Starting phenix.real_space_refine
on Tue Feb 11 21:31:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tbf_25797/02_2025/7tbf_25797.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tbf_25797/02_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_25797/02_2025/7tbf_25797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tbf_25797/02_2025/7tbf_25797.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tbf_25797/02_2025/7tbf_25797.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tbf_25797/02_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 11.03, per 1000 atoms: 1.67
  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: 1.76
  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: 0.94
  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: 2.38

  Time building geometry restraints manager: 2.09 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:             11.890
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     27.960
  Find NCS groups from input model:        0.110
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.360
-------------------------------------------------------------------------------
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  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2753
  time to fit residues: 54.2002
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  : 0.702 
-------------------------------------------------------------------------------
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 = 34)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.083137 restraints weight = 15109.630|
|-----------------------------------------------------------------------------|
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: 0.3118 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
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  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8482 (mmm) cc_final: 0.7993 (pmm)
REVERT: H   71 ARG cc_start: 0.8907 (ttp80) cc_final: 0.8703 (ttp80)
REVERT: H   72 ASP cc_start: 0.8392 (t0) cc_final: 0.7970 (t0)
REVERT: L   60 ASP cc_start: 0.8086 (t0) cc_final: 0.7876 (t0)
REVERT: L  103 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8451 (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: 0.2190
  time to fit residues: 35.9684
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  : 0.741 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 80 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3501 r_free = 0.3501 target = 0.093291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.081982 restraints weight = 15465.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.89
r_work: 0.3226 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6779  Z= 0.247
  Angle     :  0.694   9.259   9220  Z= 0.355
  Chirality :  0.045   0.155   1018
  Planarity :  0.004   0.041   1184
  Dihedral  :  5.808  56.425    976
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.73 %
    Favored  : 85.80 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.97 %
    Favored  : 85.42 %
  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: -3.14 (0.27), residues: 845
  helix: -5.21 (0.25), residues: 20
  sheet: -0.93 (0.30), residues: 327
  loop : -2.90 (0.25), residues: 498

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   0.010   0.001   PHE H 100C
 TYR   0.018   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
  139 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8516 (ttp80)
REVERT: H   72 ASP cc_start: 0.8421 (t0) cc_final: 0.8078 (t0)
REVERT: L   60 ASP cc_start: 0.7908 (t0) cc_final: 0.7563 (t0)
REVERT: L  103 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8399 (tttm)
REVERT: E   82 ASP cc_start: 0.8126 (m-30) cc_final: 0.7793 (m-30)
  outliers start: 19
  outliers final: 11
  residues processed: 130
  average time/residue: 0.2103
  time to fit residues: 35.5963
Evaluate side-chains
  120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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   11 VAL
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:    0.0050
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0070
   chunk 29 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5412

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.093461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.082256 restraints weight = 15523.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.80
r_work: 0.3238 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    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 = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6779  Z= 0.224
  Angle     :  0.693   9.673   9220  Z= 0.349
  Chirality :  0.045   0.153   1018
  Planarity :  0.004   0.042   1184
  Dihedral  :  5.662  56.072    976
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.37 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.44 %
    Favored  : 82.94 %
  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: -3.02 (0.28), residues: 845
  helix: -5.16 (0.27), residues: 20
  sheet: -0.86 (0.30), residues: 332
  loop : -2.83 (0.25), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.005   0.001   HIS L 189 
 PHE   0.009   0.001   PHE H 146 
 TYR   0.017   0.001   TYR E  49 
 ARG   0.005   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
  134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8266 (mmm) cc_final: 0.8017 (pmm)
REVERT: H   71 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8470 (ttp80)
REVERT: H   72 ASP cc_start: 0.8388 (t0) cc_final: 0.8057 (t0)
REVERT: H  135 THR cc_start: 0.6497 (OUTLIER) cc_final: 0.4573 (t)
REVERT: L   60 ASP cc_start: 0.7797 (t0) cc_final: 0.7390 (t0)
REVERT: L  103 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8413 (tttm)
REVERT: D   90 ASP cc_start: 0.7425 (m-30) cc_final: 0.7208 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 125
  average time/residue: 0.2107
  time to fit residues: 33.9593
Evaluate side-chains
  130 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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  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 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   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:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0980
   chunk 64 optimal weight:    0.9980
   chunk 59 optimal weight:    0.2980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3505 r_free = 0.3505 target = 0.093450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.082335 restraints weight = 15341.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.78
r_work: 0.3236 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6779  Z= 0.220
  Angle     :  0.679   9.531   9220  Z= 0.344
  Chirality :  0.045   0.145   1018
  Planarity :  0.004   0.042   1184
  Dihedral  :  5.580  55.932    976
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.49 %
    Favored  : 86.04 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.68 %
    Favored  : 81.16 %
  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: -2.88 (0.28), residues: 845
  helix: -5.16 (0.26), residues: 20
  sheet: -0.77 (0.30), residues: 323
  loop : -2.70 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  47 
 HIS   0.004   0.001   HIS L 189 
 PHE   0.008   0.001   PHE H 146 
 TYR   0.018   0.001   TYR E  49 
 ARG   0.006   0.000   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
  143 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8489 (ttp80)
REVERT: H   72 ASP cc_start: 0.8367 (t0) cc_final: 0.8082 (t0)
REVERT: L   60 ASP cc_start: 0.7793 (t0) cc_final: 0.7401 (t0)
REVERT: L  103 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8421 (tttm)
REVERT: D   90 ASP cc_start: 0.7373 (m-30) cc_final: 0.7139 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 134
  average time/residue: 0.1995
  time to fit residues: 35.0673
Evaluate side-chains
  132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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  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   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   22 THR
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:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 68 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.091501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.080454 restraints weight = 15492.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.78
r_work: 0.3200 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    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 = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6779  Z= 0.323
  Angle     :  0.715   9.111   9220  Z= 0.365
  Chirality :  0.046   0.152   1018
  Planarity :  0.005   0.045   1184
  Dihedral  :  5.821  56.758    976
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.61 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.64 %
    Favored  : 79.78 %
  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: -2.90 (0.28), residues: 845
  helix: -5.16 (0.26), residues: 20
  sheet: -0.79 (0.30), residues: 326
  loop : -2.71 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 148 
 HIS   0.007   0.002   HIS L 189 
 PHE   0.011   0.001   PHE H 122 
 TYR   0.019   0.001   TYR E  49 
 ARG   0.006   0.001   ARG L 107 

*********************** 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
  140 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8168 (mmm) cc_final: 0.7916 (pmm)
REVERT: H   71 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8467 (ttp80)
REVERT: H   72 ASP cc_start: 0.8345 (t0) cc_final: 0.8052 (t0)
REVERT: H  135 THR cc_start: 0.6667 (OUTLIER) cc_final: 0.4729 (t)
REVERT: L   60 ASP cc_start: 0.7824 (t0) cc_final: 0.7384 (t0)
REVERT: L  103 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8408 (tttm)
  outliers start: 26
  outliers final: 21
  residues processed: 132
  average time/residue: 0.2033
  time to fit residues: 35.0057
Evaluate side-chains
  135 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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 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  129 THR
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   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  126 SER
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:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    0.1980
   chunk 69 optimal weight:    0.3980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.092320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.081198 restraints weight = 15366.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.77
r_work: 0.3218 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6779  Z= 0.245
  Angle     :  0.692   9.291   9220  Z= 0.351
  Chirality :  0.045   0.144   1018
  Planarity :  0.004   0.042   1184
  Dihedral  :  5.681  56.416    976
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.14 %
    Favored  : 86.39 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.92 %
    Favored  : 79.23 %
  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: -2.82 (0.28), residues: 845
  helix: -5.14 (0.27), residues: 20
  sheet: -0.70 (0.30), residues: 323
  loop : -2.67 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  47 
 HIS   0.005   0.001   HIS L 189 
 PHE   0.008   0.001   PHE H 146 
 TYR   0.020   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
  142 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8466 (ttp80)
REVERT: H   72 ASP cc_start: 0.8320 (t0) cc_final: 0.8068 (t0)
REVERT: H  135 THR cc_start: 0.6608 (OUTLIER) cc_final: 0.4781 (t)
REVERT: L   60 ASP cc_start: 0.7804 (t0) cc_final: 0.7354 (t0)
REVERT: L  103 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8438 (tttm)
  outliers start: 28
  outliers final: 22
  residues processed: 133
  average time/residue: 0.1994
  time to fit residues: 34.6277
Evaluate side-chains
  135 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
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 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  124 THR
Chi-restraints excluded: chain D residue  126 SER
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0000
   chunk 60 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.6784

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.092174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.081063 restraints weight = 15531.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.78
r_work: 0.3214 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6779  Z= 0.261
  Angle     :  0.704   9.834   9220  Z= 0.355
  Chirality :  0.045   0.138   1018
  Planarity :  0.005   0.043   1184
  Dihedral  :  5.660  56.385    976
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.73 %
    Favored  : 85.80 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.78 %
    Favored  : 79.37 %
  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: -2.74 (0.28), residues: 845
  helix: -5.13 (0.28), residues: 20
  sheet: -0.62 (0.31), residues: 325
  loop : -2.64 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   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 

*********************** 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
  140 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8443 (ttp80)
REVERT: H   72 ASP cc_start: 0.8298 (t0) cc_final: 0.8009 (t0)
REVERT: H  135 THR cc_start: 0.6558 (OUTLIER) cc_final: 0.4801 (t)
REVERT: L   60 ASP cc_start: 0.7812 (t0) cc_final: 0.7507 (t0)
REVERT: L  103 LYS cc_start: 0.8761 (ttpp) cc_final: 0.8458 (tttm)
REVERT: L  124 GLN cc_start: 0.5450 (OUTLIER) cc_final: 0.5249 (mm-40)
  outliers start: 28
  outliers final: 23
  residues processed: 131
  average time/residue: 0.2027
  time to fit residues: 34.8147
Evaluate side-chains
  137 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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 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  124 GLN
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  124 THR
Chi-restraints excluded: chain D residue  126 SER
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:    0.8980
   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:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 62 optimal weight:    0.4980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.091520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.080444 restraints weight = 15594.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.77
r_work: 0.3201 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6779  Z= 0.287
  Angle     :  0.716   9.017   9220  Z= 0.362
  Chirality :  0.045   0.138   1018
  Planarity :  0.005   0.044   1184
  Dihedral  :  5.708  56.541    976
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.61 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.06 %
    Favored  : 78.95 %
  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: -2.71 (0.28), residues: 845
  helix: -5.13 (0.28), residues: 20
  sheet: -0.57 (0.31), residues: 324
  loop : -2.64 (0.26), residues: 501

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   0.009   0.001   PHE H 122 
 TYR   0.020   0.001   TYR E  49 
 ARG   0.006   0.001   ARG L 107 

*********************** REFINEMENT MACRO_CYCLE 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
  142 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8461 (ttp80)
REVERT: H   72 ASP cc_start: 0.8312 (t0) cc_final: 0.8049 (t0)
REVERT: H  135 THR cc_start: 0.6645 (OUTLIER) cc_final: 0.4855 (t)
REVERT: L   60 ASP cc_start: 0.7797 (t0) cc_final: 0.7499 (t0)
REVERT: L  103 LYS cc_start: 0.8747 (ttpp) cc_final: 0.8461 (tttm)
  outliers start: 29
  outliers final: 24
  residues processed: 132
  average time/residue: 0.2055
  time to fit residues: 35.3376
Evaluate side-chains
  136 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
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 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  129 THR
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   18 LEU
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0020
   chunk 80 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 78 optimal weight:    0.3980
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4788

-------------------------------------------------------------------------------
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 = 0.3493 r_free = 0.3493 target = 0.092656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.081316 restraints weight = 15549.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.86
r_work: 0.3222 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6779  Z= 0.217
  Angle     :  0.708  11.998   9220  Z= 0.355
  Chirality :  0.045   0.161   1018
  Planarity :  0.004   0.041   1184
  Dihedral  :  5.563  56.116    976
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.90 %
    Favored  : 86.63 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.74 %
    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: -2.62 (0.29), residues: 845
  helix: -5.11 (0.30), residues: 20
  sheet: -0.50 (0.31), residues: 324
  loop : -2.59 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  47 
 HIS   0.004   0.001   HIS L 189 
 PHE   0.008   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
  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 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8458 (ttp80)
REVERT: H   72 ASP cc_start: 0.8272 (t0) cc_final: 0.8000 (t0)
REVERT: H  135 THR cc_start: 0.6422 (OUTLIER) cc_final: 0.4737 (t)
REVERT: L   13 LEU cc_start: 0.7925 (tp) cc_final: 0.7433 (mt)
REVERT: L   60 ASP cc_start: 0.7788 (t0) cc_final: 0.7489 (t0)
REVERT: L  103 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8451 (tttm)
  outliers start: 23
  outliers final: 20
  residues processed: 128
  average time/residue: 0.2066
  time to fit residues: 34.3101
Evaluate side-chains
  131 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
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  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   18 LEU
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 SER
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:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.091453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.080192 restraints weight = 15574.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.85
r_work: 0.3183 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6779  Z= 0.297
  Angle     :  0.731  10.790   9220  Z= 0.368
  Chirality :  0.045   0.157   1018
  Planarity :  0.005   0.044   1184
  Dihedral  :  5.694  56.491    976
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 14.44 %
    Favored  : 85.09 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.74 %
    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: -2.64 (0.29), residues: 845
  helix: -5.10 (0.30), residues: 20
  sheet: -0.50 (0.31), residues: 324
  loop : -2.62 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 148 
 HIS   0.006   0.001   HIS L 189 
 PHE   0.010   0.001   PHE L 118 
 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: 3795.62 seconds
wall clock time: 68 minutes 46.23 seconds (4126.23 seconds total)