Starting phenix.real_space_refine
on Wed Sep 17 04:09:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3ktt_5148/09_2025/3ktt_5148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3ktt_5148/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/3ktt_5148/09_2025/3ktt_5148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3ktt_5148/09_2025/3ktt_5148.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/3ktt_5148/09_2025/3ktt_5148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3ktt_5148/09_2025/3ktt_5148.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.17, per 1000 atoms: 0.30
  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: 0.36
  Conformation dependent library (CDL) restraints added in 159.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.09
  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: 0.53

  Time building geometry restraints manager: 0.46 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:             0.850
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.640
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.740
-------------------------------------------------------------------------------
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= 1.436
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.015   0.001   ARG B 363 
 TYR   0.022   0.003   TYR B 284 
 PHE   0.013   0.002   PHE B 322 
 TRP   0.068   0.028   TRP B 117 
 HIS   0.005   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.01981 ( 3896)
  covalent geometry    : angle       2.86293 ( 5251)
  hydrogen bonds       : bond        0.26342 (  191)
  hydrogen bonds       : angle      10.13075 (  543)

*********************** 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  : 0.093 
Fit side-chains
   revert: symmetry clash
   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: 0.5614 (p)
REVERT: B  128 LEU cc_start: 0.6539 (mt) cc_final: 0.6052 (mt)
REVERT: B  129 LEU cc_start: 0.4424 (OUTLIER) cc_final: 0.3672 (tt)
REVERT: B  200 TYR cc_start: 0.5188 (m-80) cc_final: 0.4647 (m-80)
REVERT: B  255 GLU cc_start: 0.4800 (tm-30) cc_final: 0.4558 (tp30)
REVERT: B  296 VAL cc_start: 0.6608 (t) cc_final: 0.6291 (t)
REVERT: B  465 LEU cc_start: 0.1452 (OUTLIER) cc_final: 0.0723 (mm)
REVERT: B  475 MET cc_start: -0.1465 (tpp) cc_final: -0.2259 (mmm)
  outliers start: 32
  outliers final: 7
  residues processed: 130
  average time/residue: 0.0954
  time to fit residues: 14.3883
Evaluate side-chains
  83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
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 24 optimal weight:    0.1980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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 = 0.4903 r_free = 0.4903 target = 0.218127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.207902 restraints weight = 13912.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4810 r_free = 0.4810 target = 0.210287 restraints weight = 9545.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.211749 restraints weight = 6836.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.212944 restraints weight = 5182.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.213729 restraints weight = 4026.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.4849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3630
moved from start:          0.6241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3896  Z= 0.255
  Angle     :  1.230  19.928   5251  Z= 0.635
  Chirality :  0.067   0.439    630
  Planarity :  0.008   0.076    676
  Dihedral  : 10.434  76.882    565
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 35.14
  Ramachandran Plot:
    Outliers :  1.96 %
    Allowed  :  8.61 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 21.27 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.80 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.35), residues: 511
  helix: -0.45 (0.29), residues: 252
  sheet: -0.20 (0.70), residues: 63
  loop : -2.69 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 375 
 TYR   0.012   0.002   TYR B 443 
 PHE   0.034   0.004   PHE B 484 
 TRP   0.013   0.004   TRP B 117 
 HIS   0.014   0.003   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 3896)
  covalent geometry    : angle       1.23027 ( 5251)
  hydrogen bonds       : bond        0.07342 (  191)
  hydrogen bonds       : angle       7.03760 (  543)

*********************** 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
  113 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.7042 (t) cc_final: 0.6689 (t)
REVERT: B  143 ARG cc_start: 0.4306 (tpm170) cc_final: 0.4014 (tpm170)
REVERT: B  147 MET cc_start: 0.0764 (mpt) cc_final: 0.0439 (mpt)
REVERT: B  225 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5339 (tm)
REVERT: B  278 ILE cc_start: 0.4781 (OUTLIER) cc_final: 0.4309 (mp)
REVERT: B  496 GLU cc_start: 0.6107 (mm-30) cc_final: 0.5870 (mm-30)
  outliers start: 24
  outliers final: 6
  residues processed: 108
  average time/residue: 0.0849
  time to fit residues: 11.0084
Evaluate side-chains
  76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
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  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 15 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 46 optimal weight:    0.2980
   chunk 30 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 11 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4884 r_free = 0.4884 target = 0.216590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.204449 restraints weight = 12989.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.206783 restraints weight = 9402.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.208573 restraints weight = 7092.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.209986 restraints weight = 5505.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.210999 restraints weight = 4353.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.4816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3716
moved from start:          0.7732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3896  Z= 0.193
  Angle     :  0.998  12.484   5251  Z= 0.515
  Chirality :  0.056   0.336    630
  Planarity :  0.006   0.058    676
  Dihedral  :  8.694  73.303    552
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 27.48
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  8.81 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 25.67 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.34), residues: 511
  helix: -0.48 (0.29), residues: 257
  sheet:  0.24 (0.72), residues: 65
  loop : -3.34 (0.38), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 392 
 TYR   0.008   0.001   TYR B 443 
 PHE   0.018   0.003   PHE B 484 
 TRP   0.010   0.004   TRP B 117 
 HIS   0.011   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3896)
  covalent geometry    : angle       0.99789 ( 5251)
  hydrogen bonds       : bond        0.05492 (  191)
  hydrogen bonds       : angle       6.13936 (  543)

*********************** 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
  95 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.6862 (t) cc_final: 0.6511 (t)
REVERT: B  147 MET cc_start: 0.2074 (mpt) cc_final: 0.1382 (mpt)
  outliers start: 19
  outliers final: 11
  residues processed: 92
  average time/residue: 0.0754
  time to fit residues: 8.4858
Evaluate side-chains
  76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
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  146 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  415 THR
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 37 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0060
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    0.9802

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

Flipped N/Q/H residues before XYZ refinement:
** B 275 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 = 0.4876 r_free = 0.4876 target = 0.215000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.203555 restraints weight = 12875.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.205957 restraints weight = 8923.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.207759 restraints weight = 6532.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.208923 restraints weight = 4951.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.209999 restraints weight = 3948.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.4818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3784
moved from start:          0.8710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3896  Z= 0.180
  Angle     :  0.964  12.061   5251  Z= 0.491
  Chirality :  0.053   0.315    630
  Planarity :  0.005   0.056    676
  Dihedral  :  8.362  68.177    552
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 26.20
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  : 10.18 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 23.23 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.04 (0.34), residues: 511
  helix: -0.27 (0.30), residues: 251
  sheet:  0.03 (0.66), residues: 68
  loop : -3.42 (0.37), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 392 
 TYR   0.006   0.001   TYR B 443 
 PHE   0.018   0.002   PHE B 166 
 TRP   0.006   0.002   TRP B 117 
 HIS   0.009   0.002   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 3896)
  covalent geometry    : angle       0.96450 ( 5251)
  hydrogen bonds       : bond        0.04841 (  191)
  hydrogen bonds       : angle       5.84424 (  543)

*********************** 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
  99 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 70
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.6898 (t) cc_final: 0.6549 (t)
REVERT: B  269 ILE cc_start: 0.4559 (OUTLIER) cc_final: 0.3901 (mm)
REVERT: B  467 MET cc_start: 0.1602 (pmm) cc_final: 0.1076 (pmm)
REVERT: B  496 GLU cc_start: 0.4780 (mm-30) cc_final: 0.4495 (mm-30)
  outliers start: 29
  outliers final: 17
  residues processed: 91
  average time/residue: 0.0819
  time to fit residues: 8.8645
Evaluate side-chains
  82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
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  159 LEU
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  340 MET
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  377 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
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0970
   chunk 24 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** B 275 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 = 0.4888 r_free = 0.4888 target = 0.215533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.204134 restraints weight = 13002.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.206685 restraints weight = 9116.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4810 r_free = 0.4810 target = 0.208613 restraints weight = 6637.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.210031 restraints weight = 4984.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.210951 restraints weight = 3836.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.4831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3837
moved from start:          0.9632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3896  Z= 0.171
  Angle     :  0.927  12.400   5251  Z= 0.472
  Chirality :  0.051   0.234    630
  Planarity :  0.005   0.052    676
  Dihedral  :  8.032  60.523    552
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 22.88
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  : 10.37 %
    Favored  : 88.45 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 24.21 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.35), residues: 511
  helix: -0.17 (0.31), residues: 246
  sheet:  0.07 (0.63), residues: 75
  loop : -3.36 (0.36), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  76 
 TYR   0.008   0.001   TYR B 443 
 PHE   0.015   0.002   PHE B 166 
 TRP   0.002   0.001   TRP B 117 
 HIS   0.007   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3896)
  covalent geometry    : angle       0.92749 ( 5251)
  hydrogen bonds       : bond        0.04593 (  191)
  hydrogen bonds       : angle       5.53054 (  543)

*********************** 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
  99 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.6735 (t) cc_final: 0.6312 (t)
REVERT: B  214 ASN cc_start: 0.5015 (p0) cc_final: 0.4638 (p0)
REVERT: B  269 ILE cc_start: 0.4418 (OUTLIER) cc_final: 0.3706 (mm)
REVERT: B  341 ILE cc_start: 0.5202 (tt) cc_final: 0.4969 (tp)
REVERT: B  431 ARG cc_start: 0.4271 (OUTLIER) cc_final: 0.4006 (tpm170)
REVERT: B  467 MET cc_start: 0.1732 (pmm) cc_final: 0.1260 (pmm)
  outliers start: 27
  outliers final: 14
  residues processed: 90
  average time/residue: 0.0710
  time to fit residues: 7.9627
Evaluate side-chains
  80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   57 ILE
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  211 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  370 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
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 16 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** B 275 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 = 0.4857 r_free = 0.4857 target = 0.212552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.199675 restraints weight = 13002.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.202574 restraints weight = 9079.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.204830 restraints weight = 6600.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.206426 restraints weight = 4901.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4801 r_free = 0.4801 target = 0.207590 restraints weight = 3741.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.4799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4009
moved from start:          1.0496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3896  Z= 0.172
  Angle     :  0.944  12.351   5251  Z= 0.473
  Chirality :  0.052   0.266    630
  Planarity :  0.005   0.051    676
  Dihedral  :  7.953  51.141    552
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 24.28
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  9.00 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 26.41 %
    Favored  : 67.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.33), residues: 511
  helix: -0.26 (0.30), residues: 247
  sheet:  0.04 (0.65), residues: 65
  loop : -3.17 (0.35), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 176 
 TYR   0.012   0.001   TYR B 443 
 PHE   0.022   0.002   PHE B 166 
 TRP   0.006   0.002   TRP B 117 
 HIS   0.006   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3896)
  covalent geometry    : angle       0.94422 ( 5251)
  hydrogen bonds       : bond        0.04589 (  191)
  hydrogen bonds       : angle       5.45282 (  543)

*********************** 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
  99 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.6829 (t) cc_final: 0.6379 (t)
REVERT: B  143 ARG cc_start: 0.4038 (tpm170) cc_final: 0.3719 (tpm170)
REVERT: B  146 LEU cc_start: 0.4171 (OUTLIER) cc_final: 0.3964 (mt)
REVERT: B  215 GLN cc_start: 0.4303 (OUTLIER) cc_final: 0.2993 (pt0)
REVERT: B  403 LEU cc_start: 0.7320 (mt) cc_final: 0.7025 (mt)
REVERT: B  431 ARG cc_start: 0.4510 (OUTLIER) cc_final: 0.4103 (tpm170)
  outliers start: 26
  outliers final: 14
  residues processed: 93
  average time/residue: 0.0688
  time to fit residues: 7.9748
Evaluate side-chains
  81 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   57 ILE
Chi-restraints excluded: chain B residue  146 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  201 LEU
Chi-restraints excluded: chain B residue  215 GLN
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  366 THR
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
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 43 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    0.4980
   chunk 2 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.208598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.198609 restraints weight = 13223.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.201011 restraints weight = 8997.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.202802 restraints weight = 6427.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4764 r_free = 0.4764 target = 0.204092 restraints weight = 4718.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.205062 restraints weight = 3554.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.4769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4195
moved from start:          1.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   3896  Z= 0.213
  Angle     :  1.034  12.919   5251  Z= 0.520
  Chirality :  0.054   0.282    630
  Planarity :  0.006   0.060    676
  Dihedral  :  8.351  53.495    552
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 27.73
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  9.78 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 27.38 %
    Favored  : 66.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.19 (0.34), residues: 511
  helix: -0.48 (0.31), residues: 249
  sheet:  0.46 (0.75), residues: 52
  loop : -3.24 (0.34), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 392 
 TYR   0.022   0.002   TYR B 443 
 PHE   0.026   0.003   PHE B 166 
 TRP   0.009   0.002   TRP B 117 
 HIS   0.006   0.002   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 3896)
  covalent geometry    : angle       1.03357 ( 5251)
  hydrogen bonds       : bond        0.05221 (  191)
  hydrogen bonds       : angle       5.92116 (  543)

*********************** 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
  94 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.6755 (t) cc_final: 0.6333 (t)
REVERT: B  250 LYS cc_start: 0.4882 (mptt) cc_final: 0.4224 (mttt)
REVERT: B  431 ARG cc_start: 0.4199 (OUTLIER) cc_final: 0.3962 (tpm170)
  outliers start: 26
  outliers final: 13
  residues processed: 88
  average time/residue: 0.0676
  time to fit residues: 7.4228
Evaluate side-chains
  79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   57 ILE
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  352 VAL
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  431 ARG
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 2 optimal weight:    7.9990
   chunk 15 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 28 optimal weight:    0.3980
   chunk 25 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 HIS ** 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 = 0.4784 r_free = 0.4784 target = 0.205262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.195609 restraints weight = 12894.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.197867 restraints weight = 8952.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.199466 restraints weight = 6442.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.200718 restraints weight = 4820.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.201626 restraints weight = 3682.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.4739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4292
moved from start:          1.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3896  Z= 0.212
  Angle     :  1.033  13.066   5251  Z= 0.527
  Chirality :  0.055   0.290    630
  Planarity :  0.006   0.050    676
  Dihedral  :  8.218  52.005    549
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 26.20
  Ramachandran Plot:
    Outliers :  1.17 %
    Allowed  :  8.61 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 27.63 %
    Favored  : 66.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.42 (0.34), residues: 511
  helix: -0.60 (0.30), residues: 252
  sheet:  0.06 (0.73), residues: 52
  loop : -3.41 (0.34), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 176 
 TYR   0.028   0.002   TYR B 443 
 PHE   0.020   0.003   PHE B 166 
 TRP   0.015   0.003   TRP B 117 
 HIS   0.009   0.002   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 3896)
  covalent geometry    : angle       1.03327 ( 5251)
  hydrogen bonds       : bond        0.05228 (  191)
  hydrogen bonds       : angle       6.05477 (  543)

*********************** 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
  93 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 VAL cc_start: 0.6720 (t) cc_final: 0.6194 (t)
REVERT: B  250 LYS cc_start: 0.4826 (mptt) cc_final: 0.4321 (mttt)
REVERT: B  431 ARG cc_start: 0.4385 (OUTLIER) cc_final: 0.4034 (tpm170)
REVERT: B  467 MET cc_start: 0.1705 (OUTLIER) cc_final: 0.1321 (mtm)
  outliers start: 23
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0731
  time to fit residues: 7.6731
Evaluate side-chains
  76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   57 ILE
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  201 LEU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  431 ARG
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  467 MET
Chi-restraints excluded: chain B residue  484 PHE
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 22 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0970
   chunk 47 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0570
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 46 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
B 126 GLN
B 187 HIS
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4856 r_free = 0.4856 target = 0.210469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.202752 restraints weight = 13957.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.204502 restraints weight = 9860.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.205812 restraints weight = 7196.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4815 r_free = 0.4815 target = 0.206891 restraints weight = 5403.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.207503 restraints weight = 4101.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.4824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4067
moved from start:          1.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3896  Z= 0.185
  Angle     :  0.980  11.989   5251  Z= 0.494
  Chirality :  0.052   0.262    630
  Planarity :  0.005   0.052    676
  Dihedral  :  7.640  52.840    549
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 20.45
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  8.22 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 30.32 %
    Favored  : 65.28 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (0.35), residues: 511
  helix: -0.33 (0.31), residues: 252
  sheet:  0.39 (0.77), residues: 52
  loop : -3.47 (0.34), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  76 
 TYR   0.021   0.002   TYR B 286 
 PHE   0.013   0.002   PHE B 166 
 TRP   0.010   0.003   TRP B 117 
 HIS   0.004   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3896)
  covalent geometry    : angle       0.97985 ( 5251)
  hydrogen bonds       : bond        0.04766 (  191)
  hydrogen bonds       : angle       5.66304 (  543)

*********************** 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
  81 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.133 
Fit side-chains
REVERT: B   91 VAL cc_start: 0.6265 (t) cc_final: 0.5761 (t)
REVERT: B  431 ARG cc_start: 0.3986 (OUTLIER) cc_final: 0.3679 (tpm170)
  outliers start: 18
  outliers final: 13
  residues processed: 79
  average time/residue: 0.0782
  time to fit residues: 7.5701
Evaluate side-chains
  72 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   57 ILE
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  187 HIS
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  366 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
B 126 GLN
B 187 HIS
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4840 r_free = 0.4840 target = 0.208901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.200246 restraints weight = 13610.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.202271 restraints weight = 9400.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.203783 restraints weight = 6749.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.204908 restraints weight = 5000.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.205773 restraints weight = 3802.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.4804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4182
moved from start:          1.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3896  Z= 0.190
  Angle     :  1.027  14.927   5251  Z= 0.516
  Chirality :  0.053   0.272    630
  Planarity :  0.005   0.054    676
  Dihedral  :  7.653  49.249    549
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 22.88
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  8.81 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 32.27 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.35), residues: 511
  helix: -0.41 (0.32), residues: 251
  sheet: -0.18 (0.70), residues: 61
  loop : -3.43 (0.35), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 176 
 TYR   0.015   0.002   TYR B 443 
 PHE   0.016   0.002   PHE B 166 
 TRP   0.008   0.002   TRP B 117 
 HIS   0.005   0.001   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 3896)
  covalent geometry    : angle       1.02745 ( 5251)
  hydrogen bonds       : bond        0.04900 (  191)
  hydrogen bonds       : angle       5.79537 (  543)

********************** 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
  72 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.110 
Fit side-chains
REVERT: B  475 MET cc_start: 0.0582 (mmm) cc_final: -0.0380 (mmt)
  outliers start: 16
  outliers final: 15
  residues processed: 71
  average time/residue: 0.0710
  time to fit residues: 6.2202
Evaluate side-chains
  71 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   57 ILE
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  187 HIS
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  366 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  431 ARG
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  484 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 187 HIS
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 456 HIS ** 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 = 0.4835 r_free = 0.4835 target = 0.208324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.199299 restraints weight = 13218.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.201340 restraints weight = 9218.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.202818 restraints weight = 6691.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.203983 restraints weight = 5040.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.204757 restraints weight = 3840.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.4802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4211
moved from start:          1.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3896  Z= 0.185
  Angle     :  0.989  14.664   5251  Z= 0.496
  Chirality :  0.052   0.270    630
  Planarity :  0.005   0.051    676
  Dihedral  :  7.237  46.010    549
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 22.49
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  8.61 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 32.52 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.39 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.35), residues: 511
  helix: -0.37 (0.32), residues: 252
  sheet: -0.61 (0.69), residues: 63
  loop : -3.42 (0.35), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 176 
 TYR   0.016   0.002   TYR B 284 
 PHE   0.013   0.002   PHE B 166 
 TRP   0.003   0.001   TRP B 117 
 HIS   0.005   0.001   HIS B 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3896)
  covalent geometry    : angle       0.98937 ( 5251)
  hydrogen bonds       : bond        0.04815 (  191)
  hydrogen bonds       : angle       5.70287 (  543)

===============================================================================
Job complete
usr+sys time: 846.58 seconds
wall clock time: 15 minutes 25.58 seconds (925.58 seconds total)