Starting phenix.real_space_refine
on Tue Mar  3 15:36:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tbf_25797/03_2026/7tbf_25797.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tbf_25797/03_2026/7tbf_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_2026/7tbf_25797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tbf_25797/03_2026/7tbf_25797.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tbf_25797/03_2026/7tbf_25797.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tbf_25797/03_2026/7tbf_25797.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.52, per 1000 atoms: 0.23
  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: 0.61
  Conformation dependent library (CDL) restraints added in 249.9 milliseconds
  

  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: 0.26
  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: 1.01

  Time building geometry restraints manager: 0.79 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:             11.240
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.780
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.440
-------------------------------------------------------------------------------
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   6791  Z= 0.269
  Angle     :  0.879  26.893   9246  Z= 0.470
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.000   ARG L 142 
 TYR   0.013   0.001   TYR L 140 
 PHE   0.013   0.001   PHE A 347 
 TRP   0.007   0.001   TRP D  47 
 HIS   0.009   0.003   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00752 ( 6779)
  covalent geometry    : angle       0.87473 ( 9220)
  SS BOND              : bond        0.00720 (   10)
  SS BOND              : angle       1.61083 (   20)
  hydrogen bonds       : bond        0.30403 (  138)
  hydrogen bonds       : angle       9.87923 (  351)
  link_BETA1-4         : bond        0.00975 (    1)
  link_BETA1-4         : angle       2.72892 (    3)
  link_NAG-ASN         : bond        0.00059 (    1)
  link_NAG-ASN         : angle       2.48408 (    3)

*********************** 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  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1000
  time to fit residues: 19.6271
Evaluate side-chains
  119 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3505 r_free = 0.3505 target = 0.094063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.083112 restraints weight = 15458.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.75
r_work: 0.3244 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3247
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6791  Z= 0.162
  Angle     :  0.732   9.472   9246  Z= 0.372
  Chirality :  0.046   0.197   1018
  Planarity :  0.005   0.043   1184
  Dihedral  :  5.930  56.658    976
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.78 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.45 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.25 (0.27), residues: 845
  helix: -5.23 (0.24), residues: 20
  sheet: -1.04 (0.30), residues: 326
  loop : -2.95 (0.24), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  24 
 TYR   0.017   0.001   TYR D  80 
 PHE   0.013   0.001   PHE A 347 
 TRP   0.007   0.001   TRP D  47 
 HIS   0.006   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6779)
  covalent geometry    : angle       0.72907 ( 9220)
  SS BOND              : bond        0.00688 (   10)
  SS BOND              : angle       1.30385 (   20)
  hydrogen bonds       : bond        0.04688 (  138)
  hydrogen bonds       : angle       6.70524 (  351)
  link_BETA1-4         : bond        0.00358 (    1)
  link_BETA1-4         : angle       1.87454 (    3)
  link_NAG-ASN         : bond        0.00105 (    1)
  link_NAG-ASN         : angle       2.16476 (    3)

*********************** 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
  134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8194 (mmm) cc_final: 0.7924 (pmm)
REVERT: H   71 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8573 (ttp80)
REVERT: H   72 ASP cc_start: 0.8388 (t0) cc_final: 0.8003 (t0)
REVERT: L   60 ASP cc_start: 0.7879 (t0) cc_final: 0.7652 (t0)
REVERT: L  103 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8327 (tttm)
REVERT: L  124 GLN cc_start: 0.5819 (mm-40) cc_final: 0.5373 (mm-40)
  outliers start: 8
  outliers final: 5
  residues processed: 129
  average time/residue: 0.1006
  time to fit residues: 16.5717
Evaluate side-chains
  125 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   73 MET
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 36 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.091726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.080643 restraints weight = 15405.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.80
r_work: 0.3204 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
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 = 0.48   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 = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   6791  Z= 0.213
  Angle     :  0.736   9.077   9246  Z= 0.378
  Chirality :  0.046   0.155   1018
  Planarity :  0.005   0.044   1184
  Dihedral  :  6.017  56.635    976
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 14.32 %
    Favored  : 85.21 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 12.10 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.28), residues: 845
  helix: -5.21 (0.25), residues: 20
  sheet: -0.94 (0.30), residues: 325
  loop : -2.91 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  18 
 TYR   0.018   0.001   TYR A 396 
 PHE   0.013   0.001   PHE L 118 
 TRP   0.009   0.001   TRP D  47 
 HIS   0.010   0.002   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 6779)
  covalent geometry    : angle       0.73183 ( 9220)
  SS BOND              : bond        0.00722 (   10)
  SS BOND              : angle       1.33308 (   20)
  hydrogen bonds       : bond        0.04613 (  138)
  hydrogen bonds       : angle       6.08514 (  351)
  link_BETA1-4         : bond        0.00606 (    1)
  link_BETA1-4         : angle       1.85925 (    3)
  link_NAG-ASN         : bond        0.00346 (    1)
  link_NAG-ASN         : angle       2.50125 (    3)

*********************** 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
  140 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: H   71 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8503 (ttp80)
REVERT: H   72 ASP cc_start: 0.8410 (t0) cc_final: 0.8046 (t0)
REVERT: L   60 ASP cc_start: 0.7914 (t0) cc_final: 0.7559 (t0)
REVERT: L  103 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8405 (tttm)
REVERT: D  126 SER cc_start: 0.8899 (p) cc_final: 0.8696 (t)
REVERT: E   82 ASP cc_start: 0.8146 (m-30) cc_final: 0.7795 (m-30)
  outliers start: 23
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0941
  time to fit residues: 15.9844
Evaluate side-chains
  132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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  194 TYR
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  170 ASP
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   99 ASP
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0770
   chunk 60 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.6540

-------------------------------------------------------------------------------
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 = 0.092389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.081339 restraints weight = 15568.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.79
r_work: 0.3215 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
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 = 0.43   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 = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6791  Z= 0.166
  Angle     :  0.705   9.640   9246  Z= 0.358
  Chirality :  0.045   0.153   1018
  Planarity :  0.005   0.042   1184
  Dihedral  :  5.803  56.530    976
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.02 %
    Favored  : 86.51 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.44 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.28), residues: 845
  helix: -5.15 (0.27), residues: 20
  sheet: -0.88 (0.30), residues: 323
  loop : -2.77 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L 107 
 TYR   0.018   0.001   TYR E  49 
 PHE   0.010   0.001   PHE L 118 
 TRP   0.006   0.001   TRP D  47 
 HIS   0.006   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6779)
  covalent geometry    : angle       0.70252 ( 9220)
  SS BOND              : bond        0.00632 (   10)
  SS BOND              : angle       1.15738 (   20)
  hydrogen bonds       : bond        0.03811 (  138)
  hydrogen bonds       : angle       5.74554 (  351)
  link_BETA1-4         : bond        0.00611 (    1)
  link_BETA1-4         : angle       1.84087 (    3)
  link_NAG-ASN         : bond        0.00171 (    1)
  link_NAG-ASN         : angle       2.12115 (    3)

*********************** 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
  139 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8270 (mmm) cc_final: 0.8002 (pmm)
REVERT: H   71 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8452 (ttp80)
REVERT: H   72 ASP cc_start: 0.8387 (t0) cc_final: 0.8047 (t0)
REVERT: H  135 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.4620 (t)
REVERT: L   60 ASP cc_start: 0.7820 (t0) cc_final: 0.7420 (t0)
REVERT: L  103 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8397 (tttm)
REVERT: D  126 SER cc_start: 0.8845 (p) cc_final: 0.8637 (t)
  outliers start: 20
  outliers final: 14
  residues processed: 130
  average time/residue: 0.0912
  time to fit residues: 15.4236
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  : 0.234 
-------------------------------------------------------------------------------
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0010
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0470
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.4884

-------------------------------------------------------------------------------
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 = 0.3496 r_free = 0.3496 target = 0.092932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.081997 restraints weight = 15524.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.77
r_work: 0.3234 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    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 = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6791  Z= 0.140
  Angle     :  0.679   9.558   9246  Z= 0.343
  Chirality :  0.045   0.146   1018
  Planarity :  0.004   0.042   1184
  Dihedral  :  5.633  56.194    976
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.37 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.09 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.28), residues: 845
  helix: -5.15 (0.27), residues: 20
  sheet: -0.81 (0.30), residues: 323
  loop : -2.71 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 107 
 TYR   0.018   0.001   TYR E  49 
 PHE   0.008   0.001   PHE L 118 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.004   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6779)
  covalent geometry    : angle       0.67619 ( 9220)
  SS BOND              : bond        0.00604 (   10)
  SS BOND              : angle       1.00558 (   20)
  hydrogen bonds       : bond        0.03476 (  138)
  hydrogen bonds       : angle       5.58522 (  351)
  link_BETA1-4         : bond        0.00469 (    1)
  link_BETA1-4         : angle       1.76191 (    3)
  link_NAG-ASN         : bond        0.00115 (    1)
  link_NAG-ASN         : angle       1.99086 (    3)

*********************** 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: 23
    poor density    : 119
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8862 (m-30) cc_final: 0.8647 (m-30)
REVERT: H   71 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8465 (ttp80)
REVERT: H   72 ASP cc_start: 0.8344 (t0) cc_final: 0.8042 (t0)
REVERT: H  135 THR cc_start: 0.6500 (OUTLIER) cc_final: 0.4645 (t)
REVERT: L   60 ASP cc_start: 0.7808 (t0) cc_final: 0.7391 (t0)
REVERT: L  103 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8405 (tttm)
REVERT: D   58 GLN cc_start: 0.9319 (mp10) cc_final: 0.9109 (mp10)
REVERT: D  126 SER cc_start: 0.8844 (p) cc_final: 0.8629 (t)
  outliers start: 23
  outliers final: 18
  residues processed: 132
  average time/residue: 0.0970
  time to fit residues: 16.7656
Evaluate side-chains
  132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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  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  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 18 optimal weight:    0.2980
   chunk 64 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0670
   chunk 82 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0770
   chunk 26 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0070
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.2094

-------------------------------------------------------------------------------
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 = 0.3531 r_free = 0.3531 target = 0.094872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.083857 restraints weight = 15413.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.76
r_work: 0.3264 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6791  Z= 0.112
  Angle     :  0.656   9.689   9246  Z= 0.329
  Chirality :  0.044   0.160   1018
  Planarity :  0.004   0.039   1184
  Dihedral  :  5.362  55.405    976
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.07 %
    Favored  : 87.46 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.92 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.28), residues: 845
  helix: -5.14 (0.27), residues: 20
  sheet: -0.64 (0.30), residues: 323
  loop : -2.60 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L 107 
 TYR   0.019   0.001   TYR E  49 
 PHE   0.007   0.001   PHE L  98 
 TRP   0.007   0.001   TRP L 148 
 HIS   0.002   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6779)
  covalent geometry    : angle       0.65381 ( 9220)
  SS BOND              : bond        0.00528 (   10)
  SS BOND              : angle       0.92986 (   20)
  hydrogen bonds       : bond        0.03056 (  138)
  hydrogen bonds       : angle       5.38298 (  351)
  link_BETA1-4         : bond        0.00503 (    1)
  link_BETA1-4         : angle       1.58248 (    3)
  link_NAG-ASN         : bond        0.00086 (    1)
  link_NAG-ASN         : angle       1.67903 (    3)

*********************** 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
  141 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8843 (m-30) cc_final: 0.8620 (m-30)
REVERT: H    2 MET cc_start: 0.8171 (mmm) cc_final: 0.7850 (pmm)
REVERT: H   71 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8436 (ttp80)
REVERT: H   72 ASP cc_start: 0.8307 (t0) cc_final: 0.8017 (t0)
REVERT: L   60 ASP cc_start: 0.7749 (t0) cc_final: 0.7316 (t0)
REVERT: L  103 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8409 (tttm)
REVERT: L  145 LYS cc_start: 0.7006 (tmtt) cc_final: 0.6546 (mttp)
REVERT: D   58 GLN cc_start: 0.9300 (mp10) cc_final: 0.9081 (mp10)
REVERT: D  126 SER cc_start: 0.8767 (p) cc_final: 0.8546 (t)
  outliers start: 22
  outliers final: 16
  residues processed: 131
  average time/residue: 0.0916
  time to fit residues: 15.7047
Evaluate side-chains
  132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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 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 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 E residue   20 ILE
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 3 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    0.1980
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.092532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.081359 restraints weight = 15484.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.85
r_work: 0.3218 rms_B_bonded: 2.94 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 = 0.47   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 = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6791  Z= 0.174
  Angle     :  0.688   9.464   9246  Z= 0.347
  Chirality :  0.045   0.141   1018
  Planarity :  0.004   0.044   1184
  Dihedral  :  5.535  56.110    976
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.49 %
    Favored  : 86.04 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 16.78 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.28), residues: 845
  helix: -5.12 (0.29), residues: 20
  sheet: -0.58 (0.31), residues: 322
  loop : -2.61 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L 107 
 TYR   0.019   0.001   TYR E  49 
 PHE   0.009   0.001   PHE L 118 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.005   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 6779)
  covalent geometry    : angle       0.68613 ( 9220)
  SS BOND              : bond        0.00620 (   10)
  SS BOND              : angle       1.01674 (   20)
  hydrogen bonds       : bond        0.03663 (  138)
  hydrogen bonds       : angle       5.40629 (  351)
  link_BETA1-4         : bond        0.00406 (    1)
  link_BETA1-4         : angle       1.73985 (    3)
  link_NAG-ASN         : bond        0.00254 (    1)
  link_NAG-ASN         : angle       2.03478 (    3)

*********************** 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: 27
    poor density    : 113
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8870 (m-30) cc_final: 0.8644 (m-30)
REVERT: H    2 MET cc_start: 0.8195 (mmm) cc_final: 0.7883 (pmm)
REVERT: H   71 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8421 (ttp80)
REVERT: H   72 ASP cc_start: 0.8293 (t0) cc_final: 0.8027 (t0)
REVERT: H  135 THR cc_start: 0.6568 (OUTLIER) cc_final: 0.4752 (t)
REVERT: L   60 ASP cc_start: 0.7828 (t0) cc_final: 0.7409 (t0)
REVERT: L  103 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8419 (tttm)
REVERT: D  126 SER cc_start: 0.8879 (p) cc_final: 0.8653 (t)
  outliers start: 27
  outliers final: 24
  residues processed: 128
  average time/residue: 0.0902
  time to fit residues: 15.0146
Evaluate side-chains
  135 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
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  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   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 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 40 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.092123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.080992 restraints weight = 15614.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.79
r_work: 0.3214 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6791  Z= 0.181
  Angle     :  0.701   9.030   9246  Z= 0.353
  Chirality :  0.045   0.139   1018
  Planarity :  0.005   0.043   1184
  Dihedral  :  5.616  56.227    976
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.37 %
    Favored  : 86.15 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 17.06 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.28), residues: 845
  helix: -5.13 (0.28), residues: 20
  sheet: -0.53 (0.31), residues: 322
  loop : -2.58 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L 107 
 TYR   0.020   0.001   TYR E  49 
 PHE   0.009   0.001   PHE H 122 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.006   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 6779)
  covalent geometry    : angle       0.69656 ( 9220)
  SS BOND              : bond        0.00621 (   10)
  SS BOND              : angle       1.58014 (   20)
  hydrogen bonds       : bond        0.03701 (  138)
  hydrogen bonds       : angle       5.41290 (  351)
  link_BETA1-4         : bond        0.00534 (    1)
  link_BETA1-4         : angle       1.80758 (    3)
  link_NAG-ASN         : bond        0.00244 (    1)
  link_NAG-ASN         : angle       2.09413 (    3)

*********************** 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
  141 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8179 (mmm) cc_final: 0.7976 (pmm)
REVERT: H   71 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8436 (ttp80)
REVERT: H   72 ASP cc_start: 0.8284 (t0) cc_final: 0.8025 (t0)
REVERT: H  135 THR cc_start: 0.6599 (OUTLIER) cc_final: 0.4772 (t)
REVERT: L   60 ASP cc_start: 0.7796 (t0) cc_final: 0.7387 (t0)
REVERT: L  103 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8467 (tttm)
REVERT: L  124 GLN cc_start: 0.5469 (OUTLIER) cc_final: 0.5254 (mm-40)
REVERT: D  126 SER cc_start: 0.8890 (p) cc_final: 0.8662 (t)
  outliers start: 28
  outliers final: 24
  residues processed: 130
  average time/residue: 0.0920
  time to fit residues: 15.6654
Evaluate side-chains
  137 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
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  129 THR
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   89 ASP
Chi-restraints excluded: chain D residue   90 ASP
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 37 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.091101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.079994 restraints weight = 15620.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.86
r_work: 0.3191 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6791  Z= 0.201
  Angle     :  0.726   8.985   9246  Z= 0.368
  Chirality :  0.046   0.148   1018
  Planarity :  0.005   0.046   1184
  Dihedral  :  5.758  56.668    976
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 14.20 %
    Favored  : 85.33 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.33 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.29), residues: 845
  helix: -5.11 (0.30), residues: 20
  sheet: -0.51 (0.31), residues: 325
  loop : -2.59 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L 107 
 TYR   0.020   0.001   TYR E  49 
 PHE   0.010   0.001   PHE L 118 
 TRP   0.006   0.001   TRP D 117 
 HIS   0.006   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 6779)
  covalent geometry    : angle       0.72123 ( 9220)
  SS BOND              : bond        0.00647 (   10)
  SS BOND              : angle       1.67227 (   20)
  hydrogen bonds       : bond        0.03884 (  138)
  hydrogen bonds       : angle       5.45333 (  351)
  link_BETA1-4         : bond        0.00553 (    1)
  link_BETA1-4         : angle       1.98612 (    3)
  link_NAG-ASN         : bond        0.00322 (    1)
  link_NAG-ASN         : angle       2.25633 (    3)

*********************** 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  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.8229 (mmm) cc_final: 0.7987 (pmm)
REVERT: H   71 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8446 (ttp80)
REVERT: H   72 ASP cc_start: 0.8284 (t0) cc_final: 0.8001 (t0)
REVERT: H  135 THR cc_start: 0.6513 (OUTLIER) cc_final: 0.4761 (t)
REVERT: L   60 ASP cc_start: 0.7866 (t0) cc_final: 0.7446 (t0)
REVERT: L  103 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8475 (tttm)
REVERT: D  126 SER cc_start: 0.8914 (p) cc_final: 0.8690 (t)
  outliers start: 29
  outliers final: 24
  residues processed: 132
  average time/residue: 0.0947
  time to fit residues: 16.3155
Evaluate side-chains
  138 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  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   89 ASP
Chi-restraints excluded: chain D residue   90 ASP
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 48 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0000
   chunk 41 optimal weight:    0.0010
   chunk 28 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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
L 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.092395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.081310 restraints weight = 15589.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.79
r_work: 0.3219 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
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 = 0.47   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 = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
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   0.040   6791  Z= 0.140
  Angle     :  0.704   9.636   9246  Z= 0.356
  Chirality :  0.045   0.166   1018
  Planarity :  0.005   0.041   1184
  Dihedral  :  5.552  56.055    976
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 12.66 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.29 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.29), residues: 845
  helix: -5.09 (0.31), residues: 20
  sheet: -0.42 (0.31), residues: 324
  loop : -2.56 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L 107 
 TYR   0.020   0.001   TYR E  49 
 PHE   0.008   0.001   PHE H 146 
 TRP   0.015   0.001   TRP L 148 
 HIS   0.004   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6779)
  covalent geometry    : angle       0.70037 ( 9220)
  SS BOND              : bond        0.00522 (   10)
  SS BOND              : angle       1.43446 (   20)
  hydrogen bonds       : bond        0.03339 (  138)
  hydrogen bonds       : angle       5.33306 (  351)
  link_BETA1-4         : bond        0.00483 (    1)
  link_BETA1-4         : angle       1.85910 (    3)
  link_NAG-ASN         : bond        0.00061 (    1)
  link_NAG-ASN         : angle       1.96982 (    3)

********************** 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
  138 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: H   72 ASP cc_start: 0.8271 (t0) cc_final: 0.8013 (t0)
REVERT: H  135 THR cc_start: 0.6454 (OUTLIER) cc_final: 0.4769 (t)
REVERT: L   13 LEU cc_start: 0.7962 (tp) cc_final: 0.7526 (mt)
REVERT: L   60 ASP cc_start: 0.7812 (t0) cc_final: 0.7429 (t0)
REVERT: L  103 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8446 (tttm)
REVERT: L  145 LYS cc_start: 0.7022 (tmtt) cc_final: 0.6474 (mttp)
REVERT: L  162 SER cc_start: 0.8994 (p) cc_final: 0.8764 (t)
REVERT: D    6 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8041 (pt0)
REVERT: D  126 SER cc_start: 0.8865 (p) cc_final: 0.8638 (t)
  outliers start: 24
  outliers final: 19
  residues processed: 129
  average time/residue: 0.0921
  time to fit residues: 15.4344
Evaluate side-chains
  126 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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   90 ASP
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 17 optimal weight:    0.0970
   chunk 34 optimal weight:    3.9990
   chunk 82 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 49 optimal weight:    0.3980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN
** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.092244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.081004 restraints weight = 15461.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.85
r_work: 0.3216 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6791  Z= 0.150
  Angle     :  0.707   9.496   9246  Z= 0.354
  Chirality :  0.045   0.162   1018
  Planarity :  0.005   0.043   1184
  Dihedral  :  5.503  56.032    976
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 13.85 %
    Favored  : 85.68 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.98 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.29), residues: 845
  helix: -5.10 (0.30), residues: 20
  sheet: -0.38 (0.31), residues: 324
  loop : -2.57 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L 107 
 TYR   0.020   0.001   TYR E  49 
 PHE   0.008   0.001   PHE H 146 
 TRP   0.009   0.001   TRP L 148 
 HIS   0.004   0.001   HIS L 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6779)
  covalent geometry    : angle       0.70297 ( 9220)
  SS BOND              : bond        0.00536 (   10)
  SS BOND              : angle       1.38982 (   20)
  hydrogen bonds       : bond        0.03404 (  138)
  hydrogen bonds       : angle       5.30400 (  351)
  link_BETA1-4         : bond        0.00540 (    1)
  link_BETA1-4         : angle       1.81222 (    3)
  link_NAG-ASN         : bond        0.00111 (    1)
  link_NAG-ASN         : angle       1.97288 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1949.73 seconds
wall clock time: 34 minutes 7.52 seconds (2047.52 seconds total)