Starting phenix.real_space_refine
on Wed Mar  5 21:57:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3ktt_5148/03_2025/3ktt_5148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3ktt_5148/03_2025/3ktt_5148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/3ktt_5148/03_2025/3ktt_5148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3ktt_5148/03_2025/3ktt_5148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/3ktt_5148/03_2025/3ktt_5148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3ktt_5148/03_2025/3ktt_5148.cif"
  }
  resolution = 4.0
  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
-------------------------------------------------------------------------------
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=   0.055 sd=   0.377
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    2409      2.51       5
     N     679      2.21       5
     O     748      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3855
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 3855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 3855
          Classifications: {'peptide': 513}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 7, 'PTRANS': 9, 'TRANS': 496}
  Time building chain proxies: 3.03, per 1000 atoms: 0.79
  Number of scatterers: 3855
  At special positions: 0
  Unit cell: (75.6, 97.2, 94.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     748      8.00
     N     679      7.00
     C    2409      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.16
  Conformation dependent library (CDL) restraints added in 492.0 milliseconds
  

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  ARG B 268 "
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 6 sheets defined
      55.8% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 29
      removed outlier: 3.698A  pdb=" N   ALA B  11 " --> pdb=" O   ARG B   7 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA B  19 " --> pdb=" O   SER B  15 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE B  20 " --> pdb=" O   PHE B  16 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE B  22 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASP B  24 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LEU B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   THR B  29 " --> pdb=" O   LEU B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'B' and resid 53 through 61
      removed outlier: 4.258A  pdb=" N   ILE B  57 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 82
      removed outlier: 4.343A  pdb=" N   SER B  75 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
      removed outlier: 4.672A  pdb=" N   ARG B  76 " --> pdb=" O   VAL B  72 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   VAL B  77 " --> pdb=" O   ASP B  73 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLN B  78 " --> pdb=" O   MET B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 98
      removed outlier: 3.564A  pdb=" N   LEU B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 107
    Processing helix  chain 'B' and resid 109 through 114
    Processing helix  chain 'B' and resid 114 through 128
      removed outlier: 3.985A  pdb=" N   ARG B 118 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B 127 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 157
      removed outlier: 3.883A  pdb=" N   SER B 156 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LYS B 157 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 178
      removed outlier: 3.618A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 166 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   VAL B 171 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   GLU B 172 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 273
      removed outlier: 3.971A  pdb=" N   VAL B 251 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLU B 253 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ILE B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU B 258 " --> pdb=" O   ILE B 254 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LYS B 259 " --> pdb=" O   GLU B 255 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ARG B 268 " --> pdb=" O   GLU B 264 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU B 270 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS B 271 " --> pdb=" O   GLU B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 295
    Processing helix  chain 'B' and resid 304 through 315
      removed outlier: 3.508A  pdb=" N   GLY B 315 " --> pdb=" O   ALA B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 329
    Processing helix  chain 'B' and resid 369 through 391
      removed outlier: 4.229A  pdb=" N   HIS B 378 " --> pdb=" O   GLU B 374 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ASP B 379 " --> pdb=" O   ARG B 375 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL B 383 " --> pdb=" O   ASP B 379 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 415
      removed outlier: 3.671A  pdb=" N   GLN B 410 " --> pdb=" O   HIS B 406 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B 411 " --> pdb=" O   ALA B 407 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA B 412 " --> pdb=" O   VAL B 408 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   SER B 413 " --> pdb=" O   THR B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 430
      removed outlier: 3.522A  pdb=" N   ALA B 422 " --> pdb=" O   LYS B 418 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B 430 " --> pdb=" O   TYR B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 442
      removed outlier: 3.695A  pdb=" N   ALA B 438 " --> pdb=" O   PRO B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 459
      removed outlier: 3.619A  pdb=" N   GLY B 459 " --> pdb=" O   ALA B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 479
    Processing helix  chain 'B' and resid 483 through 504
      removed outlier: 3.657A  pdb=" N   LYS B 487 " --> pdb=" O   SER B 483 " (cutoff:3.500A)
    Processing sheet with id=A, first strand: chain 'B' and resid 4 through 6
    Processing sheet with id=B, first strand: chain 'B' and resid 37 through 40
      removed outlier: 4.203A  pdb=" N   LYS B  37 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
    Processing sheet with id=C, first strand: chain 'B' and resid 187 through 189
      removed outlier: 6.856A  pdb=" N   HIS B 187 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   LEU B 362 " --> pdb=" O   HIS B 187 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ILE B 189 " --> pdb=" O   LEU B 362 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'B' and resid 205 through 207
    Processing sheet with id=E, first strand: chain 'B' and resid 224 through 227
      removed outlier: 6.371A  pdb=" N   LEU B 225 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
    Processing sheet with id=F, first strand: chain 'B' and resid 463 through 466

    191 hydrogen bonds defined for protein.
    543 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: 1.08

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 698
        1.32 -     1.44: 1280
        1.44 -     1.57: 1879
        1.57 -     1.70: 6
        1.70 -     1.82: 33
  Bond restraints: 3896
  Sorted by residual:
  bond pdb=" C   THR B 233 "
       pdb=" N   ASP B 234 "
    ideal  model  delta    sigma   weight residual
    1.332  1.507 -0.174 1.40e-02 5.10e+03 1.55e+02
  bond pdb=" CA  GLU B 260 "
       pdb=" CB  GLU B 260 "
    ideal  model  delta    sigma   weight residual
    1.528  1.365  0.163 1.56e-02 4.11e+03 1.09e+02
  bond pdb=" CA  GLU B 317 "
       pdb=" C   GLU B 317 "
    ideal  model  delta    sigma   weight residual
    1.523  1.436  0.087 1.34e-02 5.57e+03 4.22e+01
  bond pdb=" CA  GLU B 326 "
       pdb=" C   GLU B 326 "
    ideal  model  delta    sigma   weight residual
    1.532  1.464  0.068 1.12e-02 7.97e+03 3.70e+01
  bond pdb=" CA  PHE B 142 "
       pdb=" C   PHE B 142 "
    ideal  model  delta    sigma   weight residual
    1.523  1.447  0.076 1.34e-02 5.57e+03 3.19e+01
  ... (remaining 3891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.18: 4908
        5.18 -    10.36: 307
       10.36 -    15.53: 27
       15.53 -    20.71: 6
       20.71 -    25.89: 3
  Bond angle restraints: 5251
  Sorted by residual:
  angle pdb=" N   LYS B 235 "
        pdb=" CA  LYS B 235 "
        pdb=" C   LYS B 235 "
      ideal   model   delta    sigma   weight residual
     111.07  136.96  -25.89 1.07e+00 8.73e-01 5.85e+02
  angle pdb=" C   ALA B 132 "
        pdb=" N   VAL B 133 "
        pdb=" CA  VAL B 133 "
      ideal   model   delta    sigma   weight residual
     120.88  143.46  -22.58 1.22e+00 6.72e-01 3.42e+02
  angle pdb=" C   ILE B 211 "
        pdb=" CA  ILE B 211 "
        pdb=" CB  ILE B 211 "
      ideal   model   delta    sigma   weight residual
     111.81   93.01   18.80 1.25e+00 6.40e-01 2.26e+02
  angle pdb=" CA  ASN B  52 "
        pdb=" CB  ASN B  52 "
        pdb=" CG  ASN B  52 "
      ideal   model   delta    sigma   weight residual
     112.60   99.60   13.00 1.00e+00 1.00e+00 1.69e+02
  angle pdb=" CA  PHE B 322 "
        pdb=" CB  PHE B 322 "
        pdb=" CG  PHE B 322 "
      ideal   model   delta    sigma   weight residual
     113.80  101.20   12.60 1.00e+00 1.00e+00 1.59e+02
  ... (remaining 5246 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 2199
       17.85 -    35.71: 139
       35.71 -    53.56: 28
       53.56 -    71.42: 18
       71.42 -    89.27: 11
  Dihedral angle restraints: 2395
    sinusoidal: 937
      harmonic: 1458
  Sorted by residual:
  dihedral pdb=" N   LYS B 263 "
           pdb=" C   LYS B 263 "
           pdb=" CA  LYS B 263 "
           pdb=" CB  LYS B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  166.15  -43.35     0      2.50e+00 1.60e-01 3.01e+02
  dihedral pdb=" C   LYS B 263 "
           pdb=" N   LYS B 263 "
           pdb=" CA  LYS B 263 "
           pdb=" CB  LYS B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -165.66   43.06     0      2.50e+00 1.60e-01 2.97e+02
  dihedral pdb=" C   ILE B 211 "
           pdb=" N   ILE B 211 "
           pdb=" CA  ILE B 211 "
           pdb=" CB  ILE B 211 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00  -98.49  -23.51     0      2.50e+00 1.60e-01 8.84e+01
  ... (remaining 2392 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.523: 623
       0.523 -    1.046: 5
       1.046 -    1.569: 0
       1.569 -    2.092: 1
       2.092 -    2.616: 1
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  ARG B 268 "
            pdb=" N   ARG B 268 "
            pdb=" C   ARG B 268 "
            pdb=" CB  ARG B 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -0.11    2.62 2.00e-01 2.50e+01 1.71e+02
  chirality pdb=" CA  LYS B 263 "
            pdb=" N   LYS B 263 "
            pdb=" C   LYS B 263 "
            pdb=" CB  LYS B 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.62    1.89 2.00e-01 2.50e+01 8.96e+01
  chirality pdb=" CA  LYS B  33 "
            pdb=" N   LYS B  33 "
            pdb=" C   LYS B  33 "
            pdb=" CB  LYS B  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.47    1.04 2.00e-01 2.50e+01 2.71e+01
  ... (remaining 627 not shown)

  Planarity restraints: 676
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 117 "    0.068 2.00e-02 2.50e+03   3.47e-02 3.02e+01
        pdb=" CG  TRP B 117 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 117 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 117 "   -0.026 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 117 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 117 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 117 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 117 "    0.045 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 117 "   -0.023 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 117 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 233 "    0.023 2.00e-02 2.50e+03   5.32e-02 2.83e+01
        pdb=" C   THR B 233 "   -0.092 2.00e-02 2.50e+03
        pdb=" O   THR B 233 "    0.040 2.00e-02 2.50e+03
        pdb=" N   ASP B 234 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 215 "    0.084 5.00e-02 4.00e+02   1.29e-01 2.66e+01
        pdb=" N   PRO B 216 "   -0.223 5.00e-02 4.00e+02
        pdb=" CA  PRO B 216 "    0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO B 216 "    0.067 5.00e-02 4.00e+02
  ... (remaining 673 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.30: 11
        2.30 -     2.95: 2934
        2.95 -     3.60: 6521
        3.60 -     4.25: 9660
        4.25 -     4.90: 14419
  Nonbonded interactions: 33545
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 244 "
            pdb=" O   VAL B 245 "
     model   vdw
     1.652 3.120
  nonbonded pdb=" NH1 ARG B 244 "
            pdb=" C   VAL B 245 "
     model   vdw
     2.010 3.350
  nonbonded pdb=" CZ  ARG B 244 "
            pdb=" O   VAL B 245 "
     model   vdw
     2.043 3.270
  nonbonded pdb=" CB  PHE B 142 "
            pdb=" N   ARG B 143 "
     model   vdw
     2.160 2.816
  nonbonded pdb=" O   LYS B 237 "
            pdb=" CD1 ILE B 238 "
     model   vdw
     2.207 3.460
  ... (remaining 33540 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  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:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.430
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2994
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      :  0.020   0.174   3896  Z= 1.309
  Angle     :  2.863  25.890   5251  Z= 1.937
  Chirality :  0.196   2.616    630
  Planarity :  0.014   0.129    676
  Dihedral  : 15.200  89.272   1455
  Min Nonbonded Distance : 1.652

Molprobity Statistics.
  All-atom Clashscore : 179.94
  Ramachandran Plot:
    Outliers :  4.31 %
    Allowed  :  6.26 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  7.82 %
    Allowed  : 13.20 %
    Favored  : 78.97 %
  Cbeta Deviations :  4.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    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: -0.59 (0.35), residues: 511
  helix:  0.98 (0.29), residues: 251
  sheet:  0.07 (0.88), residues: 43
  loop : -2.23 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.028   TRP B 117 
 HIS   0.005   0.001   HIS B 109 
 PHE   0.013   0.002   PHE B 322 
 TYR   0.022   0.003   TYR B 284 
 ARG   0.015   0.001   ARG B 363 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   29 THR cc_start: 0.5819 (m) cc_final: 0.5615 (p)
REVERT: B  128 LEU cc_start: 0.6539 (mt) cc_final: 0.6049 (mt)
REVERT: B  129 LEU cc_start: 0.4424 (OUTLIER) cc_final: 0.3675 (tt)
REVERT: B  200 TYR cc_start: 0.5188 (m-80) cc_final: 0.4649 (m-80)
REVERT: B  255 GLU cc_start: 0.4800 (tm-30) cc_final: 0.4563 (tp30)
REVERT: B  296 VAL cc_start: 0.6608 (t) cc_final: 0.6304 (t)
REVERT: B  465 LEU cc_start: 0.1452 (OUTLIER) cc_final: 0.0576 (mm)
REVERT: B  475 MET cc_start: -0.1465 (tpp) cc_final: -0.2293 (mmm)
  outliers start: 32
  outliers final: 7
  residues processed: 130
  average time/residue: 0.2256
  time to fit residues: 33.9613
Evaluate side-chains
  82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 LYS
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  263 LYS
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.1980
   chunk 29 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
B  60 ASN
B 182 ASN
B 272 HIS
** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 289 GLN
B 368 GLN
B 451 GLN
** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4904 r_free = 0.4904 target = 0.218710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4777 r_free = 0.4777 target = 0.207415 restraints weight = 12862.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.209991 restraints weight = 8817.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.211872 restraints weight = 6278.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.4832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3600
moved from start:          0.6046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3896  Z= 0.333
  Angle     :  1.212  19.090   5251  Z= 0.627
  Chirality :  0.067   0.433    630
  Planarity :  0.008   0.075    676
  Dihedral  : 10.516  76.426    565
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 34.12
  Ramachandran Plot:
    Outliers :  2.15 %
    Allowed  :  8.22 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 20.54 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.60 %

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: -1.78 (0.35), residues: 511
  helix: -0.31 (0.29), residues: 251
  sheet: -0.30 (0.69), residues: 63
  loop : -2.62 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B 117 
 HIS   0.013   0.002   HIS B 324 
 PHE   0.035   0.004   PHE B 484 
 TYR   0.009   0.002   TYR B 443 
 ARG   0.007   0.001   ARG B  98 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  129 LEU cc_start: 0.1431 (OUTLIER) cc_final: 0.1131 (pp)
REVERT: B  147 MET cc_start: 0.0762 (mpt) cc_final: 0.0359 (mpt)
REVERT: B  174 VAL cc_start: 0.5094 (OUTLIER) cc_final: 0.4761 (m)
REVERT: B  225 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5271 (tm)
REVERT: B  278 ILE cc_start: 0.4778 (OUTLIER) cc_final: 0.4209 (mp)
REVERT: B  467 MET cc_start: 0.1342 (pmm) cc_final: 0.1112 (pmm)
REVERT: B  496 GLU cc_start: 0.6282 (mm-30) cc_final: 0.6009 (mm-30)
  outliers start: 27
  outliers final: 8
  residues processed: 109
  average time/residue: 0.1990
  time to fit residues: 25.8222
Evaluate side-chains
  78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 148 ASN
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 489 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 = 0.4859 r_free = 0.4859 target = 0.213480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.202775 restraints weight = 12971.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.205049 restraints weight = 9134.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.206679 restraints weight = 6684.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.4780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3988
moved from start:          0.8014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3896  Z= 0.298
  Angle     :  1.098  16.735   5251  Z= 0.558
  Chirality :  0.058   0.320    630
  Planarity :  0.007   0.055    676
  Dihedral  :  9.165  73.749    556
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 31.18
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  9.20 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 25.92 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.34), residues: 511
  helix: -0.92 (0.28), residues: 253
  sheet:  0.21 (0.72), residues: 65
  loop : -3.08 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 117 
 HIS   0.012   0.002   HIS B 324 
 PHE   0.019   0.003   PHE B 166 
 TYR   0.013   0.002   TYR B 443 
 ARG   0.008   0.001   ARG B  76 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.7094 (t) cc_final: 0.6602 (t)
REVERT: B  129 LEU cc_start: 0.0455 (OUTLIER) cc_final: 0.0241 (pp)
REVERT: B  225 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5690 (tm)
REVERT: B  404 MET cc_start: 0.6866 (mtm) cc_final: 0.6535 (mtm)
REVERT: B  421 VAL cc_start: 0.7105 (m) cc_final: 0.6888 (p)
  outliers start: 23
  outliers final: 13
  residues processed: 94
  average time/residue: 0.1888
  time to fit residues: 21.3935
Evaluate side-chains
  75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  340 MET
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  431 ARG
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 37 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0970
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 HIS
B 489 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.212099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.200455 restraints weight = 12668.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.202776 restraints weight = 9001.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.204596 restraints weight = 6691.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4055
moved from start:          0.9255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3896  Z= 0.249
  Angle     :  1.000  15.802   5251  Z= 0.508
  Chirality :  0.055   0.250    630
  Planarity :  0.006   0.055    676
  Dihedral  :  8.632  69.591    556
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 27.99
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  9.20 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 25.92 %
    Favored  : 67.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.33), residues: 511
  helix: -0.62 (0.29), residues: 253
  sheet: -0.38 (0.67), residues: 63
  loop : -3.43 (0.36), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 117 
 HIS   0.008   0.002   HIS B 272 
 PHE   0.025   0.002   PHE B 166 
 TYR   0.012   0.002   TYR B 443 
 ARG   0.005   0.001   ARG B 392 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.7341 (t) cc_final: 0.6601 (t)
REVERT: B  129 LEU cc_start: 0.0578 (OUTLIER) cc_final: 0.0329 (pp)
REVERT: B  211 ILE cc_start: 0.1056 (OUTLIER) cc_final: 0.0736 (mp)
REVERT: B  225 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5566 (tm)
REVERT: B  403 LEU cc_start: 0.7368 (mt) cc_final: 0.6880 (mt)
  outliers start: 28
  outliers final: 16
  residues processed: 94
  average time/residue: 0.1639
  time to fit residues: 19.0605
Evaluate side-chains
  86 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  431 ARG
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 1 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.209066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.198404 restraints weight = 13247.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.200859 restraints weight = 9237.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.202611 restraints weight = 6662.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4164
moved from start:          1.0396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3896  Z= 0.255
  Angle     :  1.009  15.914   5251  Z= 0.503
  Chirality :  0.054   0.248    630
  Planarity :  0.006   0.050    676
  Dihedral  :  8.637  64.969    556
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 27.48
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  9.78 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 25.67 %
    Favored  : 67.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.33), residues: 511
  helix: -0.62 (0.30), residues: 245
  sheet: -0.56 (0.69), residues: 62
  loop : -3.19 (0.33), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 117 
 HIS   0.006   0.001   HIS B 324 
 PHE   0.022   0.003   PHE B 166 
 TYR   0.019   0.002   TYR B 443 
 ARG   0.007   0.001   ARG B 392 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 66
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  129 LEU cc_start: 0.0736 (OUTLIER) cc_final: 0.0450 (pp)
  outliers start: 28
  outliers final: 19
  residues processed: 86
  average time/residue: 0.1545
  time to fit residues: 16.5812
Evaluate side-chains
  80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  467 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0770
   chunk 4 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0040
   overall best weight:    0.5150

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

Flipped N/Q/H residues before XYZ refinement:
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.211697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.199559 restraints weight = 12793.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.202167 restraints weight = 8967.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.204180 restraints weight = 6587.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4050
moved from start:          1.0959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3896  Z= 0.218
  Angle     :  0.926  15.129   5251  Z= 0.463
  Chirality :  0.048   0.210    630
  Planarity :  0.005   0.048    676
  Dihedral  :  7.926  55.858    554
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 22.62
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  8.41 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 27.38 %
    Favored  : 65.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    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: -1.97 (0.35), residues: 511
  helix: -0.17 (0.32), residues: 246
  sheet: -0.21 (0.70), residues: 60
  loop : -3.15 (0.34), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B 117 
 HIS   0.005   0.001   HIS B 324 
 PHE   0.017   0.002   PHE B 166 
 TYR   0.014   0.002   TYR B 286 
 ARG   0.010   0.001   ARG B 453 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: B  129 LEU cc_start: 0.0447 (OUTLIER) cc_final: 0.0064 (pp)
REVERT: B  225 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5473 (tm)
  outliers start: 28
  outliers final: 15
  residues processed: 86
  average time/residue: 0.1481
  time to fit residues: 16.0750
Evaluate side-chains
  75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.210006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.199172 restraints weight = 12708.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.201745 restraints weight = 8637.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.203578 restraints weight = 6120.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.4746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4212
moved from start:          1.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3896  Z= 0.255
  Angle     :  0.962  15.663   5251  Z= 0.484
  Chirality :  0.051   0.256    630
  Planarity :  0.005   0.048    676
  Dihedral  :  7.463  47.672    551
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 24.03
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  8.61 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 29.58 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.34), residues: 511
  helix: -0.31 (0.31), residues: 246
  sheet: -0.24 (0.73), residues: 52
  loop : -3.23 (0.33), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 117 
 HIS   0.004   0.001   HIS B 348 
 PHE   0.016   0.002   PHE B 166 
 TYR   0.017   0.002   TYR B 443 
 ARG   0.006   0.001   ARG B 176 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 61
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  225 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5745 (tm)
  outliers start: 24
  outliers final: 17
  residues processed: 80
  average time/residue: 0.1378
  time to fit residues: 14.2115
Evaluate side-chains
  76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 126 GLN
B 215 GLN
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4823 r_free = 0.4823 target = 0.207174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.199640 restraints weight = 13526.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.201411 restraints weight = 9404.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.202723 restraints weight = 6731.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.4765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4312
moved from start:          1.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3896  Z= 0.307
  Angle     :  1.078  16.484   5251  Z= 0.538
  Chirality :  0.056   0.254    630
  Planarity :  0.006   0.051    676
  Dihedral  :  8.162  49.294    551
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 28.24
  Ramachandran Plot:
    Outliers :  1.37 %
    Allowed  :  9.59 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 28.61 %
    Favored  : 65.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.33), residues: 511
  helix: -0.58 (0.31), residues: 248
  sheet: -0.79 (0.74), residues: 54
  loop : -3.49 (0.32), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B 117 
 HIS   0.013   0.002   HIS B 456 
 PHE   0.020   0.003   PHE B 166 
 TYR   0.036   0.003   TYR B 443 
 ARG   0.011   0.001   ARG B 176 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: B  145 ASP cc_start: 0.6688 (t0) cc_final: 0.6285 (t0)
REVERT: B  262 MET cc_start: 0.1757 (ttt) cc_final: 0.1483 (ttt)
  outliers start: 25
  outliers final: 19
  residues processed: 84
  average time/residue: 0.1342
  time to fit residues: 14.5847
Evaluate side-chains
  78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  467 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 HIS
B 485 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.207470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.199846 restraints weight = 13758.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.201595 restraints weight = 9620.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.202872 restraints weight = 6952.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4306
moved from start:          1.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3896  Z= 0.274
  Angle     :  1.001  11.404   5251  Z= 0.502
  Chirality :  0.053   0.287    630
  Planarity :  0.005   0.048    676
  Dihedral  :  7.498  41.395    549
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 25.30
  Ramachandran Plot:
    Outliers :  1.37 %
    Allowed  :  9.59 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 29.58 %
    Favored  : 65.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.34), residues: 511
  helix: -0.47 (0.32), residues: 248
  sheet: -0.63 (0.75), residues: 54
  loop : -3.35 (0.34), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 117 
 HIS   0.004   0.001   HIS B 406 
 PHE   0.015   0.002   PHE B 166 
 TYR   0.018   0.002   TYR B 443 
 ARG   0.008   0.001   ARG B 176 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: B  145 ASP cc_start: 0.6758 (t0) cc_final: 0.6443 (t0)
REVERT: B  402 MET cc_start: 0.6490 (ttp) cc_final: 0.6052 (ttp)
  outliers start: 21
  outliers final: 14
  residues processed: 74
  average time/residue: 0.1469
  time to fit residues: 13.9719
Evaluate side-chains
  69 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 36 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 43 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 126 GLN
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 440 ASN
** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.211085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4767 r_free = 0.4767 target = 0.203350 restraints weight = 13669.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.205019 restraints weight = 9712.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.206257 restraints weight = 7112.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4152
moved from start:          1.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3896  Z= 0.228
  Angle     :  0.994  14.296   5251  Z= 0.489
  Chirality :  0.050   0.243    630
  Planarity :  0.005   0.056    676
  Dihedral  :  6.997  42.681    549
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 22.24
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  9.39 %
    Favored  : 89.63 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 31.05 %
    Favored  : 65.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.35), residues: 511
  helix: -0.17 (0.33), residues: 248
  sheet: -0.38 (0.76), residues: 54
  loop : -3.25 (0.34), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 117 
 HIS   0.006   0.001   HIS B 456 
 PHE   0.014   0.002   PHE B 277 
 TYR   0.007   0.001   TYR B 443 
 ARG   0.004   0.001   ARG B 176 

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 ASP cc_start: 0.6462 (t0) cc_final: 0.6183 (t0)
REVERT: B  402 MET cc_start: 0.6278 (ttp) cc_final: 0.6020 (ttp)
  outliers start: 13
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1378
  time to fit residues: 12.7004
Evaluate side-chains
  72 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 8 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 23 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0980
   chunk 10 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.212480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.204011 restraints weight = 13422.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4800 r_free = 0.4800 target = 0.205868 restraints weight = 9523.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.207261 restraints weight = 6962.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4122
moved from start:          1.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3896  Z= 0.219
  Angle     :  0.958  13.431   5251  Z= 0.470
  Chirality :  0.048   0.233    630
  Planarity :  0.005   0.056    676
  Dihedral  :  6.783  43.029    549
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  9.00 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 31.78 %
    Favored  : 65.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    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: -1.87 (0.35), residues: 511
  helix: -0.02 (0.33), residues: 250
  sheet: -0.04 (0.77), residues: 54
  loop : -3.20 (0.34), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 117 
 HIS   0.004   0.001   HIS B 456 
 PHE   0.013   0.002   PHE B 166 
 TYR   0.007   0.001   TYR B 443 
 ARG   0.004   0.000   ARG B 488 

===============================================================================
Job complete
usr+sys time: 1553.44 seconds
wall clock time: 27 minutes 50.23 seconds (1670.23 seconds total)