Starting phenix.real_space_refine
on Sun May 11 02:20:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzp_41765/05_2025/8tzp_41765.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzp_41765/05_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_41765/05_2025/8tzp_41765.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzp_41765/05_2025/8tzp_41765.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzp_41765/05_2025/8tzp_41765.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzp_41765/05_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-5687/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: 5.37, per 1000 atoms: 0.78
  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: 1.99
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.65
  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: 1.95

  Time building geometry restraints manager: 2.31 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:             2.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.830
  Find NCS groups from input model:        0.080
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.970
-------------------------------------------------------------------------------
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   7114  Z= 0.203
  Angle     :  0.734  11.763   9619  Z= 0.378
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13130 (  375)
  hydrogen bonds       : angle       5.53280 ( 1050)
  SS BOND              : bond        0.00286 (   17)
  SS BOND              : angle       1.16007 (   34)
  covalent geometry    : bond        0.00443 ( 7097)
  covalent geometry    : angle       0.73176 ( 9585)

*********************** 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  : 0.723 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1703
  time to fit residues: 23.4511
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  : 0.723 
-------------------------------------------------------------------------------
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 = 0.140604 restraints weight = 8181.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.18
r_work: 0.3520 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
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   7114  Z= 0.143
  Angle     :  0.552   8.675   9619  Z= 0.287
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  375)
  hydrogen bonds       : angle       4.36508 ( 1050)
  SS BOND              : bond        0.00369 (   17)
  SS BOND              : angle       1.22413 (   34)
  covalent geometry    : bond        0.00336 ( 7097)
  covalent geometry    : angle       0.54833 ( 9585)

*********************** 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  : 0.918 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.7681 (p90) cc_final: 0.7455 (p90)
REVERT: B  423 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8191 (mm)
  outliers start: 22
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1947
  time to fit residues: 28.3298
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  : 0.825 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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
B 470 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.180969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.138134 restraints weight = 8346.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.23
r_work: 0.3492 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7114  Z= 0.171
  Angle     :  0.552   6.989   9619  Z= 0.286
  Chirality :  0.042   0.217   1029
  Planarity :  0.005   0.070   1206
  Dihedral  :  7.824  89.551    968
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.65 %
    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:  1.07 (0.28), residues: 851
  helix:  2.08 (0.25), residues: 403
  sheet: -0.08 (0.51), residues: 109
  loop : -0.70 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 481 
 HIS   0.003   0.001   HIS A 117 
 PHE   0.011   0.001   PHE B 432 
 TYR   0.015   0.002   TYR A 318 
 ARG   0.003   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  375)
  hydrogen bonds       : angle       4.20115 ( 1050)
  SS BOND              : bond        0.00351 (   17)
  SS BOND              : angle       1.11927 (   34)
  covalent geometry    : bond        0.00406 ( 7097)
  covalent geometry    : angle       0.54904 ( 9585)

*********************** 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
  112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: A  313 TYR cc_start: 0.7759 (p90) cc_final: 0.7497 (p90)
REVERT: A  346 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6542 (m-10)
  outliers start: 23
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1799
  time to fit residues: 25.1685
Evaluate side-chains
  101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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   91 VAL
Chi-restraints excluded: chain B residue  163 THR
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  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:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 55 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.181617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.139932 restraints weight = 8419.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.08
r_work: 0.3511 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7114  Z= 0.162
  Angle     :  0.543   7.034   9619  Z= 0.282
  Chirality :  0.041   0.174   1029
  Planarity :  0.004   0.061   1206
  Dihedral  :  7.633  86.728    968
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 11.17 %
    Favored  : 84.52 %
  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:  1.20 (0.29), residues: 851
  helix:  2.21 (0.25), residues: 394
  sheet: -0.03 (0.52), residues: 109
  loop : -0.57 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.011   0.001   PHE B 432 
 TYR   0.019   0.002   TYR A 318 
 ARG   0.003   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03894 (  375)
  hydrogen bonds       : angle       4.13255 ( 1050)
  SS BOND              : bond        0.00327 (   17)
  SS BOND              : angle       1.16044 (   34)
  covalent geometry    : bond        0.00386 ( 7097)
  covalent geometry    : angle       0.53994 ( 9585)

*********************** 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
  130 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A  313 TYR cc_start: 0.7796 (p90) cc_final: 0.7571 (p90)
REVERT: A  346 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.6578 (m-10)
REVERT: B  377 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7150 (mp)
REVERT: B  423 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8200 (mm)
REVERT: C  261 TRP cc_start: 0.8350 (m100) cc_final: 0.8136 (m-90)
  outliers start: 32
  outliers final: 22
  residues processed: 118
  average time/residue: 0.1527
  time to fit residues: 25.6685
Evaluate side-chains
  114 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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  264 VAL
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:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0770
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:   30.0000
   chunk 20 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    2.4146

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

Flipped N/Q/H residues before XYZ refinement:
B 198 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.174446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.130692 restraints weight = 8409.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.26
r_work: 0.3409 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050   7114  Z= 0.310
  Angle     :  0.671   9.049   9619  Z= 0.344
  Chirality :  0.045   0.159   1029
  Planarity :  0.005   0.055   1206
  Dihedral  :  7.947  89.022    968
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.32 %
    Favored  : 82.91 %
  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:  0.75 (0.28), residues: 851
  helix:  1.78 (0.25), residues: 396
  sheet: -0.30 (0.51), residues: 109
  loop : -0.72 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 147 
 HIS   0.006   0.001   HIS A 117 
 PHE   0.016   0.002   PHE B 240 
 TYR   0.021   0.002   TYR A 318 
 ARG   0.002   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04668 (  375)
  hydrogen bonds       : angle       4.39386 ( 1050)
  SS BOND              : bond        0.00413 (   17)
  SS BOND              : angle       1.28939 (   34)
  covalent geometry    : bond        0.00757 ( 7097)
  covalent geometry    : angle       0.66762 ( 9585)

*********************** 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
  118 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 90
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7663 (pp30)
REVERT: B  377 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7137 (mp)
  outliers start: 28
  outliers final: 20
  residues processed: 109
  average time/residue: 0.1916
  time to fit residues: 28.6759
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  : 0.829 
-------------------------------------------------------------------------------
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  228 LEU
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 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  264 VAL
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
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:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.181457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.139102 restraints weight = 8375.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.16
r_work: 0.3507 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7114  Z= 0.141
  Angle     :  0.545   7.326   9619  Z= 0.283
  Chirality :  0.041   0.170   1029
  Planarity :  0.004   0.051   1206
  Dihedral  :  7.626  86.987    968
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 14.67 %
    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:  1.08 (0.29), residues: 851
  helix:  2.10 (0.24), residues: 397
  sheet: -0.25 (0.52), residues: 109
  loop : -0.57 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.026   0.002   TYR A 313 
 ARG   0.007   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  375)
  hydrogen bonds       : angle       4.09497 ( 1050)
  SS BOND              : bond        0.00301 (   17)
  SS BOND              : angle       1.12119 (   34)
  covalent geometry    : bond        0.00328 ( 7097)
  covalent geometry    : angle       0.54190 ( 9585)

*********************** 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
  115 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7659 (pp30)
REVERT: A  346 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6608 (m-10)
  outliers start: 27
  outliers final: 19
  residues processed: 106
  average time/residue: 0.1656
  time to fit residues: 24.5654
Evaluate side-chains
  106 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
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  414 LEU
Chi-restraints excluded: chain B residue  437 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 1 optimal weight:    0.7980
   chunk 78 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 80 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.179998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.138643 restraints weight = 8351.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.08
r_work: 0.3502 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7114  Z= 0.179
  Angle     :  0.563   7.740   9619  Z= 0.290
  Chirality :  0.042   0.174   1029
  Planarity :  0.004   0.050   1206
  Dihedral  :  7.618  88.871    968
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.21 %
    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:  0.96 (0.29), residues: 851
  helix:  2.04 (0.24), residues: 402
  sheet: -0.49 (0.50), residues: 116
  loop : -0.66 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.003   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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  375)
  hydrogen bonds       : angle       4.06969 ( 1050)
  SS BOND              : bond        0.00312 (   17)
  SS BOND              : angle       1.08910 (   34)
  covalent geometry    : bond        0.00426 ( 7097)
  covalent geometry    : angle       0.56075 ( 9585)

*********************** 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
  112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.821 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7672 (pp30)
REVERT: A  346 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6696 (m-10)
REVERT: B  220 ARG cc_start: 0.8313 (ttm110) cc_final: 0.7931 (mtm-85)
REVERT: B  377 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7162 (mp)
  outliers start: 24
  outliers final: 19
  residues processed: 104
  average time/residue: 0.1870
  time to fit residues: 26.9469
Evaluate side-chains
  107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 26 optimal weight:    6.9990
   chunk 81 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.182078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.140590 restraints weight = 8394.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 2.16
r_work: 0.3526 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7114  Z= 0.125
  Angle     :  0.532   6.830   9619  Z= 0.276
  Chirality :  0.041   0.166   1029
  Planarity :  0.004   0.049   1206
  Dihedral  :  7.353  89.153    968
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.80 %
    Favored  : 82.37 %
  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:  1.19 (0.29), residues: 851
  helix:  2.23 (0.24), residues: 402
  sheet: -0.37 (0.51), residues: 116
  loop : -0.55 (0.34), residues: 333

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   0.013   0.001   PHE B 432 
 TYR   0.021   0.001   TYR A 318 
 ARG   0.006   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (  375)
  hydrogen bonds       : angle       3.91767 ( 1050)
  SS BOND              : bond        0.00267 (   17)
  SS BOND              : angle       0.99289 (   34)
  covalent geometry    : bond        0.00284 ( 7097)
  covalent geometry    : angle       0.53008 ( 9585)

*********************** 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
  113 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7711 (pp30)
REVERT: A  346 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6719 (m-10)
REVERT: B  220 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7946 (mtm-85)
REVERT: C  261 TRP cc_start: 0.8241 (m100) cc_final: 0.8036 (m-90)
  outliers start: 21
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1723
  time to fit residues: 25.7678
Evaluate side-chains
  109 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
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   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  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:    0.0670
   chunk 35 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN

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 = 0.182142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.140515 restraints weight = 8332.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.21
r_work: 0.3559 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7114  Z= 0.126
  Angle     :  0.532   6.840   9619  Z= 0.276
  Chirality :  0.040   0.159   1029
  Planarity :  0.004   0.048   1206
  Dihedral  :  7.175  89.313    968
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.61 %
    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:  1.24 (0.29), residues: 851
  helix:  2.30 (0.24), residues: 402
  sheet: -0.48 (0.50), residues: 117
  loop : -0.52 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.012   0.001   PHE B 432 
 TYR   0.022   0.001   TYR A 318 
 ARG   0.005   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 (  375)
  hydrogen bonds       : angle       3.88553 ( 1050)
  SS BOND              : bond        0.00263 (   17)
  SS BOND              : angle       1.02623 (   34)
  covalent geometry    : bond        0.00289 ( 7097)
  covalent geometry    : angle       0.52958 ( 9585)

*********************** 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
  108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7733 (pp30)
REVERT: A  346 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6701 (m-10)
REVERT: B  220 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7966 (mtm-85)
REVERT: B  335 TYR cc_start: 0.8244 (m-80) cc_final: 0.7952 (m-80)
  outliers start: 21
  outliers final: 18
  residues processed: 103
  average time/residue: 0.1749
  time to fit residues: 25.1895
Evaluate side-chains
  106 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
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   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  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:    0.9980
   chunk 25 optimal weight:    0.0000
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 44 optimal weight:    0.2980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.184743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.143845 restraints weight = 8317.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 2.19
r_work: 0.3544 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7114  Z= 0.118
  Angle     :  0.530   6.694   9619  Z= 0.273
  Chirality :  0.040   0.158   1029
  Planarity :  0.004   0.048   1206
  Dihedral  :  6.975  87.916    968
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.02 %
    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:  1.34 (0.29), residues: 851
  helix:  2.38 (0.24), residues: 402
  sheet: -0.52 (0.50), residues: 117
  loop : -0.42 (0.35), residues: 332

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   0.016   0.001   PHE B 291 
 TYR   0.023   0.001   TYR A 318 
 ARG   0.005   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  375)
  hydrogen bonds       : angle       3.83712 ( 1050)
  SS BOND              : bond        0.00248 (   17)
  SS BOND              : angle       0.96537 (   34)
  covalent geometry    : bond        0.00267 ( 7097)
  covalent geometry    : angle       0.52793 ( 9585)

********************** 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
  111 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  290 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7712 (pp30)
REVERT: A  346 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.6761 (m-10)
REVERT: B  220 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7938 (mtm-85)
REVERT: B  240 PHE cc_start: 0.8073 (t80) cc_final: 0.7867 (t80)
REVERT: B  335 TYR cc_start: 0.8226 (m-80) cc_final: 0.7924 (m-80)
  outliers start: 18
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1952
  time to fit residues: 28.3549
Evaluate side-chains
  103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
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   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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 23 optimal weight:    0.0980
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.184475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.143517 restraints weight = 8232.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.18
r_work: 0.3517 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7114  Z= 0.153
  Angle     :  0.597   8.849   9619  Z= 0.305
  Chirality :  0.043   0.284   1029
  Planarity :  0.004   0.048   1206
  Dihedral  :  6.996  86.795    968
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.55 %
    Favored  : 80.89 %
  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:  2.24 (0.24), residues: 402
  sheet: -0.51 (0.50), residues: 118
  loop : -0.47 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 481 
 HIS   0.003   0.001   HIS B 322 
 PHE   0.016   0.001   PHE B 291 
 TYR   0.022   0.002   TYR A 318 
 ARG   0.005   0.000   ARG B 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  375)
  hydrogen bonds       : angle       3.88983 ( 1050)
  SS BOND              : bond        0.00259 (   17)
  SS BOND              : angle       0.94151 (   34)
  covalent geometry    : bond        0.00362 ( 7097)
  covalent geometry    : angle       0.59507 ( 9585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4195.49 seconds
wall clock time: 73 minutes 19.83 seconds (4399.83 seconds total)