Starting phenix.real_space_refine
on Wed Mar 12 04:50:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzp_41765/03_2025/8tzp_41765.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzp_41765/03_2025/8tzp_41765.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzp_41765/03_2025/8tzp_41765.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzp_41765/03_2025/8tzp_41765.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzp_41765/03_2025/8tzp_41765.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzp_41765/03_2025/8tzp_41765.cif"
  }
  resolution = 3.23
  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=   0.002 sd=   0.058
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      75      5.16       5
     C    4470      2.51       5
     N    1170      2.21       5
     O    1204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6920
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2342
          Classifications: {'peptide': 301}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 289}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 496, 4037
          Classifications: {'peptide': 496}
          Link IDs: {'PTRANS': 21, 'TRANS': 474}
    Chain: "C"
      Number of atoms: 484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 484
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 4, 'TRANS': 57}
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PAM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
  Time building chain proxies: 4.84, per 1000 atoms: 0.70
  Number of scatterers: 6920
  At special positions: 0
  Unit cell: (87.98, 92.96, 129.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      75     16.00
     P       1     15.00
     O    1204      8.00
     N    1170      7.00
     C    4470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  38 " - pdb=" SG  CYS A  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  73 " - pdb=" SG  CYS A  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 123 " - pdb=" SG  CYS A 131 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 202 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 309 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 294 " - pdb=" SG  CYS A 304 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 324 " - pdb=" SG  CYS A 339 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 336 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 332 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 216 " - pdb=" SG  CYS C 263 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 217 " - pdb=" SG  CYS C 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 225 " - pdb=" SG  CYS C 250 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.76
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 6 sheets defined
      52.7% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 41
      removed outlier: 4.293A  pdb=" N   LYS A  40 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 55 through 77
      removed outlier: 3.637A  pdb=" N   ILE A  59 " --> pdb=" O   ARG A  55 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 125
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 154 through 170
      removed outlier: 4.000A  pdb=" N   TYR A 158 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG A 170 " --> pdb=" O   PHE A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 195
    Processing helix  chain 'A' and resid 220 through 233
      removed outlier: 3.583A  pdb=" N   LEU A 224 " --> pdb=" O   GLN A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 308
    Processing helix  chain 'B' and resid 4 through 8
    Processing helix  chain 'B' and resid 10 through 35
      removed outlier: 3.835A  pdb=" N   GLY B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 81
    Processing helix  chain 'B' and resid 121 through 125
      removed outlier: 4.142A  pdb=" N   GLN B 125 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 227 through 258
      Proline residue:  B 243  - end of helix
    Processing helix  chain 'B' and resid 264 through 282
    Processing helix  chain 'B' and resid 283 through 288
    Processing helix  chain 'B' and resid 295 through 322
      removed outlier: 3.584A  pdb=" N   ILE B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 334
    Processing helix  chain 'B' and resid 335 through 357
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 358 through 362
    Processing helix  chain 'B' and resid 367 through 370
    Processing helix  chain 'B' and resid 371 through 414
      removed outlier: 3.820A  pdb=" N   SER B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER B 413 " --> pdb=" O   GLY B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 456
    Processing helix  chain 'B' and resid 469 through 492
    Processing helix  chain 'C' and resid 210 through 219
      removed outlier: 4.797A  pdb=" N   TYR C 215 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   CYS C 217 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 236
    Processing helix  chain 'C' and resid 238 through 250
    Processing helix  chain 'C' and resid 258 through 270
      removed outlier: 3.823A  pdb=" N   GLN C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER C 270 " --> pdb=" O   GLU C 266 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 202
    Processing sheet with id=AA2, first strand: chain 'A' and resid 252 through 254
      removed outlier: 5.852A  pdb=" N   VAL A 236 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294
      removed outlier: 4.193A  pdb=" N   TYR A 346 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46
      removed outlier: 6.870A  pdb=" N   ASP B 117 " --> pdb=" O   LYS B 217 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   ILE B 219 " --> pdb=" O   GLN B 115 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   GLN B 115 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ILE B 113 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLY B 223 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU B 111 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   LEU B 114 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 51
      removed outlier: 3.504A  pdb=" N   ALA B 152 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   TYR B 140 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   GLU B 150 " --> pdb=" O   TYR B 140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 462
      removed outlier: 3.619A  pdb=" N   VAL B 465 " --> pdb=" O   TRP B 462 " (cutoff:3.500A)

    375 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.86

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1085
        1.31 -     1.44: 1983
        1.44 -     1.57: 3918
        1.57 -     1.69: 3
        1.69 -     1.82: 108
  Bond restraints: 7097
  Sorted by residual:
  bond pdb=" C31 POV B 601 "
       pdb=" O31 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.418 -0.091 2.00e-02 2.50e+03 2.05e+01
  bond pdb=" C21 POV B 601 "
       pdb=" O21 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.330  1.420 -0.090 2.00e-02 2.50e+03 2.03e+01
  bond pdb="C210 POV B 601 "
       pdb="C211 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.497  1.558 -0.061 2.00e-02 2.50e+03 9.42e+00
  bond pdb=" N   POV B 601 "
       pdb=" C14 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.436  0.054 2.00e-02 2.50e+03 7.23e+00
  bond pdb=" C28 POV B 601 "
       pdb=" C29 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.497  1.548 -0.051 2.00e-02 2.50e+03 6.44e+00
  ... (remaining 7092 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 9420
        2.35 -     4.71: 128
        4.71 -     7.06: 26
        7.06 -     9.41: 9
        9.41 -    11.76: 2
  Bond angle restraints: 9585
  Sorted by residual:
  angle pdb=" CA  PRO A  56 "
        pdb=" N   PRO A  56 "
        pdb=" CD  PRO A  56 "
      ideal   model   delta    sigma   weight residual
     112.00  103.61    8.39 1.40e+00 5.10e-01 3.60e+01
  angle pdb=" C   THR A 297 "
        pdb=" N   ALA A 298 "
        pdb=" CA  ALA A 298 "
      ideal   model   delta    sigma   weight residual
     120.09  125.66   -5.57 1.25e+00 6.40e-01 1.99e+01
  angle pdb=" O13 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O14 POV B 601 "
      ideal   model   delta    sigma   weight residual
     121.11  109.35   11.76 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" O11 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O12 POV B 601 "
      ideal   model   delta    sigma   weight residual
      97.67  109.26  -11.59 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" CA  LYS B 208 "
        pdb=" CB  LYS B 208 "
        pdb=" CG  LYS B 208 "
      ideal   model   delta    sigma   weight residual
     114.10  121.79   -7.69 2.00e+00 2.50e-01 1.48e+01
  ... (remaining 9580 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.02: 3786
       18.02 -    36.04: 355
       36.04 -    54.05: 83
       54.05 -    72.07: 21
       72.07 -    90.09: 9
  Dihedral angle restraints: 4254
    sinusoidal: 1775
      harmonic: 2479
  Sorted by residual:
  dihedral pdb=" CB  CYS C 217 "
           pdb=" SG  CYS C 217 "
           pdb=" SG  CYS C 229 "
           pdb=" CB  CYS C 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.07   77.07     1      1.00e+01 1.00e-02 7.45e+01
  dihedral pdb=" CB  CYS A 324 "
           pdb=" SG  CYS A 324 "
           pdb=" SG  CYS A 339 "
           pdb=" CB  CYS A 339 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  155.26  -62.26     1      1.00e+01 1.00e-02 5.13e+01
  dihedral pdb=" CB  CYS A  38 "
           pdb=" SG  CYS A  38 "
           pdb=" SG  CYS A  52 "
           pdb=" CB  CYS A  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.52   60.52     1      1.00e+01 1.00e-02 4.87e+01
  ... (remaining 4251 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 599
       0.029 -    0.058: 283
       0.058 -    0.087: 99
       0.087 -    0.116: 38
       0.116 -    0.146: 10
  Chirality restraints: 1029
  Sorted by residual:
  chirality pdb=" CA  CYS C 250 "
            pdb=" N   CYS C 250 "
            pdb=" C   CYS C 250 "
            pdb=" CB  CYS C 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.30e-01
  chirality pdb=" CB  THR A 343 "
            pdb=" CA  THR A 343 "
            pdb=" OG1 THR A 343 "
            pdb=" CG2 THR A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  ILE A  41 "
            pdb=" N   ILE A  41 "
            pdb=" C   ILE A  41 "
            pdb=" CB  ILE A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 1026 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  55 "    0.100 5.00e-02 4.00e+02   1.46e-01 3.42e+01
        pdb=" N   PRO A  56 "   -0.253 5.00e-02 4.00e+02
        pdb=" CA  PRO A  56 "    0.077 5.00e-02 4.00e+02
        pdb=" CD  PRO A  56 "    0.076 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  67 "    0.063 5.00e-02 4.00e+02   9.46e-02 1.43e+01
        pdb=" N   PRO B  68 "   -0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO B  68 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO B  68 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 208 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.10e+00
        pdb=" C   LYS B 208 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LYS B 208 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ILE B 209 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     2.05: 2
        2.05 -     2.76: 1128
        2.76 -     3.48: 9683
        3.48 -     4.19: 15535
        4.19 -     4.90: 28735
  Nonbonded interactions: 55083
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 206 "
            pdb=" O1  PAM A 601 "
     model   vdw
     1.341 3.040
  nonbonded pdb=" OG  SER A 206 "
            pdb=" C1  PAM A 601 "
     model   vdw
     1.375 3.270
  nonbonded pdb=" O   ASN A 181 "
            pdb=" ND2 ASN A 185 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" O   LEU B 312 "
            pdb=" OH  TYR B 392 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   ARG C 231 "
            pdb=" OG  SER C 235 "
     model   vdw
     2.314 3.040
  ... (remaining 55078 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.840
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.750
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
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   0.099   7097  Z= 0.298
  Angle     :  0.732  11.763   9585  Z= 0.377
  Chirality :  0.041   0.146   1029
  Planarity :  0.006   0.146   1206
  Dihedral  : 15.231  90.091   2605
  Min Nonbonded Distance : 1.341

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 12.52 %
    Favored  : 87.21 %
  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:  1.16 (0.28), residues: 851
  helix:  2.20 (0.25), residues: 387
  sheet:  0.14 (0.53), residues: 92
  loop : -0.60 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.016   0.001   PHE B 432 
 TYR   0.011   0.001   TYR B 308 
 ARG   0.003   0.000   ARG A 170 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.819 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1707
  time to fit residues: 23.7040
Evaluate side-chains
  88 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.183117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140605 restraints weight = 8181.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.18
r_work: 0.3520 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.0763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7097  Z= 0.219
  Angle     :  0.548   8.675   9585  Z= 0.285
  Chirality :  0.041   0.164   1029
  Planarity :  0.005   0.090   1206
  Dihedral  :  8.210  88.703    968
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 11.84 %
    Favored  : 85.20 %
  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:  1.22 (0.28), residues: 851
  helix:  2.24 (0.25), residues: 394
  sheet:  0.07 (0.51), residues: 109
  loop : -0.63 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.012   0.001   TYR B 484 
 ARG   0.002   0.000   ARG B 127 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.7680 (p90) cc_final: 0.7453 (p90)
REVERT: B  423 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8192 (mm)
  outliers start: 22
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1988
  time to fit residues: 28.9313
Evaluate side-chains
  102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain B residue    8 ASN
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  110 MET
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 470 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.178004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.134892 restraints weight = 8364.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.26
r_work: 0.3462 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7097  Z= 0.325
  Angle     :  0.580   7.488   9585  Z= 0.301
  Chirality :  0.043   0.213   1029
  Planarity :  0.005   0.071   1206
  Dihedral  :  7.934  89.620    968
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.52 %
    Favored  : 84.25 %
  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:  1.04 (0.28), residues: 851
  helix:  2.08 (0.25), residues: 394
  sheet: -0.14 (0.51), residues: 109
  loop : -0.64 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 147 
 HIS   0.004   0.001   HIS A 117 
 PHE   0.012   0.001   PHE B 404 
 TYR   0.016   0.002   TYR A 318 
 ARG   0.003   0.000   ARG A 320 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
REVERT: A  313 TYR cc_start: 0.7767 (p90) cc_final: 0.7539 (p90)
REVERT: A  346 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6548 (m-10)
  outliers start: 24
  outliers final: 16
  residues processed: 103
  average time/residue: 0.1865
  time to fit residues: 26.4916
Evaluate side-chains
  105 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  488 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 13 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.182212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.140501 restraints weight = 8404.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.08
r_work: 0.3514 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7097  Z= 0.208
  Angle     :  0.528   6.768   9585  Z= 0.274
  Chirality :  0.041   0.177   1029
  Planarity :  0.004   0.061   1206
  Dihedral  :  7.619  85.997    968
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 11.57 %
    Favored  : 84.39 %
  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:  1.21 (0.29), residues: 851
  helix:  2.22 (0.25), residues: 394
  sheet: -0.05 (0.52), residues: 109
  loop : -0.57 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.010   0.001   PHE B 432 
 TYR   0.020   0.002   TYR A 318 
 ARG   0.003   0.000   ARG A 320 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 2.364 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.7803 (p90) cc_final: 0.7567 (p90)
REVERT: A  346 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6573 (m-10)
REVERT: B  377 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7148 (mp)
REVERT: B  423 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8201 (mm)
REVERT: C  261 TRP cc_start: 0.8325 (m100) cc_final: 0.8108 (m-90)
  outliers start: 30
  outliers final: 20
  residues processed: 114
  average time/residue: 0.2447
  time to fit residues: 40.2070
Evaluate side-chains
  112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  488 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    0.1980
   chunk 12 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.173128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.130359 restraints weight = 8369.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.18
r_work: 0.3498 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7097  Z= 0.378
  Angle     :  0.602   8.308   9585  Z= 0.311
  Chirality :  0.043   0.190   1029
  Planarity :  0.005   0.054   1206
  Dihedral  :  7.752  87.920    968
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.06 %
    Favored  : 83.18 %
  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:  0.91 (0.28), residues: 851
  helix:  1.94 (0.25), residues: 394
  sheet: -0.19 (0.52), residues: 109
  loop : -0.67 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 147 
 HIS   0.005   0.001   HIS A 117 
 PHE   0.015   0.002   PHE B 240 
 TYR   0.020   0.002   TYR A 318 
 ARG   0.002   0.000   ARG A 342 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7640 (pp30)
REVERT: A  313 TYR cc_start: 0.7909 (p90) cc_final: 0.7666 (p90)
REVERT: A  346 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6588 (m-10)
REVERT: B  377 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7038 (mp)
  outliers start: 28
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1684
  time to fit residues: 24.6713
Evaluate side-chains
  108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue    8 ASN
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  488 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 12 optimal weight:    0.3980
   chunk 53 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.182092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140267 restraints weight = 8357.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.17
r_work: 0.3521 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7097  Z= 0.181
  Angle     :  0.523   6.648   9585  Z= 0.271
  Chirality :  0.041   0.163   1029
  Planarity :  0.004   0.050   1206
  Dihedral  :  7.477  86.337    968
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.86 %
    Favored  : 82.50 %
  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:  1.13 (0.29), residues: 851
  helix:  2.12 (0.25), residues: 404
  sheet: -0.10 (0.53), residues: 109
  loop : -0.64 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.021   0.001   TYR A 318 
 ARG   0.011   0.000   ARG B 220 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7602 (pp30)
REVERT: A  313 TYR cc_start: 0.7881 (p90) cc_final: 0.7594 (p90)
REVERT: A  346 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6582 (m-10)
REVERT: C  261 TRP cc_start: 0.8300 (m100) cc_final: 0.8081 (m-90)
  outliers start: 27
  outliers final: 17
  residues processed: 106
  average time/residue: 0.2520
  time to fit residues: 38.1142
Evaluate side-chains
  106 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  488 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.174866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.132949 restraints weight = 8322.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.13
r_work: 0.3477 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7097  Z= 0.318
  Angle     :  0.576   7.957   9585  Z= 0.297
  Chirality :  0.042   0.173   1029
  Planarity :  0.004   0.048   1206
  Dihedral  :  7.596  89.062    968
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 14.27 %
    Favored  : 82.23 %
  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:  0.88 (0.29), residues: 851
  helix:  1.98 (0.25), residues: 400
  sheet: -0.58 (0.50), residues: 117
  loop : -0.67 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 481 
 HIS   0.004   0.001   HIS A 117 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.021   0.002   TYR A 318 
 ARG   0.007   0.000   ARG B 220 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7634 (pp30)
REVERT: A  313 TYR cc_start: 0.7929 (p90) cc_final: 0.7686 (p90)
REVERT: A  346 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6605 (m-10)
REVERT: B  220 ARG cc_start: 0.8351 (ttm110) cc_final: 0.7957 (mtm-85)
REVERT: B  377 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7098 (mp)
  outliers start: 26
  outliers final: 19
  residues processed: 107
  average time/residue: 0.2030
  time to fit residues: 29.9414
Evaluate side-chains
  108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  488 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0570
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.182705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.141758 restraints weight = 8302.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.10
r_work: 0.3539 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7097  Z= 0.179
  Angle     :  0.523   6.897   9585  Z= 0.271
  Chirality :  0.041   0.168   1029
  Planarity :  0.004   0.048   1206
  Dihedral  :  7.290  88.567    968
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.94 %
    Favored  : 81.70 %
  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:  1.18 (0.29), residues: 851
  helix:  2.22 (0.25), residues: 402
  sheet: -0.38 (0.51), residues: 115
  loop : -0.57 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 481 
 HIS   0.004   0.001   HIS B 322 
 PHE   0.013   0.001   PHE B 432 
 TYR   0.020   0.001   TYR A 318 
 ARG   0.006   0.000   ARG B 220 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7650 (pp30)
REVERT: A  313 TYR cc_start: 0.7897 (p90) cc_final: 0.7640 (p90)
REVERT: A  346 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.6616 (m-10)
REVERT: B  220 ARG cc_start: 0.8271 (ttm110) cc_final: 0.7946 (mtm-85)
REVERT: B  377 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7086 (mp)
  outliers start: 25
  outliers final: 19
  residues processed: 108
  average time/residue: 0.2068
  time to fit residues: 31.0120
Evaluate side-chains
  111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 76 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0870
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.179573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.137797 restraints weight = 8400.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.16
r_work: 0.3534 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7097  Z= 0.175
  Angle     :  0.534   8.391   9585  Z= 0.274
  Chirality :  0.041   0.157   1029
  Planarity :  0.004   0.047   1206
  Dihedral  :  7.114  89.999    968
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.80 %
    Favored  : 81.97 %
  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:  1.24 (0.29), residues: 851
  helix:  2.30 (0.25), residues: 402
  sheet: -0.47 (0.50), residues: 117
  loop : -0.52 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 481 
 HIS   0.003   0.000   HIS B 322 
 PHE   0.015   0.001   PHE B 314 
 TYR   0.022   0.001   TYR A 318 
 ARG   0.005   0.000   ARG B 220 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7693 (pp30)
REVERT: A  313 TYR cc_start: 0.7911 (p90) cc_final: 0.7649 (p90)
REVERT: A  346 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6669 (m-10)
REVERT: B  220 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7937 (mtm-85)
REVERT: B  249 MET cc_start: 0.8926 (tpp) cc_final: 0.8673 (mmm)
REVERT: B  335 TYR cc_start: 0.8215 (m-80) cc_final: 0.7920 (m-80)
REVERT: B  377 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7027 (mp)
REVERT: B  483 LEU cc_start: 0.8997 (mt) cc_final: 0.8700 (mp)
  outliers start: 24
  outliers final: 19
  residues processed: 110
  average time/residue: 0.1817
  time to fit residues: 27.4922
Evaluate side-chains
  111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:   30.0000
   chunk 44 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.183508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.141685 restraints weight = 8346.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.25
r_work: 0.3533 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7097  Z= 0.244
  Angle     :  0.582   7.480   9585  Z= 0.299
  Chirality :  0.043   0.257   1029
  Planarity :  0.004   0.047   1206
  Dihedral  :  7.166  88.495    968
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.48 %
    Favored  : 81.43 %
  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:  1.09 (0.29), residues: 851
  helix:  2.17 (0.25), residues: 402
  sheet: -0.52 (0.50), residues: 117
  loop : -0.60 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.016   0.001   PHE B 291 
 TYR   0.023   0.002   TYR A 318 
 ARG   0.005   0.000   ARG B 220 

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

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

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1702 Ramachandran restraints generated.
    851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7721 (pp30)
REVERT: A  313 TYR cc_start: 0.7971 (p90) cc_final: 0.7710 (p90)
REVERT: A  346 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6673 (m-10)
REVERT: B  220 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7985 (mtm-85)
REVERT: B  249 MET cc_start: 0.8943 (tpp) cc_final: 0.8371 (mmm)
REVERT: B  335 TYR cc_start: 0.8315 (m-80) cc_final: 0.8075 (m-80)
REVERT: B  377 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7153 (mp)
REVERT: C  240 MET cc_start: 0.7440 (pmm) cc_final: 0.7174 (pmm)
  outliers start: 23
  outliers final: 19
  residues processed: 106
  average time/residue: 0.1779
  time to fit residues: 26.0115
Evaluate side-chains
  112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  267 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  290 GLN
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0030
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.9392

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.183508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.142830 restraints weight = 8261.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.16
r_work: 0.3518 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7097  Z= 0.232
  Angle     :  0.563   6.764   9585  Z= 0.292
  Chirality :  0.042   0.225   1029
  Planarity :  0.004   0.047   1206
  Dihedral  :  7.076  87.914    968
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.48 %
    Favored  : 81.56 %
  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:  1.11 (0.29), residues: 851
  helix:  2.21 (0.25), residues: 401
  sheet: -0.53 (0.49), residues: 117
  loop : -0.60 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.015   0.001   PHE B 291 
 TYR   0.022   0.001   TYR A 318 
 ARG   0.005   0.000   ARG B 220 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4790.92 seconds
wall clock time: 86 minutes 45.56 seconds (5205.56 seconds total)