Starting phenix.real_space_refine
on Fri Oct 10 15:57:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k34_36843/10_2025/8k34_36843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k34_36843/10_2025/8k34_36843.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k34_36843/10_2025/8k34_36843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k34_36843/10_2025/8k34_36843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k34_36843/10_2025/8k34_36843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k34_36843/10_2025/8k34_36843.cif"
  }
  resolution = 2.81
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.044
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      1      5.21       5
     S      21      5.16       5
     C    4650      2.51       5
     N    1196      2.21       5
     O    1315      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7187
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3597
          Classifications: {'peptide': 429}
          Link IDs: {'PTRANS': 13, 'TRANS': 415}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 434, 3503
          Classifications: {'peptide': 434}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 409}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 86
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2}
          Link IDs: {'rna2p': 1, 'rna3p': 2}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.00, per 1000 atoms: 0.28
  Number of scatterers: 7187
  At special positions: 0
  Unit cell: (75.9, 81.4, 130.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      21     16.00
     P       4     15.00
     Mg      1     11.99
     O    1315      8.00
     N    1196      7.00
     C    4650      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: 0.61
  Conformation dependent library (CDL) restraints added in 378.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1640

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      39.2% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 28
    Processing helix  chain 'A' and resid 46 through 55
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 4.544A  pdb=" N   LYS A  70 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 89
    Processing helix  chain 'A' and resid 109 through 114
      removed outlier: 4.113A  pdb=" N   ARG A 114 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 138
    Processing helix  chain 'A' and resid 146 through 158
      removed outlier: 3.805A  pdb=" N   SER A 150 " --> pdb=" O   ASP A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 203
    Processing helix  chain 'A' and resid 220 through 224
      removed outlier: 3.690A  pdb=" N   PHE A 223 " --> pdb=" O   GLU A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 249
    Processing helix  chain 'A' and resid 257 through 280
      removed outlier: 3.587A  pdb=" N   ARG A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LYS A 278 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ASP A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 302
      No H-bonds generated for 'chain 'A' and resid 300 through 302'
    Processing helix  chain 'A' and resid 353 through 365
      removed outlier: 3.724A  pdb=" N   GLN A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 384
    Processing helix  chain 'A' and resid 420 through 438
      removed outlier: 3.824A  pdb=" N   LEU A 424 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 22 through 30
    Processing helix  chain 'B' and resid 46 through 62
      removed outlier: 3.744A  pdb=" N   LYS B  62 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 83
    Processing helix  chain 'B' and resid 115 through 132
    Processing helix  chain 'B' and resid 144 through 151
    Processing helix  chain 'B' and resid 207 through 214
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 248 through 264
    Processing helix  chain 'B' and resid 331 through 351
      removed outlier: 3.860A  pdb=" N   LYS B 336 " --> pdb=" O   PRO B 332 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ALA B 337 " --> pdb=" O   LYS B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 377
      removed outlier: 3.699A  pdb=" N   VAL B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 463
    Processing helix  chain 'B' and resid 477 through 482
      removed outlier: 4.596A  pdb=" N   PHE B 482 " --> pdb=" O   VAL B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 493
      removed outlier: 4.043A  pdb=" N   SER B 493 " --> pdb=" O   ILE B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34
      removed outlier: 5.832A  pdb=" N   ILE A   5 " --> pdb=" O   TRP A  33 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   LYS A   4 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   PHE A  60 " --> pdb=" O   LYS A   4 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   PHE A   6 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   ILE A  62 " --> pdb=" O   PHE A   6 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   SER A   8 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 165
    Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177
    Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286
    Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305
    Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 394
    Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 6
      removed outlier: 5.712A  pdb=" N   ILE B 412 " --> pdb=" O   PHE B 419 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   PHE B 419 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   GLY B 385 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   VAL B 357 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   VAL B 386 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)
      removed outlier: 5.351A  pdb=" N   ILE B 359 " --> pdb=" O   VAL B 386 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ILE B 388 " --> pdb=" O   ILE B 359 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ALA B 361 " --> pdb=" O   ILE B 388 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 20
      removed outlier: 3.775A  pdb=" N   GLN B  18 " --> pdb=" O   PHE B  14 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LYS B 270 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 95
      removed outlier: 3.608A  pdb=" N   GLY B  45 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   GLY B  42 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   ILE B 142 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL B  44 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   TRP B 139 " --> pdb=" O   GLN B 222 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   LEU B 224 " --> pdb=" O   TRP B 139 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   VAL B 141 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 321 through 322
    Processing sheet with id=AB3, first strand: chain 'B' and resid 425 through 426

    293 hydrogen bonds defined for protein.
    816 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: 1.26

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2203
        1.34 -     1.46: 1336
        1.46 -     1.58: 3792
        1.58 -     1.70: 7
        1.70 -     1.82: 31
  Bond restraints: 7369
  Sorted by residual:
  bond pdb=" CG  PRO B 319 "
       pdb=" CD  PRO B 319 "
    ideal  model  delta    sigma   weight residual
    1.503  1.384  0.119 3.40e-02 8.65e+02 1.22e+01
  bond pdb=" CG  LEU B  13 "
       pdb=" CD1 LEU B  13 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.28e+00
  bond pdb=" CB  LYS B  48 "
       pdb=" CG  LYS B  48 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 3.00e-02 1.11e+03 2.28e+00
  bond pdb=" CG  LYS B  48 "
       pdb=" CD  LYS B  48 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.04e+00
  bond pdb=" CG  LEU B  57 "
       pdb=" CD2 LEU B  57 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.00e+00
  ... (remaining 7364 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 9820
        2.58 -     5.17: 120
        5.17 -     7.75: 16
        7.75 -    10.33: 7
       10.33 -    12.92: 2
  Bond angle restraints: 9965
  Sorted by residual:
  angle pdb=" CA  LYS A 315 "
        pdb=" CB  LYS A 315 "
        pdb=" CG  LYS A 315 "
      ideal   model   delta    sigma   weight residual
     114.10  127.02  -12.92 2.00e+00 2.50e-01 4.17e+01
  angle pdb=" CA  PRO B 319 "
        pdb=" N   PRO B 319 "
        pdb=" CD  PRO B 319 "
      ideal   model   delta    sigma   weight residual
     112.00  103.09    8.91 1.40e+00 5.10e-01 4.05e+01
  angle pdb=" N   PRO B 319 "
        pdb=" CD  PRO B 319 "
        pdb=" CG  PRO B 319 "
      ideal   model   delta    sigma   weight residual
     103.20   93.83    9.37 1.50e+00 4.44e-01 3.90e+01
  angle pdb=" CB  LYS B  48 "
        pdb=" CG  LYS B  48 "
        pdb=" CD  LYS B  48 "
      ideal   model   delta    sigma   weight residual
     111.30  121.94  -10.64 2.30e+00 1.89e-01 2.14e+01
  angle pdb=" CA  GLN B 295 "
        pdb=" CB  GLN B 295 "
        pdb=" CG  GLN B 295 "
      ideal   model   delta    sigma   weight residual
     114.10  121.98   -7.88 2.00e+00 2.50e-01 1.55e+01
  ... (remaining 9960 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.42: 3676
       16.42 -    32.83: 503
       32.83 -    49.25: 169
       49.25 -    65.67: 49
       65.67 -    82.09: 10
  Dihedral angle restraints: 4407
    sinusoidal: 1875
      harmonic: 2532
  Sorted by residual:
  dihedral pdb=" CA  PRO B 393 "
           pdb=" C   PRO B 393 "
           pdb=" N   LEU B 394 "
           pdb=" CA  LEU B 394 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.69   27.31     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  SER A 173 "
           pdb=" C   SER A 173 "
           pdb=" N   ASN A 174 "
           pdb=" CA  ASN A 174 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.89   21.11     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  THR A 216 "
           pdb=" C   THR A 216 "
           pdb=" N   PHE A 217 "
           pdb=" CA  PHE A 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.70   18.30     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 4404 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 640
       0.031 -    0.062: 286
       0.062 -    0.093: 87
       0.093 -    0.124: 50
       0.124 -    0.155: 13
  Chirality restraints: 1076
  Sorted by residual:
  chirality pdb=" CA  LEU B  57 "
            pdb=" N   LEU B  57 "
            pdb=" C   LEU B  57 "
            pdb=" CB  LEU B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.02e-01
  chirality pdb=" CB  ILE B 486 "
            pdb=" CA  ILE B 486 "
            pdb=" CG1 ILE B 486 "
            pdb=" CG2 ILE B 486 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.52e-01
  chirality pdb=" CA  ILE A 391 "
            pdb=" N   ILE A 391 "
            pdb=" C   ILE A 391 "
            pdb=" CB  ILE A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 1073 not shown)

  Planarity restraints: 1242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 318 "    0.079 5.00e-02 4.00e+02   1.13e-01 2.04e+01
        pdb=" N   PRO B 319 "   -0.195 5.00e-02 4.00e+02
        pdb=" CA  PRO B 319 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO B 319 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 295 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.60e+00
        pdb=" C   GLN B 295 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLN B 295 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASN B 296 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 394 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   ASN A 394 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASN A 394 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A 395 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1239 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 80
        2.58 -     3.16: 5839
        3.16 -     3.74: 11725
        3.74 -     4.32: 16273
        4.32 -     4.90: 26684
  Nonbonded interactions: 60601
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 468 "
            pdb="MG    MG B 601 "
     model   vdw
     2.000 2.170
  nonbonded pdb=" OP1   A C   3 "
            pdb="MG    MG B 601 "
     model   vdw
     2.008 2.170
  nonbonded pdb=" OP2   A C   1 "
            pdb="MG    MG B 601 "
     model   vdw
     2.023 2.170
  nonbonded pdb=" OXT ILE B 507 "
            pdb="MG    MG B 601 "
     model   vdw
     2.088 2.170
  nonbonded pdb=" O   TRP B 269 "
            pdb=" OH  TYR B 467 "
     model   vdw
     2.144 3.040
  ... (remaining 60596 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.150
  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:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.119   7369  Z= 0.167
  Angle     :  0.737  12.915   9965  Z= 0.396
  Chirality :  0.044   0.155   1076
  Planarity :  0.005   0.113   1242
  Dihedral  : 17.750  82.086   2767
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 31.05 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.23 (0.28), residues: 845
  helix:  0.61 (0.31), residues: 280
  sheet: -0.17 (0.41), residues: 153
  loop : -0.60 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  72 
 TYR   0.021   0.001   TYR B 506 
 PHE   0.027   0.002   PHE A 305 
 TRP   0.026   0.002   TRP A  46 
 HIS   0.005   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7369)
  covalent geometry    : angle       0.73740 ( 9965)
  hydrogen bonds       : bond        0.14013 (  293)
  hydrogen bonds       : angle       6.70087 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.6775 (mp10) cc_final: 0.6572 (mp10)
REVERT: A  346 ASP cc_start: 0.7995 (m-30) cc_final: 0.7735 (m-30)
REVERT: B  356 GLU cc_start: 0.7885 (mp0) cc_final: 0.7657 (mp0)
  outliers start: 16
  outliers final: 11
  residues processed: 112
  average time/residue: 0.3654
  time to fit residues: 44.5459
Evaluate side-chains
  102 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  311 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN
A 434 ASN
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.178782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.145667 restraints weight = 10233.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 3.49
r_work: 0.4052 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7369  Z= 0.149
  Angle     :  0.587   6.948   9965  Z= 0.308
  Chirality :  0.043   0.139   1076
  Planarity :  0.004   0.065   1242
  Dihedral  :  8.169  75.488    993
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 25.36 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.12 (0.28), residues: 845
  helix:  0.75 (0.30), residues: 290
  sheet: -0.02 (0.42), residues: 149
  loop : -0.63 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  72 
 TYR   0.011   0.001   TYR A 190 
 PHE   0.023   0.002   PHE A 343 
 TRP   0.014   0.002   TRP A  46 
 HIS   0.003   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7369)
  covalent geometry    : angle       0.58667 ( 9965)
  hydrogen bonds       : bond        0.03990 (  293)
  hydrogen bonds       : angle       5.65500 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 110
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 THR cc_start: 0.7923 (m) cc_final: 0.7539 (m)
REVERT: A   31 GLU cc_start: 0.6702 (tp30) cc_final: 0.6457 (tp30)
REVERT: A   89 GLN cc_start: 0.8096 (mp10) cc_final: 0.7866 (pm20)
REVERT: A  165 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6326 (pt)
REVERT: A  345 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6488 (ppp)
REVERT: A  346 ASP cc_start: 0.7907 (m-30) cc_final: 0.7527 (m-30)
REVERT: A  371 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.6200 (m-30)
REVERT: A  394 ASN cc_start: 0.5499 (OUTLIER) cc_final: 0.5179 (p0)
REVERT: B  305 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7642 (mm)
REVERT: B  371 ASN cc_start: 0.7056 (m-40) cc_final: 0.6682 (m110)
  outliers start: 42
  outliers final: 13
  residues processed: 135
  average time/residue: 0.4561
  time to fit residues: 65.9810
Evaluate side-chains
  116 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ARG
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 68 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0670
   chunk 22 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN
B 129 ASN
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN
B 350 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.178032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.144886 restraints weight = 10152.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.4187 rms_B_bonded: 3.50
r_work: 0.4029 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7369  Z= 0.152
  Angle     :  0.587   7.422   9965  Z= 0.309
  Chirality :  0.043   0.160   1076
  Planarity :  0.004   0.050   1242
  Dihedral  :  7.515  73.569    980
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 24.71 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.18 (0.28), residues: 845
  helix:  0.76 (0.30), residues: 292
  sheet: -0.26 (0.41), residues: 149
  loop : -0.65 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 189 
 TYR   0.009   0.001   TYR B 397 
 PHE   0.022   0.002   PHE A 343 
 TRP   0.013   0.002   TRP A 368 
 HIS   0.004   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7369)
  covalent geometry    : angle       0.58700 ( 9965)
  hydrogen bonds       : bond        0.03883 (  293)
  hydrogen bonds       : angle       5.39945 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 110
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASP cc_start: 0.5778 (OUTLIER) cc_final: 0.5459 (m-30)
REVERT: A   18 THR cc_start: 0.7822 (m) cc_final: 0.7462 (m)
REVERT: A   31 GLU cc_start: 0.6791 (tp30) cc_final: 0.6498 (tp30)
REVERT: A   41 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5618 (pptt)
REVERT: A   89 GLN cc_start: 0.8125 (mp10) cc_final: 0.7895 (pm20)
REVERT: A  119 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8003 (p0)
REVERT: A  305 PHE cc_start: 0.7554 (t80) cc_final: 0.7306 (t80)
REVERT: A  345 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6405 (ppp)
REVERT: A  346 ASP cc_start: 0.7926 (m-30) cc_final: 0.7527 (m-30)
REVERT: A  371 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.6072 (m-30)
REVERT: A  394 ASN cc_start: 0.5503 (OUTLIER) cc_final: 0.5075 (p0)
REVERT: A  417 VAL cc_start: 0.7492 (t) cc_final: 0.7229 (t)
REVERT: B  305 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7663 (mm)
REVERT: B  350 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7547 (t0)
REVERT: B  371 ASN cc_start: 0.7039 (m-40) cc_final: 0.6714 (m110)
REVERT: B  474 ASP cc_start: 0.7094 (t0) cc_final: 0.6865 (t0)
  outliers start: 45
  outliers final: 16
  residues processed: 137
  average time/residue: 0.4365
  time to fit residues: 64.2866
Evaluate side-chains
  127 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  350 ASN
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  426 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 64 optimal weight:    8.9990
   chunk 48 optimal weight:    0.6980
   chunk 18 optimal weight:    0.1980
   chunk 61 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0470
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 364 GLN
A 394 ASN
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.179932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.146678 restraints weight = 10301.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.4200 rms_B_bonded: 3.54
r_work: 0.4047 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7369  Z= 0.132
  Angle     :  0.559   7.539   9965  Z= 0.293
  Chirality :  0.043   0.145   1076
  Planarity :  0.004   0.040   1242
  Dihedral  :  7.417  73.529    980
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 26.91 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.16 (0.28), residues: 845
  helix:  0.90 (0.30), residues: 292
  sheet: -0.25 (0.41), residues: 140
  loop : -0.73 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 189 
 TYR   0.012   0.001   TYR A 190 
 PHE   0.020   0.001   PHE A 343 
 TRP   0.017   0.002   TRP A 369 
 HIS   0.003   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7369)
  covalent geometry    : angle       0.55856 ( 9965)
  hydrogen bonds       : bond        0.03619 (  293)
  hydrogen bonds       : angle       5.20883 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 115
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 THR cc_start: 0.7769 (m) cc_final: 0.7423 (m)
REVERT: A   31 GLU cc_start: 0.6756 (tp30) cc_final: 0.6442 (tp30)
REVERT: A   41 LYS cc_start: 0.5942 (OUTLIER) cc_final: 0.5433 (pptt)
REVERT: A   89 GLN cc_start: 0.8101 (mp10) cc_final: 0.7875 (pm20)
REVERT: A  108 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8036 (mp)
REVERT: A  305 PHE cc_start: 0.7596 (t80) cc_final: 0.7358 (t80)
REVERT: A  345 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6400 (ppp)
REVERT: A  346 ASP cc_start: 0.7964 (m-30) cc_final: 0.7586 (m-30)
REVERT: A  371 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.6124 (m-30)
REVERT: B  286 LYS cc_start: 0.8003 (tppt) cc_final: 0.7425 (mptt)
REVERT: B  305 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7652 (mm)
REVERT: B  367 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7664 (t0)
REVERT: B  371 ASN cc_start: 0.7210 (m-40) cc_final: 0.6789 (m-40)
  outliers start: 41
  outliers final: 13
  residues processed: 138
  average time/residue: 0.4501
  time to fit residues: 66.5997
Evaluate side-chains
  121 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  233 TYR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 50 optimal weight:    0.0270
   chunk 57 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0060
   chunk 37 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.4854

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN
B 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.179409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.146689 restraints weight = 10316.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.4200 rms_B_bonded: 3.49
r_work: 0.4046 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7369  Z= 0.127
  Angle     :  0.547   7.842   9965  Z= 0.287
  Chirality :  0.042   0.143   1076
  Planarity :  0.004   0.055   1242
  Dihedral  :  7.380  73.545    980
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 26.91 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.14 (0.28), residues: 845
  helix:  0.95 (0.30), residues: 292
  sheet: -0.49 (0.40), residues: 149
  loop : -0.64 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 189 
 TYR   0.011   0.001   TYR A 293 
 PHE   0.018   0.001   PHE A 343 
 TRP   0.024   0.002   TRP A 369 
 HIS   0.004   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7369)
  covalent geometry    : angle       0.54701 ( 9965)
  hydrogen bonds       : bond        0.03514 (  293)
  hydrogen bonds       : angle       5.12906 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 112
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.7709 (m-30) cc_final: 0.6875 (m-30)
REVERT: A   18 THR cc_start: 0.7838 (m) cc_final: 0.7502 (m)
REVERT: A   41 LYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5455 (pptt)
REVERT: A   89 GLN cc_start: 0.8063 (mp10) cc_final: 0.7843 (pm20)
REVERT: A  108 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8086 (mp)
REVERT: A  119 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8027 (p0)
REVERT: A  277 MET cc_start: 0.7260 (mmp) cc_final: 0.6778 (mmp)
REVERT: A  281 ASN cc_start: 0.8341 (t0) cc_final: 0.8048 (p0)
REVERT: A  305 PHE cc_start: 0.7618 (t80) cc_final: 0.7399 (t80)
REVERT: A  315 LYS cc_start: 0.9283 (tmtt) cc_final: 0.9010 (tmmt)
REVERT: A  345 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6202 (ppp)
REVERT: A  346 ASP cc_start: 0.7939 (m-30) cc_final: 0.7541 (m-30)
REVERT: A  358 HIS cc_start: 0.7796 (m-70) cc_final: 0.7512 (m-70)
REVERT: A  371 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5950 (m-30)
REVERT: A  394 ASN cc_start: 0.5316 (OUTLIER) cc_final: 0.5077 (p0)
REVERT: B  286 LYS cc_start: 0.7930 (tppt) cc_final: 0.7365 (mptt)
REVERT: B  302 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.5884 (mp-120)
REVERT: B  350 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7617 (t0)
REVERT: B  371 ASN cc_start: 0.7135 (m-40) cc_final: 0.6770 (m-40)
REVERT: B  453 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7054 (mp10)
REVERT: B  474 ASP cc_start: 0.7136 (t0) cc_final: 0.6893 (t0)
  outliers start: 45
  outliers final: 14
  residues processed: 136
  average time/residue: 0.4376
  time to fit residues: 64.1425
Evaluate side-chains
  125 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  233 TYR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  350 ASN
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  453 GLN
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 72 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN
** B  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.179616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.146790 restraints weight = 10332.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.4195 rms_B_bonded: 3.50
r_work: 0.4041 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6662
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7369  Z= 0.134
  Angle     :  0.570   8.143   9965  Z= 0.297
  Chirality :  0.043   0.151   1076
  Planarity :  0.004   0.047   1242
  Dihedral  :  7.345  73.548    979
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 27.30 %
    Favored  : 67.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.12 (0.28), residues: 845
  helix:  1.02 (0.30), residues: 292
  sheet: -0.54 (0.40), residues: 149
  loop : -0.65 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 189 
 TYR   0.013   0.001   TYR A 190 
 PHE   0.017   0.001   PHE A 343 
 TRP   0.028   0.002   TRP A 369 
 HIS   0.004   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7369)
  covalent geometry    : angle       0.56984 ( 9965)
  hydrogen bonds       : bond        0.03487 (  293)
  hydrogen bonds       : angle       5.08380 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 112
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.7675 (m-30) cc_final: 0.6862 (m-30)
REVERT: A   18 THR cc_start: 0.7844 (m) cc_final: 0.7516 (m)
REVERT: A   41 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5427 (pptt)
REVERT: A   89 GLN cc_start: 0.8057 (mp10) cc_final: 0.7826 (pm20)
REVERT: A  108 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8098 (mp)
REVERT: A  119 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8027 (p0)
REVERT: A  277 MET cc_start: 0.7083 (mmp) cc_final: 0.6501 (mmp)
REVERT: A  281 ASN cc_start: 0.8286 (t0) cc_final: 0.8040 (p0)
REVERT: A  305 PHE cc_start: 0.7624 (t80) cc_final: 0.7420 (t80)
REVERT: A  315 LYS cc_start: 0.9299 (tmtt) cc_final: 0.9072 (tmmt)
REVERT: A  345 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6148 (ppp)
REVERT: A  346 ASP cc_start: 0.7931 (m-30) cc_final: 0.7520 (m-30)
REVERT: A  371 ASP cc_start: 0.6257 (OUTLIER) cc_final: 0.5927 (m-30)
REVERT: A  394 ASN cc_start: 0.5191 (OUTLIER) cc_final: 0.4976 (p0)
REVERT: B  286 LYS cc_start: 0.7940 (tppt) cc_final: 0.7395 (mptt)
REVERT: B  371 ASN cc_start: 0.7137 (m-40) cc_final: 0.6777 (m-40)
REVERT: B  453 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7139 (mp10)
REVERT: B  474 ASP cc_start: 0.7127 (t0) cc_final: 0.6865 (t0)
  outliers start: 37
  outliers final: 17
  residues processed: 135
  average time/residue: 0.4268
  time to fit residues: 61.9579
Evaluate side-chains
  127 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  233 TYR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  453 GLN
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0570
   chunk 54 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 320 HIS
** B  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.179312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.146422 restraints weight = 10454.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 3.52
r_work: 0.4040 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6671
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7369  Z= 0.133
  Angle     :  0.568   7.880   9965  Z= 0.296
  Chirality :  0.043   0.137   1076
  Planarity :  0.004   0.045   1242
  Dihedral  :  7.292  73.556    977
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 27.55 %
    Favored  : 67.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.14 (0.28), residues: 845
  helix:  1.01 (0.30), residues: 294
  sheet: -0.60 (0.40), residues: 154
  loop : -0.64 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 362 
 TYR   0.015   0.001   TYR B 506 
 PHE   0.018   0.001   PHE A 343 
 TRP   0.029   0.002   TRP A 369 
 HIS   0.005   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7369)
  covalent geometry    : angle       0.56816 ( 9965)
  hydrogen bonds       : bond        0.03490 (  293)
  hydrogen bonds       : angle       5.09708 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 112
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.7659 (m-30) cc_final: 0.6836 (m-30)
REVERT: A   18 THR cc_start: 0.7860 (m) cc_final: 0.7535 (m)
REVERT: A   41 LYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5496 (pptt)
REVERT: A   89 GLN cc_start: 0.8034 (mp10) cc_final: 0.7805 (pm20)
REVERT: A  108 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: A  119 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8010 (p0)
REVERT: A  277 MET cc_start: 0.7160 (mmp) cc_final: 0.6547 (mmp)
REVERT: A  281 ASN cc_start: 0.8260 (t0) cc_final: 0.8047 (p0)
REVERT: A  345 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6229 (ppp)
REVERT: A  346 ASP cc_start: 0.7966 (m-30) cc_final: 0.7580 (m-30)
REVERT: A  358 HIS cc_start: 0.7687 (m-70) cc_final: 0.7399 (m-70)
REVERT: A  369 TRP cc_start: 0.6332 (OUTLIER) cc_final: 0.5793 (m-10)
REVERT: A  371 ASP cc_start: 0.6255 (OUTLIER) cc_final: 0.5906 (m-30)
REVERT: B  229 LEU cc_start: 0.7375 (mm) cc_final: 0.6800 (mt)
REVERT: B  243 ARG cc_start: 0.7937 (ptm160) cc_final: 0.7595 (ttp-110)
REVERT: B  302 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6011 (mp-120)
REVERT: B  371 ASN cc_start: 0.7151 (m-40) cc_final: 0.6791 (m-40)
REVERT: B  453 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7084 (mp10)
  outliers start: 38
  outliers final: 17
  residues processed: 135
  average time/residue: 0.4333
  time to fit residues: 62.7220
Evaluate side-chains
  126 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  233 TYR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  369 TRP
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  453 GLN
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.178599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.145646 restraints weight = 10458.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.4182 rms_B_bonded: 3.51
r_work: 0.4033 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7369  Z= 0.147
  Angle     :  0.609   9.625   9965  Z= 0.316
  Chirality :  0.043   0.139   1076
  Planarity :  0.004   0.043   1242
  Dihedral  :  7.330  73.569    977
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 28.20 %
    Favored  : 67.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.19 (0.28), residues: 845
  helix:  0.98 (0.30), residues: 294
  sheet: -0.68 (0.40), residues: 154
  loop : -0.66 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  72 
 TYR   0.016   0.001   TYR B 506 
 PHE   0.021   0.001   PHE A 343 
 TRP   0.029   0.002   TRP A 369 
 HIS   0.006   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7369)
  covalent geometry    : angle       0.60865 ( 9965)
  hydrogen bonds       : bond        0.03580 (  293)
  hydrogen bonds       : angle       5.17903 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.7588 (m-30) cc_final: 0.6765 (m-30)
REVERT: A   18 THR cc_start: 0.7873 (m) cc_final: 0.7546 (m)
REVERT: A   41 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5516 (pptt)
REVERT: A  108 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8120 (mp)
REVERT: A  119 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8005 (p0)
REVERT: A  277 MET cc_start: 0.7173 (mmp) cc_final: 0.6581 (mmp)
REVERT: A  305 PHE cc_start: 0.7582 (t80) cc_final: 0.7352 (t80)
REVERT: A  345 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6224 (ppp)
REVERT: A  346 ASP cc_start: 0.8011 (m-30) cc_final: 0.7612 (m-30)
REVERT: A  369 TRP cc_start: 0.6342 (OUTLIER) cc_final: 0.5846 (m-10)
REVERT: A  371 ASP cc_start: 0.6217 (OUTLIER) cc_final: 0.5833 (m-30)
REVERT: B  229 LEU cc_start: 0.7412 (mm) cc_final: 0.6866 (mt)
REVERT: B  243 ARG cc_start: 0.7979 (ptm160) cc_final: 0.7580 (ttp-110)
REVERT: B  371 ASN cc_start: 0.7093 (m-40) cc_final: 0.6748 (m-40)
REVERT: B  453 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7081 (mp10)
  outliers start: 34
  outliers final: 20
  residues processed: 133
  average time/residue: 0.4194
  time to fit residues: 60.2322
Evaluate side-chains
  129 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  233 TYR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  369 TRP
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  453 GLN
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0770
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0370
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.180267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.147491 restraints weight = 10259.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 3.51
r_work: 0.4066 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7369  Z= 0.131
  Angle     :  0.622  11.002   9965  Z= 0.323
  Chirality :  0.044   0.155   1076
  Planarity :  0.004   0.041   1242
  Dihedral  :  7.278  73.518    977
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 29.62 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.14 (0.28), residues: 845
  helix:  1.05 (0.30), residues: 294
  sheet: -0.67 (0.40), residues: 154
  loop : -0.65 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 362 
 TYR   0.015   0.001   TYR B 506 
 PHE   0.023   0.001   PHE A 343 
 TRP   0.029   0.002   TRP A 369 
 HIS   0.006   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7369)
  covalent geometry    : angle       0.62161 ( 9965)
  hydrogen bonds       : bond        0.03459 (  293)
  hydrogen bonds       : angle       5.20636 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.7529 (m-30) cc_final: 0.6755 (m-30)
REVERT: A   18 THR cc_start: 0.7831 (m) cc_final: 0.7512 (m)
REVERT: A   41 LYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5490 (pptt)
REVERT: A  107 ASP cc_start: 0.8894 (t0) cc_final: 0.8547 (m-30)
REVERT: A  108 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8009 (mp)
REVERT: A  277 MET cc_start: 0.7241 (mmp) cc_final: 0.6642 (mmp)
REVERT: A  305 PHE cc_start: 0.7620 (t80) cc_final: 0.7393 (t80)
REVERT: A  345 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6195 (ppp)
REVERT: A  346 ASP cc_start: 0.8008 (m-30) cc_final: 0.7638 (m-30)
REVERT: A  358 HIS cc_start: 0.7705 (m-70) cc_final: 0.7459 (m-70)
REVERT: A  369 TRP cc_start: 0.6228 (OUTLIER) cc_final: 0.5876 (m-10)
REVERT: A  371 ASP cc_start: 0.6191 (OUTLIER) cc_final: 0.5809 (m-30)
REVERT: B  229 LEU cc_start: 0.7426 (mm) cc_final: 0.6918 (mt)
REVERT: B  243 ARG cc_start: 0.8004 (ptm160) cc_final: 0.7586 (ttp-110)
REVERT: B  302 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6222 (mp10)
REVERT: B  350 ASN cc_start: 0.7888 (t0) cc_final: 0.7665 (t0)
REVERT: B  371 ASN cc_start: 0.7074 (m-40) cc_final: 0.6744 (m-40)
REVERT: B  453 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7092 (mp10)
  outliers start: 30
  outliers final: 15
  residues processed: 132
  average time/residue: 0.4357
  time to fit residues: 61.8531
Evaluate side-chains
  127 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  233 TYR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  369 TRP
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  353 TYR
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  453 GLN
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   chunk 40 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 320 HIS
A 434 ASN
** B  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  61 GLN
B 129 ASN
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.178067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.145282 restraints weight = 10345.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.4186 rms_B_bonded: 3.49
r_work: 0.4032 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7369  Z= 0.160
  Angle     :  0.658  11.641   9965  Z= 0.341
  Chirality :  0.045   0.140   1076
  Planarity :  0.004   0.042   1242
  Dihedral  :  7.351  73.578    977
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 30.14 %
    Favored  : 66.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.25 (0.28), residues: 845
  helix:  0.90 (0.30), residues: 294
  sheet: -0.59 (0.40), residues: 152
  loop : -0.72 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 362 
 TYR   0.019   0.001   TYR B 506 
 PHE   0.018   0.002   PHE A 343 
 TRP   0.029   0.002   TRP A 369 
 HIS   0.005   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 7369)
  covalent geometry    : angle       0.65843 ( 9965)
  hydrogen bonds       : bond        0.03700 (  293)
  hydrogen bonds       : angle       5.28620 (  816)

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

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

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1690 Ramachandran restraints generated.
    845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.7592 (m-30) cc_final: 0.6903 (m-30)
REVERT: A   18 THR cc_start: 0.7983 (m) cc_final: 0.7657 (m)
REVERT: A   31 GLU cc_start: 0.6816 (tp30) cc_final: 0.6427 (tp30)
REVERT: A   41 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5748 (pptt)
REVERT: A  107 ASP cc_start: 0.8880 (t0) cc_final: 0.8575 (m-30)
REVERT: A  108 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8125 (mp)
REVERT: A  119 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8068 (p0)
REVERT: A  277 MET cc_start: 0.7355 (mmp) cc_final: 0.6738 (mmp)
REVERT: A  305 PHE cc_start: 0.7698 (t80) cc_final: 0.7490 (t80)
REVERT: A  345 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6229 (ppp)
REVERT: A  346 ASP cc_start: 0.8039 (m-30) cc_final: 0.7673 (m-30)
REVERT: A  358 HIS cc_start: 0.7735 (m-70) cc_final: 0.7502 (m-70)
REVERT: A  369 TRP cc_start: 0.6565 (OUTLIER) cc_final: 0.6056 (m-10)
REVERT: A  371 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.5980 (m-30)
REVERT: B  229 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6924 (mt)
REVERT: B  350 ASN cc_start: 0.7975 (t0) cc_final: 0.7691 (t0)
REVERT: B  371 ASN cc_start: 0.7087 (m-40) cc_final: 0.6768 (m-40)
REVERT: B  453 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7097 (mp10)
  outliers start: 29
  outliers final: 15
  residues processed: 126
  average time/residue: 0.4165
  time to fit residues: 56.7416
Evaluate side-chains
  124 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  233 TYR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  369 TRP
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  302 GLN
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  453 GLN
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.178192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.145650 restraints weight = 10303.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.4180 rms_B_bonded: 3.47
r_work: 0.4025 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7369  Z= 0.159
  Angle     :  0.666  11.760   9965  Z= 0.344
  Chirality :  0.044   0.148   1076
  Planarity :  0.004   0.040   1242
  Dihedral  :  7.365  73.570    977
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 30.40 %
    Favored  : 65.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.28 (0.28), residues: 845
  helix:  0.88 (0.30), residues: 294
  sheet: -0.63 (0.41), residues: 152
  loop : -0.75 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 362 
 TYR   0.018   0.001   TYR B 506 
 PHE   0.014   0.001   PHE A 176 
 TRP   0.030   0.002   TRP A 369 
 HIS   0.005   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7369)
  covalent geometry    : angle       0.66585 ( 9965)
  hydrogen bonds       : bond        0.03721 (  293)
  hydrogen bonds       : angle       5.32086 (  816)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2809.74 seconds
wall clock time: 48 minutes 44.68 seconds (2924.68 seconds total)