Starting phenix.real_space_refine
on Sun Sep 13 04:35:24 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6mec_9106/09_2026/6mec_9106.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mec_9106/09_2026/6mec_9106.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2026/6mec_9106.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2026/6mec_9106.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2026/6mec_9106.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2026/6mec_9106.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2026/6mec_9106.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2026/6mec_9106.cif"
  }
  resolution = 3.6
  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=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     P     832      5.49       5
     Mg     51      5.21       5
     S       8      5.16       5
     Na      1      4.78       5
     C   10129      2.51       5
     N    3918      2.21       5
     O    6337      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 21276
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 17537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 818, 17537
          Classifications: {'DNA': 1, 'RNAv2': 817}
          Modifications used: {'rna2p_pur': 53, 'rna2p_pyr': 34, 'rna3p_pur': 407, 'rna3p_pyr': 323}
          Link IDs: {'rna2p': 87, 'rna3p': 730}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 294
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "C"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3393
          Classifications: {'peptide': 414}
          Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 398}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 51
          Unusual residues: {' MG': 50, ' NA': 1}
          Classifications: {'undetermined': 51}
          Link IDs: {None: 50}
    Chain: "C"
      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: 4.78, per 1000 atoms: 0.22
  Number of scatterers: 21276
  At special positions: 0
  Unit cell: (116.13, 154.05, 237, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S       8     16.00
     P     832     15.00
     Mg     51     11.99
     Na      1     11.00
     O    6337      8.00
     N    3918      7.00
     C   10129      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 369.0 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  776

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 3 sheets defined
      53.4% alpha, 6.3% beta
      279 base pairs and 440 stacking pairs defined.
    Time for finding SS restraints: 3.44
  Creating SS restraints...
    Processing helix  chain 'C' and resid 27 through 48
      removed outlier: 4.384A  pdb=" N   ASN C  32 " --> pdb=" O   TRP C  28 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   ARG C  33 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL C  35 " --> pdb=" O   ALA C  31 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU C  48 " --> pdb=" O   LYS C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 63
    Processing helix  chain 'C' and resid 64 through 77
    Processing helix  chain 'C' and resid 93 through 105
      removed outlier: 4.176A  pdb=" N   LEU C 104 " --> pdb=" O   ALA C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 154
      Proline residue:  C 149  - end of helix
      removed outlier: 3.567A  pdb=" N   THR C 153 " --> pdb=" O   PRO C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 179
      removed outlier: 3.535A  pdb=" N   ALA C 172 " --> pdb=" O   THR C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 212 through 222
    Processing helix  chain 'C' and resid 243 through 252
      removed outlier: 3.752A  pdb=" N   LEU C 252 " --> pdb=" O   ALA C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 259
    Processing helix  chain 'C' and resid 285 through 300
      removed outlier: 3.520A  pdb=" N   GLU C 300 " --> pdb=" O   GLU C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 356
    Processing helix  chain 'C' and resid 360 through 378
      Proline residue:  C 370  - end of helix
    Processing helix  chain 'C' and resid 384 through 406
    Processing helix  chain 'C' and resid 411 through 420
    Processing helix  chain 'C' and resid 448 through 452
      removed outlier: 3.837A  pdb=" N   THR C 452 " --> pdb=" O   ALA C 449 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 115 through 119
      removed outlier: 3.994A  pdb=" N   VAL C 117 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 270 through 273
      removed outlier: 4.190A  pdb=" N   PHE C 277 " --> pdb=" O   ALA C 191 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA C 191 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 319 through 321

    163 hydrogen bonds defined for protein.
    465 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      725 hydrogen bonds
      1260 hydrogen bond angles
      0 basepair planarities
      279 basepair parallelities
      440 stacking parallelities
  Total time for adding SS restraints: 7.21

  Time building geometry restraints manager: 2.27 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2006
        1.32 -     1.44: 11160
        1.44 -     1.56: 8588
        1.56 -     1.68: 1663
        1.68 -     1.80: 12
  Bond restraints: 23429
  Sorted by residual:
  bond pdb=" C4'  DC B   8 "
       pdb=" C3'  DC B   8 "
    ideal  model  delta    sigma   weight residual
    1.529  1.478  0.051 1.00e-02 1.00e+04 2.60e+01
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.435  1.372  0.063 1.30e-02 5.92e+03 2.32e+01
  bond pdb=" C2   DT B   5 "
       pdb=" N3   DT B   5 "
    ideal  model  delta    sigma   weight residual
    1.373  1.338  0.035 8.00e-03 1.56e+04 1.86e+01
  bond pdb=" C5'  DC B   9 "
       pdb=" C4'  DC B   9 "
    ideal  model  delta    sigma   weight residual
    1.512  1.482  0.030 7.00e-03 2.04e+04 1.83e+01
  bond pdb=" N1   DT B   5 "
       pdb=" C2   DT B   5 "
    ideal  model  delta    sigma   weight residual
    1.376  1.342  0.034 8.00e-03 1.56e+04 1.81e+01
  ... (remaining 23424 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 32759
        2.49 -     4.99: 2649
        4.99 -     7.48: 323
        7.48 -     9.97: 48
        9.97 -    12.47: 10
  Bond angle restraints: 35789
  Sorted by residual:
  angle pdb=" O4'  DA B  11 "
        pdb=" C4'  DA B  11 "
        pdb=" C3'  DA B  11 "
      ideal   model   delta    sigma   weight residual
     106.00  100.97    5.03 6.00e-01 2.78e+00 7.04e+01
  angle pdb=" C3'   A A 481 "
        pdb=" O3'   A A 481 "
        pdb=" P     U A 482 "
      ideal   model   delta    sigma   weight residual
     119.70  128.24   -8.54 1.20e+00 6.94e-01 5.06e+01
  angle pdb=" C3'   U A 545 "
        pdb=" O3'   U A 545 "
        pdb=" P     C A 546 "
      ideal   model   delta    sigma   weight residual
     119.70  127.78   -8.08 1.20e+00 6.94e-01 4.54e+01
  angle pdb=" C3'   A A 462 "
        pdb=" O3'   A A 462 "
        pdb=" P     U A 463 "
      ideal   model   delta    sigma   weight residual
     119.70  127.58   -7.88 1.20e+00 6.94e-01 4.31e+01
  angle pdb=" O4'  DG B  12 "
        pdb=" C4'  DG B  12 "
        pdb=" C3'  DG B  12 "
      ideal   model   delta    sigma   weight residual
     106.00  102.17    3.83 6.00e-01 2.78e+00 4.07e+01
  ... (remaining 35784 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.34: 10352
       35.34 -    70.67: 1599
       70.67 -   106.01: 77
      106.01 -   141.34: 4
      141.34 -   176.68: 8
  Dihedral angle restraints: 12040
    sinusoidal: 10842
      harmonic: 1198
  Sorted by residual:
  dihedral pdb=" C4'   A A 401 "
           pdb=" C3'   A A 401 "
           pdb=" C2'   A A 401 "
           pdb=" C1'   A A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -42.70   79.05     1      3.10e+00 1.04e-01 8.09e+02
  dihedral pdb=" C4'   A A 130 "
           pdb=" C3'   A A 130 "
           pdb=" C2'   A A 130 "
           pdb=" C1'   A A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -41.71   78.06     1      3.10e+00 1.04e-01 7.92e+02
  dihedral pdb=" C4'   U A 286 "
           pdb=" C3'   U A 286 "
           pdb=" C2'   U A 286 "
           pdb=" C1'   U A 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -41.33   77.68     1      3.10e+00 1.04e-01 7.86e+02
  ... (remaining 12037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 3307
       0.101 -    0.202: 661
       0.202 -    0.303: 620
       0.303 -    0.404: 53
       0.404 -    0.504: 3
  Chirality restraints: 4644
  Sorted by residual:
  chirality pdb=" P     C A 543 "
            pdb=" OP1   C A 543 "
            pdb=" OP2   C A 543 "
            pdb=" O5'   C A 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.68   -0.50 2.00e-01 2.50e+01 6.36e+00
  chirality pdb=" C1'   A A 401 "
            pdb=" O4'   A A 401 "
            pdb=" C2'   A A 401 "
            pdb=" N9    A A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.00    0.46 2.00e-01 2.50e+01 5.22e+00
  chirality pdb=" C2'   U A 790 "
            pdb=" C3'   U A 790 "
            pdb=" O2'   U A 790 "
            pdb=" C1'   U A 790 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.38   -0.41 2.00e-01 2.50e+01 4.18e+00
  ... (remaining 4641 not shown)

  Planarity restraints: 1417
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 238 "   -0.049 2.00e-02 2.50e+03   2.15e-02 1.27e+01
        pdb=" N9    A A 238 "    0.047 2.00e-02 2.50e+03
        pdb=" C8    A A 238 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    A A 238 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A A 238 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    A A 238 "   -0.008 2.00e-02 2.50e+03
        pdb=" N6    A A 238 "   -0.013 2.00e-02 2.50e+03
        pdb=" N1    A A 238 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    A A 238 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    A A 238 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A A 238 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 407 "    0.057 5.00e-02 4.00e+02   8.68e-02 1.20e+01
        pdb=" N   PRO C 408 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO C 408 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C 408 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 401 "    0.044 2.00e-02 2.50e+03   1.84e-02 9.34e+00
        pdb=" N9    A A 401 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8    A A 401 "   -0.007 2.00e-02 2.50e+03
        pdb=" N7    A A 401 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    A A 401 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A A 401 "    0.010 2.00e-02 2.50e+03
        pdb=" N6    A A 401 "    0.011 2.00e-02 2.50e+03
        pdb=" N1    A A 401 "    0.008 2.00e-02 2.50e+03
        pdb=" C2    A A 401 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    A A 401 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A A 401 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1414 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 75
        2.31 -     2.96: 9335
        2.96 -     3.60: 36914
        3.60 -     4.25: 64238
        4.25 -     4.90: 82886
  Nonbonded interactions: 193448
  Sorted by model distance:
  nonbonded pdb=" CZ2 TRP C  28 "
            pdb=" CD  LYS C  73 "
     model   vdw
     1.659 3.740
  nonbonded pdb=" NE  ARG C 380 "
            pdb=" OE1 GLN C 455 "
     model   vdw
     1.667 3.120
  nonbonded pdb=" P     U A   1 "
            pdb=" O2'   A A 860 "
     model   vdw
     1.676 3.400
  nonbonded pdb=" O   LEU C 356 "
            pdb=" CH2 TRP C 402 "
     model   vdw
     1.793 3.340
  nonbonded pdb=" O2'   A A 428 "
            pdb=" OP1   A A 429 "
     model   vdw
     1.851 3.040
  ... (remaining 193443 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     24.570
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
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      :  0.011   0.099  23429  Z= 0.534
  Angle     :  1.440  12.467  35789  Z= 0.609
  Chirality :  0.121   0.504   4644
  Planarity :  0.008   0.087   1417
  Dihedral  : 22.796 176.679  11264
  Min Nonbonded Distance : 1.659

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.73 %
    Favored  : 86.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.50 %

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 are not related in a simple way.
  whole: -4.93 (0.32), residues: 408
  helix: -3.26 (0.23), residues: 212
  sheet: -1.60 (0.94), residues: 34
  loop : -3.49 (0.42), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG C 163 
 TYR   0.035   0.004   TYR C 378 
 PHE   0.051   0.006   PHE C 231 
 TRP   0.040   0.006   TRP C 324 
 HIS   0.018   0.006   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01052 /  0.53 (23429)
  covalent geometry    : angle       1.43976 /  0.61 (35789)
  hydrogen bonds       : bond        0.14282 /  7.25 (  888)
  hydrogen bonds       : angle       4.69836 /  1.89 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: C  231 PHE cc_start: 0.8259 (p90) cc_final: 0.7871 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2132
  time to fit residues: 31.2443
Evaluate side-chains
  47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 202 HIS
C 269 ASN
C 341 ASN
C 346 HIS
** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 407 HIS
C 417 ASN
C 455 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.123344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.096704 restraints weight = 58464.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.097881 restraints weight = 41756.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.098676 restraints weight = 25993.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.098819 restraints weight = 23546.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.098722 restraints weight = 21694.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  23429  Z= 0.288
  Angle     :  1.726  24.721  35789  Z= 0.676
  Chirality :  0.151   1.854   4644
  Planarity :  0.007   0.063   1417
  Dihedral  : 21.036 179.195  10401
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 10.42 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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 are not related in a simple way.
  whole: -3.62 (0.36), residues: 408
  helix: -1.81 (0.30), residues: 215
  sheet: -1.74 (0.82), residues: 36
  loop : -3.31 (0.44), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 413 
 TYR   0.019   0.003   TYR C  66 
 PHE   0.032   0.003   PHE C 231 
 TRP   0.044   0.004   TRP C 396 
 HIS   0.009   0.003   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00569 /  0.29 (23429)
  covalent geometry    : angle       1.72603 /  0.68 (35789)
  hydrogen bonds       : bond        0.08124 /  4.12 (  888)
  hydrogen bonds       : angle       3.30143 /  1.28 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.342 
Fit side-chains
REVERT: C  231 PHE cc_start: 0.8292 (p90) cc_final: 0.7876 (p90)
  outliers start: 8
  outliers final: 4
  residues processed: 69
  average time/residue: 0.2000
  time to fit residues: 19.9865
Evaluate side-chains
  49 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   65 PHE
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  417 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 116 optimal weight:    0.4980
   chunk 74 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    3.8988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 GLN
C 269 ASN
** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 346 HIS
** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.119525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.092966 restraints weight = 59548.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.093659 restraints weight = 45189.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.094481 restraints weight = 32240.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.094656 restraints weight = 26772.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.094624 restraints weight = 25830.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.097  23429  Z= 0.426
  Angle     :  1.549  18.263  35789  Z= 0.609
  Chirality :  0.119   1.262   4644
  Planarity :  0.007   0.058   1417
  Dihedral  : 20.945 175.292  10401
  Min Nonbonded Distance : 1.680

Molprobity Statistics.
  All-atom Clashscore : 17.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.99 %
    Favored  : 87.01 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 12.96 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -3.25 (0.38), residues: 408
  helix: -1.38 (0.32), residues: 215
  sheet: -0.94 (0.84), residues: 32
  loop : -3.48 (0.44), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG C 327 
 TYR   0.020   0.003   TYR C 109 
 PHE   0.026   0.003   PHE C 231 
 TRP   0.028   0.004   TRP C 433 
 HIS   0.012   0.003   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00868 /  0.43 (23429)
  covalent geometry    : angle       1.54935 /  0.61 (35789)
  hydrogen bonds       : bond        0.09260 /  4.71 (  888)
  hydrogen bonds       : angle       3.37794 /  1.34 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 49
  time to evaluate  : 0.261 
Fit side-chains
REVERT: C   94 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.5963 (mt0)
  outliers start: 23
  outliers final: 16
  residues processed: 66
  average time/residue: 0.1852
  time to fit residues: 17.9081
Evaluate side-chains
  60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   65 PHE
Chi-restraints excluded: chain C residue   94 GLN
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 ASP
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 92 optimal weight:    0.1980
   chunk 18 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 100 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.124193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.104542 restraints weight = 59114.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.104387 restraints weight = 67981.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.105589 restraints weight = 43261.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.105573 restraints weight = 31242.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.107680 restraints weight = 26518.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  23429  Z= 0.195
  Angle     :  1.267  15.279  35789  Z= 0.498
  Chirality :  0.098   1.167   4644
  Planarity :  0.005   0.043   1417
  Dihedral  : 20.750 179.104  10401
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.59 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -2.38 (0.40), residues: 408
  helix: -0.49 (0.35), residues: 215
  sheet: -0.71 (0.84), residues: 32
  loop : -3.33 (0.46), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  33 
 TYR   0.015   0.003   TYR C 143 
 PHE   0.022   0.002   PHE C 231 
 TRP   0.053   0.003   TRP C  91 
 HIS   0.007   0.002   HIS C 397 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.20 (23429)
  covalent geometry    : angle       1.26714 /  0.50 (35789)
  hydrogen bonds       : bond        0.07584 /  3.83 (  888)
  hydrogen bonds       : angle       2.94673 /  1.16 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.251 
Fit side-chains
  outliers start: 11
  outliers final: 6
  residues processed: 61
  average time/residue: 0.1878
  time to fit residues: 16.9403
Evaluate side-chains
  50 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  127 ARG
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 119 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.7586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.123331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.097284 restraints weight = 59118.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.097507 restraints weight = 45538.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.097863 restraints weight = 35174.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.098197 restraints weight = 30376.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.098290 restraints weight = 27583.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  23429  Z= 0.245
  Angle     :  1.223  14.613  35789  Z= 0.481
  Chirality :  0.090   0.899   4644
  Planarity :  0.005   0.049   1417
  Dihedral  : 20.503 176.419  10401
  Min Nonbonded Distance : 1.789

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 19.15 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -2.04 (0.41), residues: 408
  helix: -0.16 (0.35), residues: 214
  sheet: -0.69 (0.86), residues: 32
  loop : -3.21 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 456 
 TYR   0.016   0.003   TYR C 143 
 PHE   0.018   0.002   PHE C 231 
 TRP   0.024   0.003   TRP C  59 
 HIS   0.008   0.003   HIS C  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00496 /  0.25 (23429)
  covalent geometry    : angle       1.22310 /  0.48 (35789)
  hydrogen bonds       : bond        0.07732 /  3.91 (  888)
  hydrogen bonds       : angle       2.86192 /  1.14 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 47
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: C  246 MET cc_start: 0.8161 (tpp) cc_final: 0.7948 (ttm)
  outliers start: 20
  outliers final: 13
  residues processed: 61
  average time/residue: 0.1816
  time to fit residues: 16.7315
Evaluate side-chains
  56 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  127 ARG
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 120 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  63 HIS
** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.121265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.093750 restraints weight = 59142.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.095707 restraints weight = 41095.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.095580 restraints weight = 27064.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.095856 restraints weight = 23383.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.095879 restraints weight = 22426.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.074  23429  Z= 0.337
  Angle     :  1.303  14.716  35789  Z= 0.513
  Chirality :  0.094   0.984   4644
  Planarity :  0.006   0.054   1417
  Dihedral  : 20.536 178.599  10401
  Min Nonbonded Distance : 1.767

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 18.59 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -2.27 (0.40), residues: 408
  helix: -0.30 (0.35), residues: 216
  sheet: -0.63 (0.89), residues: 32
  loop : -3.47 (0.45), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 405 
 TYR   0.014   0.003   TYR C 109 
 PHE   0.021   0.003   PHE C 231 
 TRP   0.034   0.003   TRP C  91 
 HIS   0.010   0.003   HIS C  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00686 /  0.34 (23429)
  covalent geometry    : angle       1.30283 /  0.51 (35789)
  hydrogen bonds       : bond        0.08293 /  4.20 (  888)
  hydrogen bonds       : angle       3.01208 /  1.19 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 0.305 
Fit side-chains
REVERT: C   50 ARG cc_start: 0.8190 (mmp-170) cc_final: 0.7887 (mmp-170)
REVERT: C   70 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8255 (mm)
REVERT: C  282 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7133 (mp0)
  outliers start: 24
  outliers final: 15
  residues processed: 64
  average time/residue: 0.1650
  time to fit residues: 16.0807
Evaluate side-chains
  61 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  127 ARG
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 ASP
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 96 optimal weight:    0.7980
   chunk 63 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 60 optimal weight:   10.0000
   chunk 94 optimal weight:    0.3980
   chunk 43 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.9784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.123182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.095970 restraints weight = 59248.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.097063 restraints weight = 40645.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.097424 restraints weight = 25427.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.097760 restraints weight = 23641.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.097685 restraints weight = 21486.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  23429  Z= 0.245
  Angle     :  1.195  13.823  35789  Z= 0.470
  Chirality :  0.088   0.873   4644
  Planarity :  0.005   0.046   1417
  Dihedral  : 20.429 177.891  10401
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 21.13 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -1.97 (0.41), residues: 408
  helix: -0.08 (0.35), residues: 215
  sheet: -0.52 (0.89), residues: 32
  loop : -3.27 (0.46), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  33 
 TYR   0.012   0.002   TYR C 143 
 PHE   0.019   0.002   PHE C 231 
 TRP   0.021   0.002   TRP C  59 
 HIS   0.006   0.001   HIS C 397 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00494 /  0.24 (23429)
  covalent geometry    : angle       1.19501 /  0.47 (35789)
  hydrogen bonds       : bond        0.07670 /  3.87 (  888)
  hydrogen bonds       : angle       2.86505 /  1.13 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.375 
Fit side-chains
  outliers start: 17
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1682
  time to fit residues: 16.3930
Evaluate side-chains
  56 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  127 ARG
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 100 optimal weight:    0.5980
   chunk 48 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.5186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.122302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.095233 restraints weight = 58932.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.096210 restraints weight = 47386.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.096910 restraints weight = 28475.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.096949 restraints weight = 25456.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.097014 restraints weight = 23336.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  23429  Z= 0.294
  Angle     :  1.229  13.827  35789  Z= 0.484
  Chirality :  0.089   0.925   4644
  Planarity :  0.005   0.048   1417
  Dihedral  : 20.414 177.137  10401
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.54 %
    Favored  : 89.46 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 21.13 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -1.98 (0.41), residues: 408
  helix: -0.04 (0.35), residues: 216
  sheet: -0.36 (0.90), residues: 32
  loop : -3.41 (0.45), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 405 
 TYR   0.012   0.003   TYR C 143 
 PHE   0.017   0.002   PHE C 231 
 TRP   0.026   0.003   TRP C  59 
 HIS   0.006   0.002   HIS C 346 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00601 /  0.29 (23429)
  covalent geometry    : angle       1.22924 /  0.48 (35789)
  hydrogen bonds       : bond        0.07911 /  4.00 (  888)
  hydrogen bonds       : angle       2.89020 /  1.14 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.436 
Fit side-chains
REVERT: C   70 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (mm)
  outliers start: 15
  outliers final: 12
  residues processed: 56
  average time/residue: 0.1734
  time to fit residues: 14.8865
Evaluate side-chains
  59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  127 ARG
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 51 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    2.9588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.120300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.092655 restraints weight = 57809.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.093617 restraints weight = 36646.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.093650 restraints weight = 25403.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.094896 restraints weight = 24062.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.094769 restraints weight = 19905.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  23429  Z= 0.329
  Angle     :  1.291  14.390  35789  Z= 0.507
  Chirality :  0.091   0.974   4644
  Planarity :  0.006   0.051   1417
  Dihedral  : 20.485 175.382  10401
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 17.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 22.25 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -2.05 (0.41), residues: 408
  helix: -0.12 (0.35), residues: 216
  sheet: -0.13 (0.93), residues: 32
  loop : -3.47 (0.46), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 405 
 TYR   0.015   0.003   TYR C 329 
 PHE   0.015   0.002   PHE C 231 
 TRP   0.042   0.003   TRP C  59 
 HIS   0.009   0.002   HIS C  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00672 /  0.33 (23429)
  covalent geometry    : angle       1.29092 /  0.51 (35789)
  hydrogen bonds       : bond        0.08455 /  4.29 (  888)
  hydrogen bonds       : angle       3.02423 /  1.20 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.292 
Fit side-chains
REVERT: C   59 TRP cc_start: 0.8561 (t-100) cc_final: 0.7723 (t-100)
REVERT: C   70 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8306 (mm)
  outliers start: 16
  outliers final: 12
  residues processed: 59
  average time/residue: 0.1778
  time to fit residues: 15.8271
Evaluate side-chains
  60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  127 ARG
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  340 LYS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0570
   chunk 62 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 116 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 91 optimal weight:    0.3980
   overall best weight:    1.4502

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.123232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.095710 restraints weight = 58395.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.097203 restraints weight = 34099.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.097436 restraints weight = 22384.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.097889 restraints weight = 22513.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.097677 restraints weight = 18787.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  23429  Z= 0.209
  Angle     :  1.155  13.129  35789  Z= 0.454
  Chirality :  0.084   0.790   4644
  Planarity :  0.005   0.035   1417
  Dihedral  : 20.404 177.124  10401
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 22.25 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -1.69 (0.42), residues: 408
  helix:  0.22 (0.35), residues: 215
  sheet: -0.41 (0.93), residues: 32
  loop : -3.23 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  50 
 TYR   0.013   0.002   TYR C 160 
 PHE   0.017   0.002   PHE C 231 
 TRP   0.024   0.002   TRP C  59 
 HIS   0.006   0.001   HIS C 397 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.21 (23429)
  covalent geometry    : angle       1.15501 /  0.45 (35789)
  hydrogen bonds       : bond        0.07509 /  3.79 (  888)
  hydrogen bonds       : angle       2.76298 /  1.09 ( 1725)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   70 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8083 (mm)
  outliers start: 15
  outliers final: 13
  residues processed: 62
  average time/residue: 0.1685
  time to fit residues: 16.0848
Evaluate side-chains
  63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   65 PHE
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  127 ARG
Chi-restraints excluded: chain C residue  135 LYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  215 VAL
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  433 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 69 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 76 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 45 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.9586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.122666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.094987 restraints weight = 57986.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.096248 restraints weight = 35750.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.096349 restraints weight = 25557.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.096700 restraints weight = 24740.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.096731 restraints weight = 22701.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  23429  Z= 0.243
  Angle     :  1.173  13.007  35789  Z= 0.461
  Chirality :  0.084   0.805   4644
  Planarity :  0.005   0.038   1417
  Dihedral  : 20.371 176.942  10401
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.10 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 are not related in a simple way.
  whole: -1.73 (0.42), residues: 408
  helix:  0.23 (0.35), residues: 215
  sheet: -0.43 (0.92), residues: 32
  loop : -3.32 (0.47), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 405 
 TYR   0.012   0.002   TYR C 143 
 PHE   0.016   0.002   PHE C 231 
 TRP   0.026   0.002   TRP C  59 
 HIS   0.005   0.001   HIS C 397 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00494 /  0.24 (23429)
  covalent geometry    : angle       1.17264 /  0.46 (35789)
  hydrogen bonds       : bond        0.07643 /  3.87 (  888)
  hydrogen bonds       : angle       2.77649 /  1.10 ( 1725)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2982.34 seconds
wall clock time: 52 minutes 53.00 seconds (3173.00 seconds total)