Starting phenix.real_space_refine
on Tue Feb 11 04:01:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ymh_33928/02_2025/7ymh_33928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ymh_33928/02_2025/7ymh_33928.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ymh_33928/02_2025/7ymh_33928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ymh_33928/02_2025/7ymh_33928.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ymh_33928/02_2025/7ymh_33928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ymh_33928/02_2025/7ymh_33928.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.051
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      24      5.16       5
     C    2577      2.51       5
     N     657      2.21       5
     O     690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3948
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2038
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 14, 'TRANS': 255}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 52
    Chain: "B"
      Number of atoms: 1389
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 197, 1384
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 6, 'TRANS': 190}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 257
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 219
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 183
      Conformer: "B"
        Number of residues, atoms: 197, 1384
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 6, 'TRANS': 190}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 257
          Unresolved non-hydrogen angles: 319
          Unresolved non-hydrogen dihedrals: 219
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 183
          bond proxies already assigned to first conformer: 1403
    Chain: "D"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 509
          Classifications: {'peptide': 75}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 157
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 87
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'E5E': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AALA B 158 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA B 158 " occ=0.50
  Time building chain proxies: 3.57, per 1000 atoms: 0.90
  Number of scatterers: 3948
  At special positions: 0
  Unit cell: (58.1887, 61.4824, 139.433, 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      24     16.00
     O     690      8.00
     N     657      7.00
     C    2577      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 176 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 790.7 milliseconds
  

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1026

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 4 sheets defined
      53.9% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 50
    Processing helix  chain 'A' and resid 59 through 90
      removed outlier: 3.636A  pdb=" N   LEU A  68 " --> pdb=" O   TYR A  64 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   THR A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   LEU A  80 " --> pdb=" O   THR A  76 " (cutoff:3.500A)
      Proline residue:  A  81  - end of helix
    Processing helix  chain 'A' and resid 96 through 129
      removed outlier: 3.719A  pdb=" N   ALA A 104 " --> pdb=" O   ASN A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 159
    Processing helix  chain 'A' and resid 160 through 163
      removed outlier: 3.734A  pdb=" N   PHE A 163 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 160 through 163'
    Processing helix  chain 'A' and resid 183 through 191
      removed outlier: 3.889A  pdb=" N   PHE A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 211
    Processing helix  chain 'A' and resid 263 through 274
      removed outlier: 3.915A  pdb=" N   LYS A 269 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ALA A 270 " --> pdb=" O   ARG A 266 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   THR A 273 " --> pdb=" O   LYS A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 298
      removed outlier: 4.635A  pdb=" N   PHE A 281 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
      Proline residue:  A 293  - end of helix
    Processing helix  chain 'A' and resid 304 through 329
      removed outlier: 3.946A  pdb=" N   GLY A 315 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   TYR A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   CYS A 320 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
      Proline residue:  A 323  - end of helix
      removed outlier: 3.576A  pdb=" N   TYR A 326 " --> pdb=" O   ASN A 322 " (cutoff:3.500A)
      Proline residue:  A 327  - end of helix
    Processing helix  chain 'A' and resid 331 through 339
    Processing helix  chain 'B' and resid 27 through 33
      removed outlier: 3.556A  pdb=" N   LYS B  33 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 81
      removed outlier: 4.380A  pdb=" N   GLN B  80 " --> pdb=" O   ARG B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 112
    Processing helix  chain 'B' and resid 127 through 136
      removed outlier: 3.605A  pdb=" N   GLU B 133 " --> pdb=" O   ASP B 129 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU B 136 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 146
    Processing helix  chain 'B' and resid 165 through 184
    Processing helix  chain 'B' and resid 205 through 225
    Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20
    Processing sheet with id=AA2, first strand: chain 'B' and resid 88 through 93
    Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58
      removed outlier: 6.275A  pdb=" N   PHE D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ARG D  38 " --> pdb=" O   PHE D  47 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   VAL D  91 " --> pdb=" O   GLN D  39 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 66 through 69

    224 hydrogen bonds defined for protein.
    663 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.92

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1232
        1.34 -     1.46: 961
        1.46 -     1.58: 1813
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 4037
  Sorted by residual:
  bond pdb=" CAJ E5E A 401 "
       pdb=" OAC E5E A 401 "
    ideal  model  delta    sigma   weight residual
    1.350  1.399 -0.049 2.00e-02 2.50e+03 6.09e+00
  bond pdb=" CAI E5E A 401 "
       pdb=" OAB E5E A 401 "
    ideal  model  delta    sigma   weight residual
    1.354  1.400 -0.046 2.00e-02 2.50e+03 5.31e+00
  bond pdb=" N   PRO A 299 "
       pdb=" CA  PRO A 299 "
    ideal  model  delta    sigma   weight residual
    1.469  1.482 -0.013 7.40e-03 1.83e+04 3.25e+00
  bond pdb=" CAH E5E A 401 "
       pdb=" NAA E5E A 401 "
    ideal  model  delta    sigma   weight residual
    1.486  1.451  0.035 2.00e-02 2.50e+03 3.03e+00
  bond pdb=" C   LEU A  80 "
       pdb=" N   PRO A  81 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.23e-02 6.61e+03 2.47e+00
  ... (remaining 4032 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 5268
        1.60 -     3.21: 204
        3.21 -     4.81: 38
        4.81 -     6.41: 10
        6.41 -     8.02: 4
  Bond angle restraints: 5524
  Sorted by residual:
  angle pdb=" N   ILE A 159 "
        pdb=" CA  ILE A 159 "
        pdb=" C   ILE A 159 "
      ideal   model   delta    sigma   weight residual
     111.91  106.40    5.51 8.90e-01 1.26e+00 3.83e+01
  angle pdb=" N   ASP A 300 "
        pdb=" CA  ASP A 300 "
        pdb=" C   ASP A 300 "
      ideal   model   delta    sigma   weight residual
     114.31  108.59    5.72 1.29e+00 6.01e-01 1.97e+01
  angle pdb=" N   ILE A 178 "
        pdb=" CA  ILE A 178 "
        pdb=" C   ILE A 178 "
      ideal   model   delta    sigma   weight residual
     110.05  106.05    4.00 1.09e+00 8.42e-01 1.35e+01
  angle pdb=" C   ILE A 321 "
        pdb=" N   ASN A 322 "
        pdb=" CA  ASN A 322 "
      ideal   model   delta    sigma   weight residual
     120.06  124.17   -4.11 1.19e+00 7.06e-01 1.19e+01
  angle pdb=" N   LEU A  80 "
        pdb=" CA  LEU A  80 "
        pdb=" C   LEU A  80 "
      ideal   model   delta    sigma   weight residual
     109.81  116.27   -6.46 2.21e+00 2.05e-01 8.54e+00
  ... (remaining 5519 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.48: 2063
       15.48 -    30.95: 209
       30.95 -    46.43: 49
       46.43 -    61.90: 4
       61.90 -    77.38: 4
  Dihedral angle restraints: 2329
    sinusoidal: 744
      harmonic: 1585
  Sorted by residual:
  dihedral pdb=" CA  PRO A 161 "
           pdb=" C   PRO A 161 "
           pdb=" N   LEU A 162 "
           pdb=" CA  LEU A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.63   19.37     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  ILE A 325 "
           pdb=" C   ILE A 325 "
           pdb=" N   TYR A 326 "
           pdb=" CA  TYR A 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.88  -19.12     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  PHE A 193 "
           pdb=" C   PHE A 193 "
           pdb=" N   TYR A 194 "
           pdb=" CA  TYR A 194 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.80  -18.20     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 2326 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 393
       0.038 -    0.075: 190
       0.075 -    0.113: 56
       0.113 -    0.151: 21
       0.151 -    0.189: 6
  Chirality restraints: 666
  Sorted by residual:
  chirality pdb=" CB  ILE A 159 "
            pdb=" CA  ILE A 159 "
            pdb=" CG1 ILE A 159 "
            pdb=" CG2 ILE A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.19 2.00e-01 2.50e+01 8.89e-01
  chirality pdb=" CAL E5E A 401 "
            pdb=" CAH E5E A 401 "
            pdb=" CAK E5E A 401 "
            pdb=" OAD E5E A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -2.49    0.18 2.00e-01 2.50e+01 8.11e-01
  chirality pdb=" CA  TYR A 326 "
            pdb=" N   TYR A 326 "
            pdb=" C   TYR A 326 "
            pdb=" CB  TYR A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 663 not shown)

  Planarity restraints: 688
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 322 "    0.050 5.00e-02 4.00e+02   7.53e-02 9.07e+00
        pdb=" N   PRO A 323 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 323 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 323 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 326 "    0.043 5.00e-02 4.00e+02   6.40e-02 6.55e+00
        pdb=" N   PRO A 327 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 327 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 327 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 286 "   -0.040 5.00e-02 4.00e+02   5.95e-02 5.66e+00
        pdb=" N   PRO A 287 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 287 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 287 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 685 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1341
        2.84 -     3.35: 3524
        3.35 -     3.87: 6319
        3.87 -     4.38: 6842
        4.38 -     4.90: 12224
  Nonbonded interactions: 30250
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 194 "
            pdb=" OD2 ASP B 215 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OD1 ASP A 172 "
            pdb=" OH  TYR D  37 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" OG  SER D  69 "
            pdb=" O   TYR D  78 "
     model   vdw
     2.383 3.040
  nonbonded pdb=" O   THR A 139 "
            pdb=" N   GLY A 143 "
     model   vdw
     2.383 3.120
  nonbonded pdb=" O   ASP A  72 "
            pdb=" OG1 THR A  76 "
     model   vdw
     2.417 3.040
  ... (remaining 30245 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.230
  Find NCS groups from input model:        0.030
  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:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
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      :  0.004   0.050   4037  Z= 0.264
  Angle     :  0.780   8.018   5524  Z= 0.448
  Chirality :  0.050   0.189    666
  Planarity :  0.007   0.075    688
  Dihedral  : 13.786  77.379   1300
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.54 (0.28), residues: 527
  helix: -2.63 (0.23), residues: 283
  sheet: -3.00 (0.49), residues: 67
  loop : -3.32 (0.39), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 111 
 HIS   0.006   0.001   HIS B 191 
 PHE   0.012   0.002   PHE A 308 
 TYR   0.018   0.001   TYR A 134 
 ARG   0.002   0.000   ARG B 207 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.8592 (mp) cc_final: 0.8371 (mp)
REVERT: A  165 TRP cc_start: 0.4361 (m100) cc_final: 0.4151 (m100)
REVERT: A  272 LYS cc_start: 0.8785 (tppp) cc_final: 0.8292 (tptt)
REVERT: B  215 ASP cc_start: 0.8499 (t70) cc_final: 0.7595 (t0)
REVERT: D  100 TYR cc_start: 0.8228 (p90) cc_final: 0.7856 (p90)
REVERT: D  102 ASP cc_start: 0.8443 (t70) cc_final: 0.7816 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2000
  time to fit residues: 27.7923
Evaluate side-chains
  87 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0040
   chunk 30 optimal weight:    0.0970
   chunk 48 optimal weight:   10.0000
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 179 ASN
A 318 ASN
A 331 GLN
B  16 HIS
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 GLN
B 226 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.145311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.110403 restraints weight = 5994.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110461 restraints weight = 3670.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.112186 restraints weight = 2941.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4037  Z= 0.168
  Angle     :  0.547   6.042   5524  Z= 0.297
  Chirality :  0.040   0.129    666
  Planarity :  0.005   0.043    688
  Dihedral  :  4.402  17.981    583
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.35 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.33), residues: 527
  helix: -0.77 (0.29), residues: 282
  sheet: -2.45 (0.54), residues: 67
  loop : -2.95 (0.39), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 102 
 HIS   0.004   0.001   HIS B  16 
 PHE   0.008   0.001   PHE B 197 
 TYR   0.012   0.001   TYR A 326 
 ARG   0.008   0.000   ARG B 176 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8043 (mtp) cc_final: 0.7648 (mtt)
REVERT: A  165 TRP cc_start: 0.4037 (m100) cc_final: 0.3641 (m100)
REVERT: A  272 LYS cc_start: 0.8717 (tppp) cc_final: 0.8218 (tptt)
REVERT: B  215 ASP cc_start: 0.8526 (t70) cc_final: 0.7832 (t0)
REVERT: D  100 TYR cc_start: 0.8195 (p90) cc_final: 0.7915 (p90)
  outliers start: 5
  outliers final: 2
  residues processed: 101
  average time/residue: 0.1835
  time to fit residues: 22.4589
Evaluate side-chains
  91 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain D residue   61 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 24 optimal weight:    0.2980
   chunk 31 optimal weight:    7.9990
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.144963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.106084 restraints weight = 5812.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.109538 restraints weight = 3302.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.111684 restraints weight = 2426.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4037  Z= 0.175
  Angle     :  0.526   5.670   5524  Z= 0.281
  Chirality :  0.040   0.127    666
  Planarity :  0.004   0.038    688
  Dihedral  :  4.172  17.425    583
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.80 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.35), residues: 527
  helix:  0.15 (0.31), residues: 281
  sheet: -2.24 (0.55), residues: 69
  loop : -2.76 (0.41), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 111 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.015   0.001   PHE A 187 
 TYR   0.012   0.001   TYR A 326 
 ARG   0.007   0.000   ARG B 176 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.7932 (mtp) cc_final: 0.7555 (mtt)
REVERT: A  165 TRP cc_start: 0.4035 (m100) cc_final: 0.3590 (m100)
REVERT: A  272 LYS cc_start: 0.8701 (tppp) cc_final: 0.8183 (tptt)
REVERT: B  215 ASP cc_start: 0.8495 (t70) cc_final: 0.7778 (t0)
REVERT: D  100 TYR cc_start: 0.8106 (p90) cc_final: 0.7882 (p90)
  outliers start: 13
  outliers final: 7
  residues processed: 97
  average time/residue: 0.1983
  time to fit residues: 23.0849
Evaluate side-chains
  93 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain D residue   61 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0060
   chunk 46 optimal weight:    0.0270
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.4254

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
A 179 ASN
B 226 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.146347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.107556 restraints weight = 5900.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.111122 restraints weight = 3301.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.113309 restraints weight = 2410.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3403
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3403
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4037  Z= 0.146
  Angle     :  0.496   5.410   5524  Z= 0.261
  Chirality :  0.039   0.127    666
  Planarity :  0.004   0.033    688
  Dihedral  :  3.842  14.698    583
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.71 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.37), residues: 527
  helix:  0.75 (0.32), residues: 284
  sheet: -2.00 (0.56), residues: 69
  loop : -2.62 (0.42), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 111 
 HIS   0.004   0.001   HIS B 191 
 PHE   0.010   0.001   PHE A 297 
 TYR   0.010   0.001   TYR A 326 
 ARG   0.007   0.000   ARG B 176 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.7223 (m-10) cc_final: 0.6976 (m-10)
REVERT: A  165 TRP cc_start: 0.4007 (m100) cc_final: 0.3767 (m100)
REVERT: A  272 LYS cc_start: 0.8675 (tppp) cc_final: 0.8146 (tptt)
REVERT: B  215 ASP cc_start: 0.8427 (t70) cc_final: 0.7713 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1923
  time to fit residues: 22.9966
Evaluate side-chains
  95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   91 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    7.9990
   chunk 23 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0980
   chunk 28 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
B 126 ASN
B 226 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.145458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.108671 restraints weight = 6079.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109836 restraints weight = 3580.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.111678 restraints weight = 2882.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4037  Z= 0.170
  Angle     :  0.504   5.443   5524  Z= 0.265
  Chirality :  0.040   0.127    666
  Planarity :  0.004   0.029    688
  Dihedral  :  3.846  15.651    583
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.71 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.37), residues: 527
  helix:  0.89 (0.32), residues: 285
  sheet: -1.78 (0.58), residues: 69
  loop : -2.44 (0.43), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 111 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.016   0.001   PHE A 187 
 TYR   0.013   0.001   TYR A  91 
 ARG   0.007   0.000   ARG B 176 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A   63 TYR cc_start: 0.7252 (m-10) cc_final: 0.7032 (m-10)
REVERT: A  165 TRP cc_start: 0.4053 (m100) cc_final: 0.3650 (m100)
REVERT: A  272 LYS cc_start: 0.8686 (tppp) cc_final: 0.8224 (tptt)
REVERT: A  292 MET cc_start: 0.8027 (ttm) cc_final: 0.7720 (tpt)
REVERT: B  215 ASP cc_start: 0.8445 (t70) cc_final: 0.7743 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 95
  average time/residue: 0.1907
  time to fit residues: 21.9275
Evaluate side-chains
  95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain B residue  226 ASN
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   91 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0000
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.145450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.106206 restraints weight = 5923.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.109712 restraints weight = 3370.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.111869 restraints weight = 2471.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3378
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3378
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4037  Z= 0.173
  Angle     :  0.512   7.346   5524  Z= 0.266
  Chirality :  0.040   0.126    666
  Planarity :  0.003   0.029    688
  Dihedral  :  3.790  15.957    583
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 19.62 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.37), residues: 527
  helix:  1.01 (0.32), residues: 285
  sheet: -1.77 (0.58), residues: 70
  loop : -2.29 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 102 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.008   0.001   PHE A 193 
 TYR   0.012   0.001   TYR A  91 
 ARG   0.006   0.000   ARG B 176 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A  140 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7482 (mp10)
REVERT: A  272 LYS cc_start: 0.8661 (tppp) cc_final: 0.8181 (tptt)
REVERT: A  292 MET cc_start: 0.7896 (ttm) cc_final: 0.7570 (tpt)
REVERT: A  313 TRP cc_start: 0.8806 (m100) cc_final: 0.8588 (m100)
REVERT: B  215 ASP cc_start: 0.8450 (t70) cc_final: 0.7754 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 99
  average time/residue: 0.1799
  time to fit residues: 21.4607
Evaluate side-chains
  101 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   91 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   chunk 14 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0270
   chunk 10 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.145256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.105725 restraints weight = 5968.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.109205 restraints weight = 3402.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111339 restraints weight = 2507.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4037  Z= 0.170
  Angle     :  0.508   8.469   5524  Z= 0.262
  Chirality :  0.040   0.125    666
  Planarity :  0.003   0.028    688
  Dihedral  :  3.721  15.029    583
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.98 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.38), residues: 527
  helix:  1.10 (0.32), residues: 286
  sheet: -1.67 (0.58), residues: 70
  loop : -2.15 (0.45), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 102 
 HIS   0.004   0.001   HIS B 191 
 PHE   0.008   0.001   PHE A 193 
 TYR   0.010   0.001   TYR A 326 
 ARG   0.005   0.000   ARG B 176 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  140 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7484 (mp10)
REVERT: A  145 MET cc_start: 0.7551 (mmm) cc_final: 0.7078 (mtt)
REVERT: A  272 LYS cc_start: 0.8668 (tppp) cc_final: 0.8198 (tptt)
REVERT: B   35 MET cc_start: 0.7581 (pmm) cc_final: 0.7367 (pmm)
REVERT: B  215 ASP cc_start: 0.8449 (t70) cc_final: 0.7754 (t0)
  outliers start: 14
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1756
  time to fit residues: 22.2046
Evaluate side-chains
  101 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  291 VAL
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   91 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 40 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0970
   chunk 0 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
B  71 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.145421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.106067 restraints weight = 5895.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.109519 restraints weight = 3346.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.111725 restraints weight = 2465.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3378
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3378
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4037  Z= 0.173
  Angle     :  0.520   9.084   5524  Z= 0.268
  Chirality :  0.040   0.185    666
  Planarity :  0.003   0.029    688
  Dihedral  :  3.739  14.929    583
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.71 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.38), residues: 527
  helix:  1.12 (0.32), residues: 286
  sheet: -1.61 (0.58), residues: 70
  loop : -2.06 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 102 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.008   0.001   PHE A 193 
 TYR   0.011   0.001   TYR D  99 
 ARG   0.005   0.000   ARG B 176 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  140 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7456 (mp10)
REVERT: A  145 MET cc_start: 0.7550 (mmm) cc_final: 0.7110 (mtt)
REVERT: A  181 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8002 (tm-30)
REVERT: A  272 LYS cc_start: 0.8649 (tppp) cc_final: 0.8162 (tptt)
REVERT: B   35 MET cc_start: 0.7736 (pmm) cc_final: 0.7495 (pmm)
REVERT: B  215 ASP cc_start: 0.8450 (t70) cc_final: 0.7745 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.1785
  time to fit residues: 21.3144
Evaluate side-chains
  99 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain A residue  334 LYS
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   91 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0010
   chunk 46 optimal weight:    0.0170
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.3424

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.147178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.107894 restraints weight = 5868.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.111423 restraints weight = 3339.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.113592 restraints weight = 2461.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3405
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3405 r_free = 0.3405    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3405 r_free = 0.3405    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3405
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4037  Z= 0.141
  Angle     :  0.506   9.639   5524  Z= 0.258
  Chirality :  0.039   0.126    666
  Planarity :  0.003   0.029    688
  Dihedral  :  3.654  14.792    583
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.16 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.38), residues: 527
  helix:  1.27 (0.32), residues: 286
  sheet: -1.42 (0.59), residues: 70
  loop : -1.96 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 111 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.007   0.001   PHE A 193 
 TYR   0.014   0.001   TYR A  91 
 ARG   0.005   0.000   ARG B 176 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A   89 LEU cc_start: 0.8542 (mp) cc_final: 0.8178 (mp)
REVERT: A  140 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7317 (mp10)
REVERT: A  145 MET cc_start: 0.7484 (mmm) cc_final: 0.7077 (mtt)
REVERT: A  272 LYS cc_start: 0.8626 (tppp) cc_final: 0.8142 (tptt)
REVERT: A  313 TRP cc_start: 0.8666 (m100) cc_final: 0.8384 (m100)
REVERT: B   35 MET cc_start: 0.7737 (pmm) cc_final: 0.7518 (pmm)
REVERT: B  215 ASP cc_start: 0.8407 (t70) cc_final: 0.7713 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 110
  average time/residue: 0.2006
  time to fit residues: 26.2518
Evaluate side-chains
  105 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   91 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 25 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 21 optimal weight:    0.3980
   chunk 13 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
B  71 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.146103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.109794 restraints weight = 5910.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.109795 restraints weight = 3742.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.111581 restraints weight = 3046.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4037  Z= 0.169
  Angle     :  0.527   9.733   5524  Z= 0.269
  Chirality :  0.040   0.137    666
  Planarity :  0.004   0.032    688
  Dihedral  :  3.685  14.116    583
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 20.98 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.38), residues: 527
  helix:  1.26 (0.32), residues: 286
  sheet: -1.38 (0.60), residues: 70
  loop : -1.91 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 111 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.008   0.001   PHE A 193 
 TYR   0.009   0.001   TYR A 326 
 ARG   0.008   0.001   ARG A 206 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   89 LEU cc_start: 0.8563 (mp) cc_final: 0.8141 (mp)
REVERT: A  140 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7399 (mp10)
REVERT: A  145 MET cc_start: 0.7506 (mmm) cc_final: 0.7103 (mtt)
REVERT: A  272 LYS cc_start: 0.8620 (tppp) cc_final: 0.8127 (tptt)
REVERT: B   35 MET cc_start: 0.7774 (pmm) cc_final: 0.7560 (pmm)
REVERT: B  215 ASP cc_start: 0.8421 (t70) cc_final: 0.7756 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 106
  average time/residue: 0.2117
  time to fit residues: 26.6415
Evaluate side-chains
  109 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain D residue   61 SER
Chi-restraints excluded: chain D residue   91 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0040
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8594

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.144012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.107037 restraints weight = 5948.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.107167 restraints weight = 3785.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.108851 restraints weight = 3086.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4037  Z= 0.222
  Angle     :  0.552   9.587   5524  Z= 0.284
  Chirality :  0.041   0.139    666
  Planarity :  0.004   0.032    688
  Dihedral  :  3.824  15.748    583
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.53 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.38), residues: 527
  helix:  1.21 (0.32), residues: 286
  sheet: -1.43 (0.61), residues: 70
  loop : -1.88 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 102 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.009   0.001   PHE B 107 
 TYR   0.023   0.001   TYR A  91 
 ARG   0.008   0.001   ARG A 206 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1795.08 seconds
wall clock time: 32 minutes 37.03 seconds (1957.03 seconds total)