Starting phenix.real_space_refine
on Mon Sep 23 17:26:45 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/09_2024/9eme_19818.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/09_2024/9eme_19818.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/09_2024/9eme_19818.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/09_2024/9eme_19818.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/09_2024/9eme_19818.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/09_2024/9eme_19818.cif"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2562      2.51       5
     N     714      2.21       5
     O     852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 4140
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 690
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 1, 'TRANS': 90}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.39, per 1000 atoms: 0.58
  Number of scatterers: 4140
  At special positions: 0
  Unit cell: (79.04, 92.56, 52, 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      12     16.00
     O     852      8.00
     N     714      7.00
     C    2562      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  87 " distance=2.02

  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: 0.91
  Conformation dependent library (CDL) restraints added in 494.0 milliseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  984

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23
      removed outlier: 6.582A  pdb=" N   GLN A  16 " --> pdb=" O   THR B  17 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ARG B  19 " --> pdb=" O   GLN A  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL A  18 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   THR B  21 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE A  20 " --> pdb=" O   THR B  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN B  23 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   CYS A  22 " --> pdb=" O   GLN B  23 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLN B  16 " --> pdb=" O   THR C  17 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ARG C  19 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL B  18 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   THR C  21 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE B  20 " --> pdb=" O   THR C  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN C  23 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   CYS B  22 " --> pdb=" O   GLN C  23 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLN C  16 " --> pdb=" O   THR D  17 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ARG D  19 " --> pdb=" O   GLN C  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL C  18 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   THR D  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE C  20 " --> pdb=" O   THR D  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN D  23 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   CYS C  22 " --> pdb=" O   GLN D  23 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   GLN D  16 " --> pdb=" O   THR E  17 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ARG E  19 " --> pdb=" O   GLN D  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL D  18 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   THR E  21 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE D  20 " --> pdb=" O   THR E  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN E  23 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   CYS D  22 " --> pdb=" O   GLN E  23 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   GLN E  16 " --> pdb=" O   THR F  17 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   ARG F  19 " --> pdb=" O   GLN E  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL E  18 " --> pdb=" O   ARG F  19 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   THR F  21 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE E  20 " --> pdb=" O   THR F  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN F  23 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   CYS E  22 " --> pdb=" O   GLN F  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 30
    Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37
    Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 47
      removed outlier: 6.844A  pdb=" N   LEU A  45 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU B  45 " --> pdb=" O   VAL C  46 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU C  45 " --> pdb=" O   VAL D  46 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU D  45 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU E  45 " --> pdb=" O   VAL F  46 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68
    Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 78
      removed outlier: 6.757A  pdb=" N   ALA B  77 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN A  78 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA C  77 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN B  78 " --> pdb=" O   ALA C  77 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA D  77 " --> pdb=" O   GLY C  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN C  78 " --> pdb=" O   ALA D  77 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA E  77 " --> pdb=" O   GLY D  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN D  78 " --> pdb=" O   ALA E  77 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA F  77 " --> pdb=" O   GLY E  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN E  78 " --> pdb=" O   ALA F  77 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83
      removed outlier: 8.450A  pdb=" N   ASP A  81 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP B  81 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP C  81 " --> pdb=" O   GLU D  82 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP D  81 " --> pdb=" O   GLU E  82 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP E  81 " --> pdb=" O   GLU F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 106

    80 hydrogen bonds defined for protein.
    240 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 690
        1.30 -     1.43: 1224
        1.43 -     1.55: 2286
        1.55 -     1.68: 0
        1.68 -     1.81: 12
  Bond restraints: 4212
  Sorted by residual:
  bond pdb=" C   VAL A  46 "
       pdb=" O   VAL A  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.47e+01
  bond pdb=" C   VAL F  46 "
       pdb=" O   VAL F  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.46e+01
  bond pdb=" C   VAL E  46 "
       pdb=" O   VAL E  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.46e+01
  bond pdb=" C   VAL D  46 "
       pdb=" O   VAL D  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.45e+01
  bond pdb=" C   VAL B  46 "
       pdb=" O   VAL B  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.45e+01
  ... (remaining 4207 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 3919
        1.92 -     3.84: 1269
        3.84 -     5.76: 458
        5.76 -     7.68: 60
        7.68 -     9.61: 6
  Bond angle restraints: 5712
  Sorted by residual:
  angle pdb=" N   SER F  64 "
        pdb=" CA  SER F  64 "
        pdb=" C   SER F  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.58   -9.61 1.09e+00 8.42e-01 7.77e+01
  angle pdb=" N   SER C  64 "
        pdb=" CA  SER C  64 "
        pdb=" C   SER C  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.56   -9.59 1.09e+00 8.42e-01 7.75e+01
  angle pdb=" N   SER D  64 "
        pdb=" CA  SER D  64 "
        pdb=" C   SER D  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.54   -9.57 1.09e+00 8.42e-01 7.71e+01
  angle pdb=" N   SER E  64 "
        pdb=" CA  SER E  64 "
        pdb=" C   SER E  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.53   -9.56 1.09e+00 8.42e-01 7.70e+01
  angle pdb=" N   SER A  64 "
        pdb=" CA  SER A  64 "
        pdb=" C   SER A  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.53   -9.56 1.09e+00 8.42e-01 7.69e+01
  ... (remaining 5707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.03: 2145
       14.03 -    28.06: 156
       28.06 -    42.09: 84
       42.09 -    56.12: 24
       56.12 -    70.15: 6
  Dihedral angle restraints: 2415
    sinusoidal: 849
      harmonic: 1566
  Sorted by residual:
  dihedral pdb=" C   HIS E  95 "
           pdb=" N   HIS E  95 "
           pdb=" CA  HIS E  95 "
           pdb=" CB  HIS E  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.87    9.27     0      2.50e+00 1.60e-01 1.38e+01
  dihedral pdb=" C   HIS F  95 "
           pdb=" N   HIS F  95 "
           pdb=" CA  HIS F  95 "
           pdb=" CB  HIS F  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.86    9.26     0      2.50e+00 1.60e-01 1.37e+01
  dihedral pdb=" C   HIS C  95 "
           pdb=" N   HIS C  95 "
           pdb=" CA  HIS C  95 "
           pdb=" CB  HIS C  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.86    9.26     0      2.50e+00 1.60e-01 1.37e+01
  ... (remaining 2412 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 228
       0.062 -    0.124: 186
       0.124 -    0.186: 142
       0.186 -    0.248: 62
       0.248 -    0.310: 18
  Chirality restraints: 636
  Sorted by residual:
  chirality pdb=" CA  HIS B  95 "
            pdb=" N   HIS B  95 "
            pdb=" C   HIS B  95 "
            pdb=" CB  HIS B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CA  HIS A  95 "
            pdb=" N   HIS A  95 "
            pdb=" C   HIS A  95 "
            pdb=" CB  HIS A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  HIS D  95 "
            pdb=" N   HIS D  95 "
            pdb=" C   HIS D  95 "
            pdb=" CB  HIS D  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 633 not shown)

  Planarity restraints: 738
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E 100 "    0.021 2.00e-02 2.50e+03   4.19e-02 1.76e+01
        pdb=" C   GLY E 100 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   GLY E 100 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLY E 101 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 100 "    0.021 2.00e-02 2.50e+03   4.18e-02 1.75e+01
        pdb=" C   GLY B 100 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   GLY B 100 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLY B 101 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 100 "    0.021 2.00e-02 2.50e+03   4.18e-02 1.75e+01
        pdb=" C   GLY C 100 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   GLY C 100 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLY C 101 "    0.025 2.00e-02 2.50e+03
  ... (remaining 735 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 23
        2.59 -     3.17: 3317
        3.17 -     3.75: 6377
        3.75 -     4.32: 8956
        4.32 -     4.90: 17467
  Nonbonded interactions: 36140
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B  22 "
            pdb=" SG  CYS B  87 "
     model   vdw
     2.019 3.760
  nonbonded pdb=" SG  CYS C  22 "
            pdb=" SG  CYS C  87 "
     model   vdw
     2.019 3.760
  nonbonded pdb=" SG  CYS E  22 "
            pdb=" SG  CYS E  87 "
     model   vdw
     2.019 3.760
  nonbonded pdb=" SG  CYS D  22 "
            pdb=" SG  CYS D  87 "
     model   vdw
     2.019 3.760
  nonbonded pdb=" SG  CYS F  22 "
            pdb=" SG  CYS F  87 "
     model   vdw
     2.019 3.760
  ... (remaining 36135 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.290
  Find NCS groups from input model:        0.110
  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:12.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5839
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      :  0.015   0.065   4212  Z= 0.991
  Angle     :  2.116   9.606   5712  Z= 1.591
  Chirality :  0.121   0.310    636
  Planarity :  0.012   0.042    738
  Dihedral  : 14.206  70.153   1428
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.40 (0.21), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.16), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.005   TRP C  34 
 HIS   0.007   0.003   HIS B  95 
 PHE   0.006   0.002   PHE C  61 
 TYR   0.014   0.002   TYR B  30 
 ARG   0.007   0.002   ARG E  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A   23 GLN cc_start: 0.7914 (tt0) cc_final: 0.6979 (tm-30)
REVERT: A   89 SER cc_start: 0.6068 (t) cc_final: 0.5827 (t)
REVERT: B   23 GLN cc_start: 0.6604 (tt0) cc_final: 0.5670 (tm-30)
REVERT: C   19 ARG cc_start: 0.5982 (ttm170) cc_final: 0.5702 (ttm170)
REVERT: C   23 GLN cc_start: 0.6797 (tt0) cc_final: 0.5708 (tm-30)
REVERT: C   27 LEU cc_start: 0.6638 (tt) cc_final: 0.6275 (mp)
REVERT: D   23 GLN cc_start: 0.7023 (tt0) cc_final: 0.5726 (tm-30)
REVERT: D   33 SER cc_start: 0.7831 (p) cc_final: 0.7617 (p)
REVERT: D   38 LYS cc_start: 0.7392 (mttt) cc_final: 0.7167 (mtpp)
REVERT: D   78 GLN cc_start: 0.7055 (mt0) cc_final: 0.6721 (mt0)
REVERT: F   23 GLN cc_start: 0.6897 (tt0) cc_final: 0.6431 (tm-30)
REVERT: F   78 GLN cc_start: 0.7283 (mt0) cc_final: 0.6979 (mt0)
REVERT: F   80 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6218 (tt0)
REVERT: F   90 ARG cc_start: 0.6815 (ttt180) cc_final: 0.6035 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 1.0348
  time to fit residues: 128.8490
Evaluate side-chains
  61 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
A  68 ASN
A  78 GLN
B  52 ASN
B  68 ASN
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
C  78 GLN
D  68 ASN
E  16 GLN
E  68 ASN
E  78 GLN
F  65 ASN
F  68 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5893
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4212  Z= 0.175
  Angle     :  0.568   6.836   5712  Z= 0.320
  Chirality :  0.045   0.121    636
  Planarity :  0.002   0.032    738
  Dihedral  :  5.041  17.926    600
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.89 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.47 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.20), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP C  34 
 HIS   0.002   0.001   HIS E  95 
 PHE   0.004   0.001   PHE E  61 
 TYR   0.011   0.002   TYR A  31 
 ARG   0.003   0.000   ARG E  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7811 (mttt)
REVERT: A   81 ASP cc_start: 0.6707 (m-30) cc_final: 0.6444 (m-30)
REVERT: B   31 TYR cc_start: 0.8019 (m-80) cc_final: 0.7727 (m-80)
REVERT: D   22 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7603 (m)
REVERT: D   78 GLN cc_start: 0.6648 (mt0) cc_final: 0.6414 (mt0)
REVERT: D   86 TYR cc_start: 0.7584 (m-80) cc_final: 0.7328 (m-80)
REVERT: E   90 ARG cc_start: 0.6316 (ttp80) cc_final: 0.5948 (ttp80)
REVERT: F   23 GLN cc_start: 0.7207 (tt0) cc_final: 0.6375 (tm-30)
REVERT: F   78 GLN cc_start: 0.7081 (mt0) cc_final: 0.6790 (mt0)
REVERT: F   80 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6477 (tt0)
REVERT: F   90 ARG cc_start: 0.6439 (ttt180) cc_final: 0.5650 (tpm170)
  outliers start: 13
  outliers final: 2
  residues processed: 60
  average time/residue: 1.1152
  time to fit residues: 69.5339
Evaluate side-chains
  48 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain F residue   49 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
B  51 ASN
B  68 ASN
B  78 GLN
D  51 ASN
D  68 ASN
E  78 GLN
F  68 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5978
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   4212  Z= 0.422
  Angle     :  0.648   6.870   5712  Z= 0.362
  Chirality :  0.046   0.126    636
  Planarity :  0.003   0.030    738
  Dihedral  :  5.588  18.513    600
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.79 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.46 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP D  34 
 HIS   0.009   0.003   HIS D  95 
 PHE   0.007   0.001   PHE A  99 
 TYR   0.018   0.003   TYR A  30 
 ARG   0.003   0.000   ARG D  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.404 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7658 (mttt)
REVERT: A   81 ASP cc_start: 0.6498 (m-30) cc_final: 0.6283 (m-30)
REVERT: A   82 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7278 (mt-10)
REVERT: A   90 ARG cc_start: 0.6799 (ttp80) cc_final: 0.6402 (ttp80)
REVERT: B   31 TYR cc_start: 0.8062 (m-80) cc_final: 0.7729 (m-80)
REVERT: C   19 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5651 (ttm170)
REVERT: C   82 GLU cc_start: 0.6728 (mt-10) cc_final: 0.5948 (mt-10)
REVERT: E   82 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6631 (mt-10)
REVERT: F   90 ARG cc_start: 0.6127 (ttt180) cc_final: 0.5154 (tpm170)
  outliers start: 9
  outliers final: 2
  residues processed: 52
  average time/residue: 1.2910
  time to fit residues: 69.5075
Evaluate side-chains
  45 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain C residue   19 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    0.1980
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
D  78 GLN
F  68 ASN
** F  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   4212  Z= 0.220
  Angle     :  0.537   5.493   5712  Z= 0.302
  Chirality :  0.045   0.168    636
  Planarity :  0.002   0.020    738
  Dihedral  :  5.052  18.012    600
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 18.24 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  34 
 HIS   0.003   0.001   HIS D  95 
 PHE   0.003   0.001   PHE A  99 
 TYR   0.010   0.001   TYR A  30 
 ARG   0.004   0.000   ARG E  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7761 (mttt)
REVERT: A   81 ASP cc_start: 0.6623 (m-30) cc_final: 0.6365 (m-30)
REVERT: A   82 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7242 (mt-10)
REVERT: A   90 ARG cc_start: 0.6766 (ttp80) cc_final: 0.6328 (ttp80)
REVERT: B   31 TYR cc_start: 0.8018 (m-80) cc_final: 0.7654 (m-80)
REVERT: E   90 ARG cc_start: 0.6152 (ttp80) cc_final: 0.5789 (ttp80)
REVERT: F   80 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6404 (tt0)
REVERT: F   90 ARG cc_start: 0.6512 (ttt180) cc_final: 0.5222 (ttm170)
  outliers start: 7
  outliers final: 2
  residues processed: 46
  average time/residue: 1.3207
  time to fit residues: 62.9449
Evaluate side-chains
  44 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   62 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   chunk 26 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
E  78 GLN
F  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5928
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4212  Z= 0.178
  Angle     :  0.507   4.912   5712  Z= 0.282
  Chirality :  0.044   0.147    636
  Planarity :  0.002   0.033    738
  Dihedral  :  4.726  17.370    600
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 20.27 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  34 
 HIS   0.003   0.001   HIS D  95 
 PHE   0.003   0.001   PHE E  61 
 TYR   0.010   0.001   TYR A  35 
 ARG   0.003   0.000   ARG E  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7024 (mmpt)
REVERT: A   81 ASP cc_start: 0.6735 (m-30) cc_final: 0.6530 (m-30)
REVERT: A   82 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7345 (mt-10)
REVERT: A   90 ARG cc_start: 0.6857 (ttp80) cc_final: 0.6547 (ttp80)
REVERT: B   31 TYR cc_start: 0.7966 (m-80) cc_final: 0.7591 (m-80)
REVERT: C   19 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5809 (ttm170)
REVERT: E   90 ARG cc_start: 0.6163 (ttp80) cc_final: 0.5832 (ttp80)
REVERT: F   80 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6421 (tt0)
REVERT: F   90 ARG cc_start: 0.6443 (ttt180) cc_final: 0.5188 (tpt170)
  outliers start: 7
  outliers final: 2
  residues processed: 43
  average time/residue: 1.2689
  time to fit residues: 56.7318
Evaluate side-chains
  43 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain C residue   19 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 12 optimal weight:    0.2980
   chunk 52 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
E  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5962
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4212  Z= 0.282
  Angle     :  0.553   5.222   5712  Z= 0.306
  Chirality :  0.045   0.147    636
  Planarity :  0.002   0.023    738
  Dihedral  :  5.091  18.106    600
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 20.50 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  34 
 HIS   0.005   0.002   HIS D  95 
 PHE   0.005   0.001   PHE B  99 
 TYR   0.013   0.002   TYR F  30 
 ARG   0.003   0.000   ARG C  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7644 (mttt)
REVERT: A   82 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7183 (mt-10)
REVERT: A   90 ARG cc_start: 0.6835 (ttp80) cc_final: 0.6605 (ttp80)
REVERT: B   31 TYR cc_start: 0.8038 (m-80) cc_final: 0.7647 (m-80)
REVERT: C   19 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5716 (ttm170)
REVERT: E   82 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6633 (mt-10)
REVERT: E   91 ASP cc_start: 0.7032 (m-30) cc_final: 0.6798 (m-30)
REVERT: F   80 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6367 (tt0)
REVERT: F   90 ARG cc_start: 0.6390 (ttt180) cc_final: 0.5134 (ttm170)
  outliers start: 5
  outliers final: 2
  residues processed: 43
  average time/residue: 1.2810
  time to fit residues: 57.1878
Evaluate side-chains
  44 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain C residue   19 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    0.4980
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
E  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5930
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4212  Z= 0.181
  Angle     :  0.506   6.252   5712  Z= 0.277
  Chirality :  0.044   0.116    636
  Planarity :  0.002   0.027    738
  Dihedral  :  4.676  17.163    600
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 21.85 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  34 
 HIS   0.002   0.001   HIS D  95 
 PHE   0.003   0.001   PHE E  61 
 TYR   0.011   0.001   TYR A  35 
 ARG   0.004   0.000   ARG C  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7624 (mttt)
REVERT: A   82 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7240 (mt-10)
REVERT: A   90 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6617 (ttp80)
REVERT: B   31 TYR cc_start: 0.7977 (m-80) cc_final: 0.7582 (m-80)
REVERT: C   19 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5704 (ttm170)
REVERT: E   90 ARG cc_start: 0.6250 (ttp80) cc_final: 0.5748 (ptm160)
REVERT: F   80 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6491 (tt0)
REVERT: F   90 ARG cc_start: 0.6352 (ttt180) cc_final: 0.5063 (tpm170)
  outliers start: 6
  outliers final: 4
  residues processed: 40
  average time/residue: 1.3547
  time to fit residues: 56.2297
Evaluate side-chains
  43 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain C residue   19 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
E  78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5955
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4212  Z= 0.253
  Angle     :  0.540   6.708   5712  Z= 0.297
  Chirality :  0.045   0.125    636
  Planarity :  0.002   0.030    738
  Dihedral  :  4.911  17.664    600
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 21.62 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  34 
 HIS   0.005   0.001   HIS D  95 
 PHE   0.004   0.001   PHE B  99 
 TYR   0.012   0.002   TYR A  30 
 ARG   0.004   0.000   ARG D  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7259 (mt-10)
REVERT: A   90 ARG cc_start: 0.6911 (ttp80) cc_final: 0.6654 (ttp80)
REVERT: B   31 TYR cc_start: 0.8049 (m-80) cc_final: 0.7649 (m-80)
REVERT: C   19 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5726 (ttm170)
REVERT: C   82 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.5768 (mt-10)
REVERT: D   38 LYS cc_start: 0.7970 (mttp) cc_final: 0.7732 (mptt)
REVERT: D   90 ARG cc_start: 0.6463 (ptt90) cc_final: 0.6087 (ptt90)
REVERT: E   82 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6688 (mt-10)
REVERT: E   90 ARG cc_start: 0.6218 (ttp80) cc_final: 0.5581 (ptm160)
REVERT: F   80 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6422 (tt0)
REVERT: F   90 ARG cc_start: 0.6412 (ttt180) cc_final: 0.5272 (ttm170)
  outliers start: 8
  outliers final: 5
  residues processed: 46
  average time/residue: 1.3823
  time to fit residues: 65.8182
Evaluate side-chains
  48 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain C residue   19 ARG
Chi-restraints excluded: chain C residue   82 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5988
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   4212  Z= 0.380
  Angle     :  0.607   6.975   5712  Z= 0.335
  Chirality :  0.046   0.141    636
  Planarity :  0.003   0.029    738
  Dihedral  :  5.365  18.386    600
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 22.52 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  34 
 HIS   0.007   0.002   HIS D  95 
 PHE   0.007   0.001   PHE B  99 
 TYR   0.018   0.002   TYR F  30 
 ARG   0.005   0.001   ARG C  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A   82 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7187 (mt-10)
REVERT: A   90 ARG cc_start: 0.6890 (ttp80) cc_final: 0.6636 (ttp80)
REVERT: B   31 TYR cc_start: 0.8034 (m-80) cc_final: 0.7670 (m-80)
REVERT: C   19 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5702 (ttm170)
REVERT: C   82 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5778 (mt-10)
REVERT: D   90 ARG cc_start: 0.6569 (ptt90) cc_final: 0.6196 (ptt90)
REVERT: E   82 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6767 (mt-10)
REVERT: E   90 ARG cc_start: 0.6123 (ttp80) cc_final: 0.5478 (ptm160)
REVERT: F   80 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6413 (tt0)
REVERT: F   90 ARG cc_start: 0.6410 (ttt180) cc_final: 0.5255 (ttm170)
  outliers start: 5
  outliers final: 3
  residues processed: 42
  average time/residue: 1.3870
  time to fit residues: 60.3557
Evaluate side-chains
  44 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain C residue   19 ARG
Chi-restraints excluded: chain C residue   82 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5940
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4212  Z= 0.188
  Angle     :  0.523   7.175   5712  Z= 0.285
  Chirality :  0.044   0.120    636
  Planarity :  0.002   0.025    738
  Dihedral  :  4.754  17.390    600
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 22.07 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  34 
 HIS   0.003   0.001   HIS D  95 
 PHE   0.004   0.001   PHE E  61 
 TYR   0.011   0.001   TYR A  35 
 ARG   0.004   0.000   ARG D  90 

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7199 (mt-10)
REVERT: A   90 ARG cc_start: 0.6947 (ttp80) cc_final: 0.6700 (ttp80)
REVERT: B   31 TYR cc_start: 0.8040 (m-80) cc_final: 0.7692 (m-80)
REVERT: C   19 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5710 (ttm170)
REVERT: D   38 LYS cc_start: 0.7922 (mttp) cc_final: 0.7130 (mptt)
REVERT: D   90 ARG cc_start: 0.6428 (ptt90) cc_final: 0.6150 (ptt90)
REVERT: E   90 ARG cc_start: 0.6076 (ttp80) cc_final: 0.5413 (ptm160)
REVERT: F   80 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6425 (tt0)
REVERT: F   90 ARG cc_start: 0.6457 (ttt180) cc_final: 0.5256 (tpm170)
  outliers start: 6
  outliers final: 4
  residues processed: 42
  average time/residue: 1.3647
  time to fit residues: 59.4177
Evaluate side-chains
  43 residues out of total 444 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain C residue   19 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0770
   chunk 37 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.9344

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.118263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.106745 restraints weight = 5780.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.09
r_work: 0.3794 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3690 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4212  Z= 0.201
  Angle     :  0.524   7.253   5712  Z= 0.286
  Chirality :  0.044   0.121    636
  Planarity :  0.002   0.031    738
  Dihedral  :  4.732  17.263    600
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 22.07 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  34 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.003   0.001   PHE E  61 
 TYR   0.011   0.001   TYR A  35 
 ARG   0.005   0.000   ARG C  90 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1944.26 seconds
wall clock time: 38 minutes 19.61 seconds (2299.61 seconds total)