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.016   0.002   PHE A 108 
 TYR   0.012   0.001   TYR B 100 
 ARG   0.002   0.000   ARG B 367 

*********************** 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
  106 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.471 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9011 (m100) cc_final: 0.8508 (m100)
REVERT: A   48 ASN cc_start: 0.8615 (t0) cc_final: 0.8185 (t0)
REVERT: A   82 LYS cc_start: 0.8767 (mttt) cc_final: 0.8325 (mmmt)
REVERT: A  166 ASP cc_start: 0.8486 (t70) cc_final: 0.8089 (t70)
REVERT: B  110 GLN cc_start: 0.8594 (tt0) cc_final: 0.8277 (tm-30)
REVERT: B  132 CYS cc_start: 0.9278 (p) cc_final: 0.8671 (p)
REVERT: B  134 ASP cc_start: 0.7592 (p0) cc_final: 0.7232 (p0)
REVERT: B  152 CYS cc_start: 0.7901 (t) cc_final: 0.6581 (t)
REVERT: B  206 VAL cc_start: 0.8757 (m) cc_final: 0.8469 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1379
  time to fit residues: 19.2238
Evaluate side-chains
  85 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 2 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3007 r_free = 0.3007 target = 0.102562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.089722 restraints weight = 6808.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.091272 restraints weight = 4878.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.092260 restraints weight = 3832.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.6699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4463  Z= 0.335
  Angle     :  0.655   8.149   6074  Z= 0.339
  Chirality :  0.047   0.140    673
  Planarity :  0.005   0.052    782
  Dihedral  :  4.658  18.088    594
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  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: -0.60 (0.35), residues: 550
  helix: -1.83 (0.69), residues: 47
  sheet:  0.66 (0.39), residues: 188
  loop : -0.83 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 115 
 HIS   0.005   0.001   HIS B 283 
 PHE   0.027   0.002   PHE B 275 
 TYR   0.014   0.002   TYR B 241 
 ARG   0.008   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
  93 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9051 (m100) cc_final: 0.8434 (m100)
REVERT: A   82 LYS cc_start: 0.8842 (mttt) cc_final: 0.8400 (mmmt)
REVERT: A  166 ASP cc_start: 0.8655 (t70) cc_final: 0.8340 (t70)
REVERT: B   36 MET cc_start: 0.8493 (ptt) cc_final: 0.8278 (ptt)
REVERT: B  110 GLN cc_start: 0.8667 (tt0) cc_final: 0.8356 (tm-30)
REVERT: B  132 CYS cc_start: 0.9106 (p) cc_final: 0.8815 (p)
REVERT: B  152 CYS cc_start: 0.8352 (t) cc_final: 0.7732 (t)
REVERT: B  206 VAL cc_start: 0.8890 (m) cc_final: 0.8592 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1289
  time to fit residues: 16.0913
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  : 0.497 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0040
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.5996

-------------------------------------------------------------------------------
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 = 0.3040 r_free = 0.3040 target = 0.105762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.092459 restraints weight = 6839.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.094187 restraints weight = 4775.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.095205 restraints weight = 3684.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.6829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4463  Z= 0.211
  Angle     :  0.593   5.857   6074  Z= 0.313
  Chirality :  0.045   0.143    673
  Planarity :  0.004   0.051    782
  Dihedral  :  4.510  17.398    594
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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: -0.63 (0.35), residues: 550
  helix: -1.80 (0.66), residues: 50
  sheet:  0.76 (0.39), residues: 183
  loop : -0.90 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 115 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.021   0.002   PHE B 275 
 TYR   0.011   0.001   TYR B  46 
 ARG   0.006   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
  90 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   47 TRP cc_start: 0.9007 (m100) cc_final: 0.8442 (m100)
REVERT: A   48 ASN cc_start: 0.8682 (t0) cc_final: 0.8215 (t0)
REVERT: A   82 LYS cc_start: 0.8872 (mttt) cc_final: 0.8525 (mmmt)
REVERT: A  166 ASP cc_start: 0.8591 (t70) cc_final: 0.8238 (t70)
REVERT: B  110 GLN cc_start: 0.8580 (tt0) cc_final: 0.8166 (tm-30)
REVERT: B  132 CYS cc_start: 0.9121 (p) cc_final: 0.8808 (p)
REVERT: B  152 CYS cc_start: 0.8097 (t) cc_final: 0.7417 (t)
REVERT: B  206 VAL cc_start: 0.8900 (m) cc_final: 0.8594 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1208
  time to fit residues: 15.1839
Evaluate side-chains
  80 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 40 optimal weight:    0.4980
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0770
   chunk 46 optimal weight:    0.5980
   chunk 34 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.109084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.096074 restraints weight = 6546.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.097731 restraints weight = 4593.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.098917 restraints weight = 3553.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.6939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   4463  Z= 0.162
  Angle     :  0.584   8.148   6074  Z= 0.299
  Chirality :  0.044   0.141    673
  Planarity :  0.004   0.051    782
  Dihedral  :  4.176  17.425    594
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  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 (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 (0.36), residues: 550
  helix: -1.85 (0.68), residues: 50
  sheet:  0.66 (0.39), residues: 190
  loop : -0.81 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 170 
 HIS   0.002   0.000   HIS B 283 
 PHE   0.023   0.002   PHE B 275 
 TYR   0.008   0.001   TYR B 100 
 ARG   0.006   0.000   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
  100 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A    8 SER cc_start: 0.7414 (t) cc_final: 0.7034 (m)
REVERT: A   47 TRP cc_start: 0.8926 (m100) cc_final: 0.8416 (m100)
REVERT: A   48 ASN cc_start: 0.8587 (t0) cc_final: 0.8187 (t0)
REVERT: A   82 LYS cc_start: 0.8850 (mttt) cc_final: 0.8554 (mmmt)
REVERT: A  119 ASN cc_start: 0.8683 (m-40) cc_final: 0.8459 (m-40)
REVERT: A  122 PHE cc_start: 0.9093 (p90) cc_final: 0.8800 (p90)
REVERT: A  166 ASP cc_start: 0.8532 (t70) cc_final: 0.8139 (t70)
REVERT: B  113 MET cc_start: 0.7079 (tmm) cc_final: 0.6794 (tpp)
REVERT: B  132 CYS cc_start: 0.9159 (p) cc_final: 0.8807 (p)
REVERT: B  152 CYS cc_start: 0.7842 (t) cc_final: 0.7045 (t)
REVERT: B  206 VAL cc_start: 0.8880 (m) cc_final: 0.8591 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1188
  time to fit residues: 16.3090
Evaluate side-chains
  77 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 25 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0870
   chunk 52 optimal weight:    0.3980
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0370
   chunk 40 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.2836

-------------------------------------------------------------------------------
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 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.110684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.097837 restraints weight = 6610.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.099460 restraints weight = 4582.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.100560 restraints weight = 3535.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.7025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   4463  Z= 0.152
  Angle     :  0.572  10.569   6074  Z= 0.295
  Chirality :  0.044   0.153    673
  Planarity :  0.004   0.050    782
  Dihedral  :  4.099  18.477    594
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  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: -0.76 (0.36), residues: 550
  helix: -2.05 (0.65), residues: 54
  sheet:  0.53 (0.38), residues: 195
  loop : -0.89 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 235 
 HIS   0.001   0.000   HIS B 283 
 PHE   0.020   0.002   PHE B 275 
 TYR   0.009   0.001   TYR B 105 
 ARG   0.006   0.000   ARG B 315 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1771.83 seconds
wall clock time: 32 minutes 39.50 seconds (1959.50 seconds total)