Starting phenix.real_space_refine
on Wed Jul 23 18:34:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ymh_33928/07_2025/7ymh_33928.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ymh_33928/07_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_33928/07_2025/7ymh_33928.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_2025/7ymh_33928.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_2025/7ymh_33928.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ymh_33928/07_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 3.80, per 1000 atoms: 0.96
  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: 1.05
  Conformation dependent library (CDL) restraints added in 884.9 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: 0.38
  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: 0.95

  Time building geometry restraints manager: 1.23 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:             0.570
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.200
-------------------------------------------------------------------------------
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   4038  Z= 0.204
  Angle     :  0.780   8.018   5526  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13040 (  224)
  hydrogen bonds       : angle       6.89403 (  663)
  SS BOND              : bond        0.00295 (    1)
  SS BOND              : angle       0.61919 (    2)
  covalent geometry    : bond        0.00420 ( 4037)
  covalent geometry    : angle       0.77982 ( 5524)

*********************** 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  : 0.462 
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: 0.2019
  time to fit residues: 27.9697
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  : 0.440 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 30 optimal weight:    0.0970
   chunk 48 optimal weight:   10.0000
   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  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 = 0.3814 r_free = 0.3814 target = 0.145409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.110454 restraints weight = 5992.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.110696 restraints weight = 3618.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.112372 restraints weight = 2911.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    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 = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4038  Z= 0.124
  Angle     :  0.550   6.005   5526  Z= 0.299
  Chirality :  0.040   0.128    666
  Planarity :  0.005   0.043    688
  Dihedral  :  4.397  17.938    583
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.35 %
    Favored  : 82.56 %
  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: -0.76 (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 191 
 PHE   0.008   0.001   PHE B 197 
 TYR   0.012   0.001   TYR A 326 
 ARG   0.008   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  224)
  hydrogen bonds       : angle       4.69874 (  663)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       0.29210 (    2)
  covalent geometry    : bond        0.00266 ( 4037)
  covalent geometry    : angle       0.54979 ( 5524)

*********************** 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
  105 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.8037 (mtp) cc_final: 0.7642 (mtt)
REVERT: A  165 TRP cc_start: 0.4042 (m100) cc_final: 0.3769 (m100)
REVERT: A  272 LYS cc_start: 0.8717 (tppp) cc_final: 0.8215 (tptt)
REVERT: B  215 ASP cc_start: 0.8529 (t70) cc_final: 0.7807 (t0)
REVERT: D  100 TYR cc_start: 0.8196 (p90) cc_final: 0.7914 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 101
  average time/residue: 0.1922
  time to fit residues: 23.5252
Evaluate side-chains
  92 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 31 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.144337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.105332 restraints weight = 5843.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.108761 restraints weight = 3345.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.110847 restraints weight = 2465.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4038  Z= 0.133
  Angle     :  0.534   5.693   5526  Z= 0.285
  Chirality :  0.040   0.126    666
  Planarity :  0.004   0.038    688
  Dihedral  :  4.200  17.772    583
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 17.44 %
    Favored  : 77.93 %
  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: -1.77 (0.35), residues: 527
  helix:  0.12 (0.30), residues: 281
  sheet: -2.30 (0.55), residues: 69
  loop : -2.75 (0.41), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 102 
 HIS   0.004   0.001   HIS B 191 
 PHE   0.014   0.001   PHE A 187 
 TYR   0.012   0.001   TYR A 326 
 ARG   0.007   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04076 (  224)
  hydrogen bonds       : angle       4.44832 (  663)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       0.42418 (    2)
  covalent geometry    : bond        0.00300 ( 4037)
  covalent geometry    : angle       0.53356 ( 5524)

*********************** 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
  107 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.7996 (mtp) cc_final: 0.7619 (mtt)
REVERT: A  165 TRP cc_start: 0.4063 (m100) cc_final: 0.3821 (m100)
REVERT: A  272 LYS cc_start: 0.8716 (tppp) cc_final: 0.8197 (tptt)
REVERT: B  215 ASP cc_start: 0.8583 (t70) cc_final: 0.7838 (t0)
REVERT: D  100 TYR cc_start: 0.8119 (p90) cc_final: 0.7895 (p90)
  outliers start: 17
  outliers final: 10
  residues processed: 96
  average time/residue: 0.1959
  time to fit residues: 22.4680
Evaluate side-chains
  97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   78 THR
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  291 VAL
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  333 PHE
Chi-restraints excluded: chain B residue   68 VAL
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:    7.9990
   chunk 40 optimal weight:    0.0670
   chunk 3 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 43 optimal weight:    0.3980
   chunk 32 optimal weight:    0.2980
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.3118

-------------------------------------------------------------------------------
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  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.147086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.108320 restraints weight = 5874.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.111919 restraints weight = 3269.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.114106 restraints weight = 2376.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    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 = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4038  Z= 0.099
  Angle     :  0.493   5.506   5526  Z= 0.260
  Chirality :  0.039   0.128    666
  Planarity :  0.004   0.034    688
  Dihedral  :  3.850  15.130    583
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.25 %
    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: -1.11 (0.37), residues: 527
  helix:  0.72 (0.32), residues: 284
  sheet: -2.01 (0.56), residues: 69
  loop : -2.65 (0.42), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 111 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.010   0.001   PHE A 297 
 TYR   0.009   0.001   TYR A 326 
 ARG   0.006   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03635 (  224)
  hydrogen bonds       : angle       4.09172 (  663)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.23345 (    2)
  covalent geometry    : bond        0.00211 ( 4037)
  covalent geometry    : angle       0.49275 ( 5524)

*********************** 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
  106 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 TYR cc_start: 0.7215 (m-10) cc_final: 0.6968 (m-10)
REVERT: A  272 LYS cc_start: 0.8678 (tppp) cc_final: 0.8223 (tptt)
REVERT: B  215 ASP cc_start: 0.8457 (t70) cc_final: 0.7721 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 99
  average time/residue: 0.1956
  time to fit residues: 23.1776
Evaluate side-chains
  93 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  205 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0970
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   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 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 = 0.145266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.105843 restraints weight = 6085.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.109369 restraints weight = 3423.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.111503 restraints weight = 2500.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3377
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    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 = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3377
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4038  Z= 0.119
  Angle     :  0.505   5.454   5526  Z= 0.266
  Chirality :  0.040   0.130    666
  Planarity :  0.003   0.030    688
  Dihedral  :  3.840  15.561    583
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  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: -0.81 (0.37), residues: 527
  helix:  0.84 (0.32), residues: 290
  sheet: -1.86 (0.57), residues: 70
  loop : -2.37 (0.44), residues: 167

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   0.016   0.001   PHE A 187 
 TYR   0.013   0.001   TYR A  91 
 ARG   0.004   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  224)
  hydrogen bonds       : angle       4.02772 (  663)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       0.16148 (    2)
  covalent geometry    : bond        0.00271 ( 4037)
  covalent geometry    : angle       0.50492 ( 5524)

*********************** 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
  107 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A   63 TYR cc_start: 0.7256 (m-10) cc_final: 0.7008 (m-10)
REVERT: A  272 LYS cc_start: 0.8684 (tppp) cc_final: 0.8141 (tptt)
REVERT: A  292 MET cc_start: 0.7911 (ttm) cc_final: 0.7600 (tpt)
REVERT: B  215 ASP cc_start: 0.8489 (t70) cc_final: 0.7748 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1847
  time to fit residues: 22.1566
Evaluate side-chains
  96 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
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  163 PHE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  205 CYS
Chi-restraints excluded: chain A residue  262 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.2980
   chunk 19 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 40 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
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 = 0.144997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.105549 restraints weight = 5943.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109029 restraints weight = 3387.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.110943 restraints weight = 2493.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4038  Z= 0.124
  Angle     :  0.514   7.236   5526  Z= 0.268
  Chirality :  0.040   0.125    666
  Planarity :  0.004   0.029    688
  Dihedral  :  3.808  15.721    583
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.89 %
    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: -0.67 (0.37), residues: 527
  helix:  0.97 (0.32), residues: 286
  sheet: -1.79 (0.57), residues: 70
  loop : -2.27 (0.44), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 102 
 HIS   0.004   0.001   HIS B 191 
 PHE   0.009   0.001   PHE A 297 
 TYR   0.012   0.001   TYR A  91 
 ARG   0.005   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  224)
  hydrogen bonds       : angle       4.00298 (  663)
  SS BOND              : bond        0.00354 (    1)
  SS BOND              : angle       0.25885 (    2)
  covalent geometry    : bond        0.00285 ( 4037)
  covalent geometry    : angle       0.51405 ( 5524)

*********************** 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
  104 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A   63 TYR cc_start: 0.7320 (m-10) cc_final: 0.7046 (m-10)
REVERT: A  140 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7527 (mp10)
REVERT: A  272 LYS cc_start: 0.8667 (tppp) cc_final: 0.8191 (tptt)
REVERT: B  215 ASP cc_start: 0.8464 (t70) cc_final: 0.7764 (t0)
REVERT: B  226 ASN cc_start: 0.8350 (t0) cc_final: 0.8113 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 96
  average time/residue: 0.1802
  time to fit residues: 20.9370
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  : 0.433 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 33 optimal weight:    0.4980
   chunk 14 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3807 r_free = 0.3807 target = 0.144710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.105131 restraints weight = 5978.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.108572 restraints weight = 3396.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110707 restraints weight = 2505.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4038  Z= 0.128
  Angle     :  0.528   8.454   5526  Z= 0.272
  Chirality :  0.040   0.183    666
  Planarity :  0.003   0.029    688
  Dihedral  :  3.814  15.395    583
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 19.89 %
    Favored  : 75.48 %
  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: -0.53 (0.38), residues: 527
  helix:  1.04 (0.32), residues: 286
  sheet: -1.75 (0.58), residues: 70
  loop : -2.12 (0.45), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 313 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.008   0.001   PHE A 297 
 TYR   0.010   0.001   TYR A 326 
 ARG   0.005   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  224)
  hydrogen bonds       : angle       4.00184 (  663)
  SS BOND              : bond        0.00331 (    1)
  SS BOND              : angle       0.40991 (    2)
  covalent geometry    : bond        0.00294 ( 4037)
  covalent geometry    : angle       0.52787 ( 5524)

*********************** 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
  109 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A   63 TYR cc_start: 0.7309 (m-10) cc_final: 0.7055 (m-10)
REVERT: A  145 MET cc_start: 0.7577 (mmm) cc_final: 0.7094 (mtt)
REVERT: A  272 LYS cc_start: 0.8668 (tppp) cc_final: 0.8180 (tptt)
REVERT: B  215 ASP cc_start: 0.8466 (t70) cc_final: 0.7753 (t0)
REVERT: B  226 ASN cc_start: 0.8321 (t0) cc_final: 0.8046 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1851
  time to fit residues: 21.9986
Evaluate side-chains
  101 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
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  163 PHE
Chi-restraints excluded: chain A residue  174 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0770
   chunk 46 optimal weight:    0.0870
   chunk 0 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.145604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.106365 restraints weight = 5884.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.109856 restraints weight = 3344.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.112010 restraints weight = 2447.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    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 = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4038  Z= 0.113
  Angle     :  0.513   9.124   5526  Z= 0.263
  Chirality :  0.039   0.127    666
  Planarity :  0.003   0.029    688
  Dihedral  :  3.726  14.946    583
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 19.89 %
    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: -0.38 (0.38), residues: 527
  helix:  1.13 (0.32), residues: 286
  sheet: -1.61 (0.59), residues: 70
  loop : -2.01 (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   0.010   0.001   TYR D  99 
 ARG   0.005   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  224)
  hydrogen bonds       : angle       3.95728 (  663)
  SS BOND              : bond        0.00289 (    1)
  SS BOND              : angle       0.40396 (    2)
  covalent geometry    : bond        0.00254 ( 4037)
  covalent geometry    : angle       0.51314 ( 5524)

*********************** 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
  112 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A  140 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7459 (mp10)
REVERT: A  145 MET cc_start: 0.7535 (mmm) cc_final: 0.7085 (mtt)
REVERT: A  181 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: A  272 LYS cc_start: 0.8644 (tppp) cc_final: 0.8148 (tptt)
REVERT: B   35 MET cc_start: 0.7581 (pmm) cc_final: 0.7352 (pmm)
REVERT: B  215 ASP cc_start: 0.8443 (t70) cc_final: 0.7742 (t0)
REVERT: B  226 ASN cc_start: 0.8305 (t0) cc_final: 0.8032 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 105
  average time/residue: 0.1736
  time to fit residues: 22.0120
Evaluate side-chains
  103 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
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  162 LEU
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  200 ILE
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:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0570
   chunk 2 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.144666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.105130 restraints weight = 5913.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.108538 restraints weight = 3395.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.110630 restraints weight = 2514.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4038  Z= 0.125
  Angle     :  0.526   9.285   5526  Z= 0.270
  Chirality :  0.040   0.125    666
  Planarity :  0.003   0.029    688
  Dihedral  :  3.769  15.261    583
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 20.16 %
    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: -0.36 (0.38), residues: 527
  helix:  1.13 (0.32), residues: 285
  sheet: -1.61 (0.59), residues: 70
  loop : -1.94 (0.46), 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 B 107 
 TYR   0.014   0.001   TYR A  91 
 ARG   0.004   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  224)
  hydrogen bonds       : angle       4.00352 (  663)
  SS BOND              : bond        0.00322 (    1)
  SS BOND              : angle       0.41808 (    2)
  covalent geometry    : bond        0.00288 ( 4037)
  covalent geometry    : angle       0.52604 ( 5524)

*********************** 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
  109 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A  140 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7492 (mp10)
REVERT: A  145 MET cc_start: 0.7550 (mmm) cc_final: 0.7132 (mtt)
REVERT: A  272 LYS cc_start: 0.8682 (tppp) cc_final: 0.8291 (tptt)
REVERT: B   35 MET cc_start: 0.7743 (pmm) cc_final: 0.7502 (pmm)
REVERT: B  215 ASP cc_start: 0.8461 (t70) cc_final: 0.7745 (t0)
  outliers start: 15
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1950
  time to fit residues: 23.9122
Evaluate side-chains
  104 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  200 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 51 optimal weight:    0.0060
   chunk 21 optimal weight:    0.0770
   chunk 13 optimal weight:    0.0070
   chunk 47 optimal weight:    2.9990
   chunk 23 optimal weight:    0.2980
   chunk 39 optimal weight:    0.3980
   chunk 48 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0370
   overall best weight:    0.0850

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.152155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112125 restraints weight = 5663.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.116156 restraints weight = 2974.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118527 restraints weight = 2122.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4038  Z= 0.097
  Angle     :  0.509  10.405   5526  Z= 0.259
  Chirality :  0.039   0.127    666
  Planarity :  0.003   0.031    688
  Dihedral  :  3.503  14.011    583
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 22.89 %
    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:  0.00 (0.39), residues: 527
  helix:  1.50 (0.33), residues: 280
  sheet: -1.36 (0.59), residues: 70
  loop : -1.87 (0.46), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 111 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.006   0.001   PHE A 297 
 TYR   0.010   0.001   TYR A 125 
 ARG   0.004   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03253 (  224)
  hydrogen bonds       : angle       3.77863 (  663)
  SS BOND              : bond        0.00195 (    1)
  SS BOND              : angle       0.24357 (    2)
  covalent geometry    : bond        0.00201 ( 4037)
  covalent geometry    : angle       0.50877 ( 5524)

********************** 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
  109 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 LEU cc_start: 0.8469 (mp) cc_final: 0.8086 (mp)
REVERT: A  140 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7395 (mp10)
REVERT: A  145 MET cc_start: 0.7377 (mmm) cc_final: 0.7007 (mtt)
REVERT: A  181 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8048 (tm-30)
REVERT: A  272 LYS cc_start: 0.8545 (tppp) cc_final: 0.8067 (tptt)
REVERT: A  333 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8069 (t80)
REVERT: B  215 ASP cc_start: 0.8349 (t70) cc_final: 0.7636 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 107
  average time/residue: 0.1949
  time to fit residues: 24.7997
Evaluate side-chains
  97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  140 GLN
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:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3818 r_free = 0.3818 target = 0.145243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.105502 restraints weight = 5949.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.108808 restraints weight = 3409.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.110618 restraints weight = 2542.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4038  Z= 0.141
  Angle     :  0.556   9.497   5526  Z= 0.284
  Chirality :  0.040   0.123    666
  Planarity :  0.004   0.029    688
  Dihedral  :  3.629  13.630    583
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 23.98 %
    Favored  : 74.39 %
  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: -0.10 (0.38), residues: 527
  helix:  1.38 (0.33), residues: 280
  sheet: -1.40 (0.59), residues: 70
  loop : -1.86 (0.46), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 102 
 HIS   0.003   0.001   HIS B 191 
 PHE   0.009   0.001   PHE A 193 
 TYR   0.011   0.001   TYR A 125 
 ARG   0.008   0.001   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03837 (  224)
  hydrogen bonds       : angle       3.95596 (  663)
  SS BOND              : bond        0.00410 (    1)
  SS BOND              : angle       0.51850 (    2)
  covalent geometry    : bond        0.00333 ( 4037)
  covalent geometry    : angle       0.55618 ( 5524)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1914.65 seconds
wall clock time: 33 minutes 43.11 seconds (2023.11 seconds total)