Starting phenix.real_space_refine
on Tue Mar 11 21:03:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tbf_25797/03_2025/7tbf_25797.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tbf_25797/03_2025/7tbf_25797.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tbf_25797/03_2025/7tbf_25797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tbf_25797/03_2025/7tbf_25797.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tbf_25797/03_2025/7tbf_25797.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tbf_25797/03_2025/7tbf_25797.cif"
  }
  resolution = 3.1
  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=   0.007
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      29      5.16       5
     C    4181      2.51       5
     N    1114      2.21       5
     O    1293      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6617
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1551
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "H"
      Number of atoms: 1611
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 215, 1611
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 202}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "L"
      Number of atoms: 1641
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 213, 1641
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200}
    Chain: "D"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 973
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 2, 'TRANS': 123}
    Chain: "E"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 813
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.55, per 1000 atoms: 0.84
  Number of scatterers: 6617
  At special positions: 0
  Unit cell: (88.173, 104.76, 138.807, 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      29     16.00
     O    1293      8.00
     N    1114      7.00
     C    4181      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  97 " - pdb=" SG  CYS H 100B" distance=2.03
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.04

  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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1574

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 20 sheets defined
      2.7% alpha, 25.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 417 through 422
      removed outlier: 3.529A  pdb=" N   TYR A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 65
      No H-bonds generated for 'chain 'H' and resid 63 through 65'
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.524A  pdb=" N   SER D  31 " --> pdb=" O   THR D  28 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.532A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.695A  pdb=" N   TYR H  91 " --> pdb=" O   VAL H  37 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.514A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
    Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 98
      removed outlier: 3.954A  pdb=" N   SER H 100A" --> pdb=" O   SER H  98 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 121
    Processing sheet with id=AA9, first strand: chain 'H' and resid 137 through 139
    Processing sheet with id=AB1, first strand: chain 'H' and resid 150 through 154
      removed outlier: 3.586A  pdb=" N   ASN H 197 " --> pdb=" O   SER H 153 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   THR H 205 " --> pdb=" O   HIS H 200 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.760A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR L  87 " --> pdb=" O   TYR L  36 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.760A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 19 through 22
    Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 117
      removed outlier: 3.566A  pdb=" N   SER L 176 " --> pdb=" O   SER L 162 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER L 162 " --> pdb=" O   SER L 176 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 18 through 23
      removed outlier: 3.628A  pdb=" N   LEU D  79 " --> pdb=" O   CYS D  22 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 58 through 60
      removed outlier: 3.701A  pdb=" N   TYR D  59 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   VAL D  50 " --> pdb=" O   PHE D  34 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   PHE D  34 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   HIS D  35 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA D  97 " --> pdb=" O   HIS D  35 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN D  39 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 102 through 104
    Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 7
    Processing sheet with id=AC1, first strand: chain 'E' and resid 34 through 37
      removed outlier: 6.605A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 85 through 86

    145 hydrogen bonds defined for protein.
    351 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: 1.85

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.04 -     1.20: 1
        1.20 -     1.36: 2146
        1.36 -     1.52: 3616
        1.52 -     1.69: 980
        1.69 -     1.85: 36
  Bond restraints: 6779
  Sorted by residual:
  bond pdb=" CG  PRO A 384 "
       pdb=" CD  PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.503  1.042  0.461 3.40e-02 8.65e+02 1.84e+02
  bond pdb=" N   PRO A 384 "
       pdb=" CD  PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.473  1.521 -0.048 1.40e-02 5.10e+03 1.19e+01
  bond pdb=" CB  PRO A 384 "
       pdb=" CG  PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.492  1.338  0.154 5.00e-02 4.00e+02 9.43e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.41e+00
  bond pdb=" CB  PRO A 337 "
       pdb=" CG  PRO A 337 "
    ideal  model  delta    sigma   weight residual
    1.492  1.570 -0.078 5.00e-02 4.00e+02 2.44e+00
  ... (remaining 6774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.38: 9204
        5.38 -    10.76: 13
       10.76 -    16.14: 0
       16.14 -    21.51: 1
       21.51 -    26.89: 2
  Bond angle restraints: 9220
  Sorted by residual:
  angle pdb=" N   PRO A 384 "
        pdb=" CD  PRO A 384 "
        pdb=" CG  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     103.20   76.31   26.89 1.50e+00 4.44e-01 3.21e+02
  angle pdb=" CA  PRO A 384 "
        pdb=" CB  PRO A 384 "
        pdb=" CG  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     104.50   84.12   20.38 1.90e+00 2.77e-01 1.15e+02
  angle pdb=" CB  PRO A 384 "
        pdb=" CG  PRO A 384 "
        pdb=" CD  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     106.10  132.40  -26.30 3.20e+00 9.77e-02 6.76e+01
  angle pdb=" CA  PRO A 384 "
        pdb=" N   PRO A 384 "
        pdb=" CD  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     112.00  101.89   10.11 1.40e+00 5.10e-01 5.21e+01
  angle pdb=" N   ASP H 144 "
        pdb=" CA  ASP H 144 "
        pdb=" C   ASP H 144 "
      ideal   model   delta    sigma   weight residual
     110.91  116.10   -5.19 1.17e+00 7.31e-01 1.97e+01
  ... (remaining 9215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 3571
       16.05 -    32.10: 369
       32.10 -    48.15: 75
       48.15 -    64.20: 15
       64.20 -    80.25: 7
  Dihedral angle restraints: 4037
    sinusoidal: 1565
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.23  -57.23     1      1.00e+01 1.00e-02 4.40e+01
  dihedral pdb=" CB  CYS E  23 "
           pdb=" SG  CYS E  23 "
           pdb=" SG  CYS E  88 "
           pdb=" CB  CYS E  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.21  -57.21     1      1.00e+01 1.00e-02 4.40e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  96 "
           pdb=" CB  CYS D  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.52   56.48     1      1.00e+01 1.00e-02 4.30e+01
  ... (remaining 4034 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 571
       0.031 -    0.062: 280
       0.062 -    0.093: 99
       0.093 -    0.124: 56
       0.124 -    0.154: 12
  Chirality restraints: 1018
  Sorted by residual:
  chirality pdb=" CA  VAL H 211 "
            pdb=" N   VAL H 211 "
            pdb=" C   VAL H 211 "
            pdb=" CB  VAL H 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 5.96e-01
  chirality pdb=" CA  VAL L 132 "
            pdb=" N   VAL L 132 "
            pdb=" C   VAL L 132 "
            pdb=" CB  VAL L 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  chirality pdb=" CA  PRO E  40 "
            pdb=" N   PRO E  40 "
            pdb=" C   PRO E  40 "
            pdb=" CB  PRO E  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 1015 not shown)

  Planarity restraints: 1185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 383 "   -0.070 5.00e-02 4.00e+02   9.80e-02 1.54e+01
        pdb=" N   PRO A 384 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO A 384 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 384 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 336 "   -0.052 5.00e-02 4.00e+02   7.72e-02 9.53e+00
        pdb=" N   PRO A 337 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 337 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 337 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  14 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.67e+00
        pdb=" N   PRO L  15 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO L  15 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO L  15 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1182 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 62
        2.63 -     3.20: 5629
        3.20 -     3.77: 8740
        3.77 -     4.33: 12681
        4.33 -     4.90: 22334
  Nonbonded interactions: 49446
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN L 124 "
            pdb=" O   THR L 129 "
     model   vdw
     2.064 3.120
  nonbonded pdb=" N   THR H 135 "
            pdb=" O   VAL H 184 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OH  TYR E  36 "
            pdb=" OE1 GLN E  89 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD1 ASP L  60 "
            pdb=" N   ARG L  61 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" OD1 ASP L 167 "
            pdb=" N   ASP L 170 "
     model   vdw
     2.297 3.120
  ... (remaining 49441 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.630
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.730
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
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      :  0.008   0.461   6779  Z= 0.528
  Angle     :  0.875  26.893   9220  Z= 0.469
  Chirality :  0.046   0.154   1018
  Planarity :  0.006   0.098   1184
  Dihedral  : 13.385  80.248   2433
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 14.91 %
    Favored  : 84.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -3.53 (0.27), residues: 845
  helix: -5.25 (0.24), residues: 20
  sheet: -1.34 (0.30), residues: 316
  loop : -3.03 (0.24), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  47 
 HIS   0.009   0.003   HIS L 189 
 PHE   0.013   0.001   PHE A 347 
 TYR   0.013   0.001   TYR L 140 
 ARG   0.006   0.000   ARG L 142 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2228
  time to fit residues: 43.5862
Evaluate side-chains
  120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0040
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 388 ASN
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** 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 = 0.3506 r_free = 0.3506 target = 0.093970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.083136 restraints weight = 15109.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.70
r_work: 0.3239 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6779  Z= 0.259
  Angle     :  0.737   9.393   9220  Z= 0.377
  Chirality :  0.046   0.194   1018
  Planarity :  0.005   0.043   1184
  Dihedral  :  5.975  56.363    976
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.14 %
    Favored  : 86.39 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.73 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -3.27 (0.27), residues: 845
  helix: -5.24 (0.24), residues: 20
  sheet: -1.07 (0.30), residues: 328
  loop : -2.95 (0.24), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  47 
 HIS   0.006   0.001   HIS L 189 
 PHE   0.012   0.001   PHE A 347 
 TYR   0.018   0.001   TYR D  80 
 ARG   0.004   0.001   ARG E  24 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8483 (mmm) cc_final: 0.7993 (pmm)
REVERT: H   71 ARG cc_start: 0.8907 (ttp80) cc_final: 0.8702 (ttp80)
REVERT: H   72 ASP cc_start: 0.8391 (t0) cc_final: 0.7969 (t0)
REVERT: L   60 ASP cc_start: 0.8087 (t0) cc_final: 0.7877 (t0)
REVERT: L  103 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8450 (tttm)
REVERT: D   58 GLN cc_start: 0.9135 (mp10) cc_final: 0.8503 (mp10)
  outliers start: 8
  outliers final: 6
  residues processed: 128
  average time/residue: 0.2202
  time to fit residues: 36.4250
Evaluate side-chains
  124 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   73 MET
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  124 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 80 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 63 optimal weight:    0.0470
   chunk 61 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 81 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.2878

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.095736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.084419 restraints weight = 15451.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.82
r_work: 0.3268 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6779  Z= 0.180
  Angle     :  0.664   9.573   9220  Z= 0.336
  Chirality :  0.044   0.165   1018
  Planarity :  0.004   0.037   1184
  Dihedral  :  5.513  55.473    976
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 11.83 %
    Favored  : 87.69 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 11.83 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -3.06 (0.28), residues: 845
  helix: -5.22 (0.25), residues: 20
  sheet: -0.90 (0.30), residues: 333
  loop : -2.84 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 436 
 HIS   0.003   0.001   HIS L 189 
 PHE   0.008   0.001   PHE L  98 
 TYR   0.016   0.001   TYR A 396 
 ARG   0.004   0.001   ARG L 142 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8531 (ttp80)
REVERT: H   72 ASP cc_start: 0.8413 (t0) cc_final: 0.8077 (t0)
REVERT: L   60 ASP cc_start: 0.7804 (t0) cc_final: 0.7445 (t0)
REVERT: L  103 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8391 (tttm)
REVERT: L  124 GLN cc_start: 0.5452 (mm-40) cc_final: 0.4949 (mm-40)
REVERT: D  126 SER cc_start: 0.8785 (p) cc_final: 0.8583 (t)
REVERT: E   82 ASP cc_start: 0.8075 (m-30) cc_final: 0.7757 (m-30)
  outliers start: 18
  outliers final: 10
  residues processed: 134
  average time/residue: 0.2156
  time to fit residues: 38.1475
Evaluate side-chains
  122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   73 MET
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  194 TYR
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   99 ASP
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   63 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0050
   overall best weight:    1.1198

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.091192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.080100 restraints weight = 15617.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.80
r_work: 0.3189 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   6779  Z= 0.385
  Angle     :  0.754   9.450   9220  Z= 0.386
  Chirality :  0.047   0.151   1018
  Planarity :  0.005   0.045   1184
  Dihedral  :  5.968  56.900    976
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 14.44 %
    Favored  : 85.09 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 13.20 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -3.10 (0.27), residues: 845
  helix: -5.20 (0.26), residues: 20
  sheet: -0.84 (0.30), residues: 323
  loop : -2.92 (0.24), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  47 
 HIS   0.010   0.002   HIS L 189 
 PHE   0.015   0.001   PHE L 118 
 TYR   0.017   0.002   TYR E  49 
 ARG   0.004   0.001   ARG L 142 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: H   72 ASP cc_start: 0.8368 (t0) cc_final: 0.8055 (t0)
REVERT: H  135 THR cc_start: 0.6703 (OUTLIER) cc_final: 0.4614 (t)
REVERT: L   60 ASP cc_start: 0.7858 (t0) cc_final: 0.7459 (t0)
REVERT: L  103 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8386 (tttm)
REVERT: D  126 SER cc_start: 0.8929 (p) cc_final: 0.8721 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 123
  average time/residue: 0.2090
  time to fit residues: 33.3481
Evaluate side-chains
  133 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  194 TYR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain D residue    6 GLU
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   89 ASP
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   63 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9980
   chunk 51 optimal weight:    0.1980
   chunk 68 optimal weight:    0.0070
   chunk 64 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN
D 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.093166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.082129 restraints weight = 15366.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.76
r_work: 0.3234 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6779  Z= 0.198
  Angle     :  0.678   9.692   9220  Z= 0.343
  Chirality :  0.045   0.151   1018
  Planarity :  0.004   0.041   1184
  Dihedral  :  5.606  56.204    976
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.31 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.13 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -2.87 (0.28), residues: 845
  helix: -5.15 (0.27), residues: 20
  sheet: -0.76 (0.30), residues: 323
  loop : -2.69 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 117 
 HIS   0.004   0.001   HIS L 189 
 PHE   0.008   0.001   PHE H 146 
 TYR   0.019   0.001   TYR E  49 
 ARG   0.005   0.001   ARG L 107 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8225 (mmm) cc_final: 0.7952 (pmm)
REVERT: H   71 ARG cc_start: 0.8726 (ttp80) cc_final: 0.7817 (ttp80)
REVERT: H   72 ASP cc_start: 0.8354 (t0) cc_final: 0.8055 (t0)
REVERT: L   60 ASP cc_start: 0.7789 (t0) cc_final: 0.7390 (t0)
REVERT: L  103 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8413 (tttm)
REVERT: D  126 SER cc_start: 0.8838 (p) cc_final: 0.8625 (t)
  outliers start: 24
  outliers final: 14
  residues processed: 133
  average time/residue: 0.1998
  time to fit residues: 34.5947
Evaluate side-chains
  128 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain H residue  152 VAL
Chi-restraints excluded: chain H residue  194 TYR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain D residue    6 GLU
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   63 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 77 optimal weight:    0.2980
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0770
   chunk 34 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8340

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.091602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.080486 restraints weight = 15467.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.85
r_work: 0.3204 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   6779  Z= 0.302
  Angle     :  0.702   9.177   9220  Z= 0.358
  Chirality :  0.045   0.153   1018
  Planarity :  0.005   0.044   1184
  Dihedral  :  5.759  56.516    976
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.96 %
    Favored  : 85.56 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.64 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -2.86 (0.28), residues: 845
  helix: -5.15 (0.27), residues: 20
  sheet: -0.74 (0.30), residues: 326
  loop : -2.69 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  47 
 HIS   0.007   0.001   HIS L 189 
 PHE   0.010   0.001   PHE H 122 
 TYR   0.019   0.001   TYR E  49 
 ARG   0.006   0.001   ARG H  71 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8250 (mmm) cc_final: 0.7936 (pmm)
REVERT: H   71 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8391 (ttp80)
REVERT: H   72 ASP cc_start: 0.8361 (t0) cc_final: 0.8092 (t0)
REVERT: L   60 ASP cc_start: 0.7858 (t0) cc_final: 0.7410 (t0)
REVERT: L  103 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8421 (tttm)
REVERT: D  124 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.8016 (p)
REVERT: D  126 SER cc_start: 0.8923 (p) cc_final: 0.8698 (t)
  outliers start: 23
  outliers final: 21
  residues processed: 125
  average time/residue: 0.2121
  time to fit residues: 34.5849
Evaluate side-chains
  134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain H residue   73 MET
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  152 VAL
Chi-restraints excluded: chain H residue  194 TYR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain D residue    6 GLU
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   18 LEU
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue  119 GLN
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   63 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 27 optimal weight:    0.0870
   chunk 54 optimal weight:    0.0000
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.1980
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.3562

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.093383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.082355 restraints weight = 15310.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.76
r_work: 0.3247 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6779  Z= 0.193
  Angle     :  0.665   9.527   9220  Z= 0.337
  Chirality :  0.044   0.145   1018
  Planarity :  0.004   0.039   1184
  Dihedral  :  5.475  55.811    976
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.43 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 17.33 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -2.69 (0.28), residues: 845
  helix: -5.11 (0.29), residues: 20
  sheet: -0.62 (0.31), residues: 325
  loop : -2.58 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 148 
 HIS   0.003   0.001   HIS L 189 
 PHE   0.007   0.001   PHE H 146 
 TYR   0.019   0.001   TYR E  49 
 ARG   0.006   0.001   ARG L 107 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8155 (mmm) cc_final: 0.7950 (pmm)
REVERT: H   71 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8455 (ttp80)
REVERT: H   72 ASP cc_start: 0.8250 (t0) cc_final: 0.7997 (t0)
REVERT: H  135 THR cc_start: 0.6485 (OUTLIER) cc_final: 0.4787 (t)
REVERT: L   60 ASP cc_start: 0.7758 (t0) cc_final: 0.7312 (t0)
REVERT: L  103 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8454 (tttm)
REVERT: D  126 SER cc_start: 0.8840 (p) cc_final: 0.8621 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 129
  average time/residue: 0.1940
  time to fit residues: 32.5798
Evaluate side-chains
  131 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain H residue   73 MET
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  152 VAL
Chi-restraints excluded: chain H residue  194 TYR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  189 HIS
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain D residue    6 GLU
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue  119 GLN
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   63 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 51 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.091821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.080586 restraints weight = 15494.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.85
r_work: 0.3208 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6779  Z= 0.275
  Angle     :  0.698   9.706   9220  Z= 0.353
  Chirality :  0.045   0.137   1018
  Planarity :  0.005   0.044   1184
  Dihedral  :  5.605  56.271    976
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.73 %
    Favored  : 85.80 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.88 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -2.68 (0.28), residues: 845
  helix: -5.12 (0.29), residues: 20
  sheet: -0.55 (0.31), residues: 325
  loop : -2.62 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  47 
 HIS   0.006   0.001   HIS L 189 
 PHE   0.009   0.001   PHE H 122 
 TYR   0.020   0.001   TYR E  49 
 ARG   0.006   0.001   ARG L 107 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8207 (mmm) cc_final: 0.7960 (pmm)
REVERT: H   71 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8449 (ttp80)
REVERT: H   72 ASP cc_start: 0.8276 (t0) cc_final: 0.8025 (t0)
REVERT: H  135 THR cc_start: 0.6569 (OUTLIER) cc_final: 0.4748 (t)
REVERT: L   60 ASP cc_start: 0.7851 (t0) cc_final: 0.7552 (t0)
REVERT: L  103 LYS cc_start: 0.8758 (ttpp) cc_final: 0.8465 (tttm)
REVERT: D  126 SER cc_start: 0.8909 (p) cc_final: 0.8677 (t)
  outliers start: 24
  outliers final: 22
  residues processed: 127
  average time/residue: 0.2025
  time to fit residues: 33.4807
Evaluate side-chains
  136 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain H residue   73 MET
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  152 VAL
Chi-restraints excluded: chain H residue  194 TYR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  189 HIS
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain D residue    6 GLU
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   90 ASP
Chi-restraints excluded: chain D residue  119 GLN
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   63 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0970
   chunk 72 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 49 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0870
   overall best weight:    0.2756

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.094019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.082675 restraints weight = 15484.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.87
r_work: 0.3247 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3253
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6779  Z= 0.185
  Angle     :  0.678   9.359   9220  Z= 0.340
  Chirality :  0.044   0.140   1018
  Planarity :  0.004   0.038   1184
  Dihedral  :  5.352  55.513    976
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.43 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.57 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -2.56 (0.28), residues: 845
  helix: -5.09 (0.31), residues: 20
  sheet: -0.38 (0.32), residues: 309
  loop : -2.56 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 148 
 HIS   0.002   0.001   HIS L 189 
 PHE   0.007   0.001   PHE L  98 
 TYR   0.020   0.001   TYR E  49 
 ARG   0.006   0.001   ARG L 107 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8171 (mmm) cc_final: 0.7964 (pmm)
REVERT: H   72 ASP cc_start: 0.8289 (t0) cc_final: 0.8059 (t0)
REVERT: H  135 THR cc_start: 0.6395 (OUTLIER) cc_final: 0.4755 (t)
REVERT: L   60 ASP cc_start: 0.7752 (t0) cc_final: 0.7465 (t0)
REVERT: L  103 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8451 (tttm)
REVERT: D  126 SER cc_start: 0.8847 (p) cc_final: 0.8618 (t)
  outliers start: 22
  outliers final: 17
  residues processed: 128
  average time/residue: 0.2006
  time to fit residues: 33.5044
Evaluate side-chains
  126 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   73 MET
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  152 VAL
Chi-restraints excluded: chain H residue  194 TYR
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  189 HIS
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain D residue    6 GLU
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  119 GLN
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   63 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 80 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0870
   chunk 32 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0470
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.094027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.082719 restraints weight = 15586.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.89
r_work: 0.3246 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6779  Z= 0.197
  Angle     :  0.692  11.758   9220  Z= 0.343
  Chirality :  0.044   0.137   1018
  Planarity :  0.004   0.040   1184
  Dihedral  :  5.323  55.471    976
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.66 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.84 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -2.52 (0.28), residues: 845
  helix: -5.09 (0.31), residues: 20
  sheet: -0.30 (0.32), residues: 309
  loop : -2.56 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 436 
 HIS   0.003   0.001   HIS L 189 
 PHE   0.007   0.001   PHE H 146 
 TYR   0.020   0.001   TYR E  49 
 ARG   0.007   0.001   ARG L 107 

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8129 (mmm) cc_final: 0.7881 (pmm)
REVERT: H   72 ASP cc_start: 0.8290 (t0) cc_final: 0.8073 (t0)
REVERT: H  135 THR cc_start: 0.6388 (OUTLIER) cc_final: 0.4741 (t)
REVERT: L   13 LEU cc_start: 0.7920 (tp) cc_final: 0.7419 (mt)
REVERT: L   60 ASP cc_start: 0.7778 (t0) cc_final: 0.7488 (t0)
REVERT: L  103 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8473 (tttm)
REVERT: L  145 LYS cc_start: 0.6906 (tmtt) cc_final: 0.6583 (tmtt)
REVERT: D  126 SER cc_start: 0.8875 (p) cc_final: 0.8632 (t)
  outliers start: 21
  outliers final: 19
  residues processed: 124
  average time/residue: 0.2077
  time to fit residues: 33.5351
Evaluate side-chains
  129 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain H residue   73 MET
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain H residue  152 VAL
Chi-restraints excluded: chain H residue  194 TYR
Chi-restraints excluded: chain H residue  198 VAL
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  189 HIS
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain D residue    6 GLU
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  119 GLN
Chi-restraints excluded: chain E residue   20 ILE
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   63 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 65 optimal weight:    0.3980
   chunk 66 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.092264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.081134 restraints weight = 15572.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.79
r_work: 0.3206 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3225 r_free = 0.3225    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6779  Z= 0.270
  Angle     :  0.713  10.824   9220  Z= 0.357
  Chirality :  0.045   0.139   1018
  Planarity :  0.005   0.042   1184
  Dihedral  :  5.504  55.911    976
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.85 %
    Favored  : 85.68 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.29 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    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: -2.49 (0.29), residues: 845
  helix: -5.09 (0.31), residues: 20
  sheet: -0.33 (0.31), residues: 323
  loop : -2.55 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  47 
 HIS   0.005   0.001   HIS L 189 
 PHE   0.009   0.001   PHE H 146 
 TYR   0.020   0.001   TYR E  49 
 ARG   0.006   0.001   ARG L 107 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4015.74 seconds
wall clock time: 69 minutes 33.60 seconds (4173.60 seconds total)