Starting phenix.real_space_refine
on Thu Sep 18 22:42:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mec_9106/09_2025/6mec_9106.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mec_9106/09_2025/6mec_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_2025/6mec_9106.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2025/6mec_9106.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2025/6mec_9106.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mec_9106/09_2025/6mec_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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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, 'RNA': 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: 5.34, per 1000 atoms: 0.25
  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: 1.87
  Conformation dependent library (CDL) restraints added in 366.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 4.30
  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: 8.35

  Time building geometry restraints manager: 2.61 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=" N   PRO C 132 "
       pdb=" CD  PRO C 132 "
    ideal  model  delta    sigma   weight residual
    1.473  1.416  0.057 1.40e-02 5.10e+03 1.64e+01
  bond pdb=" N   PRO C 245 "
       pdb=" CD  PRO C 245 "
    ideal  model  delta    sigma   weight residual
    1.473  1.430  0.043 1.40e-02 5.10e+03 9.60e+00
  bond pdb=" CB  ASN C 389 "
       pdb=" CG  ASN C 389 "
    ideal  model  delta    sigma   weight residual
    1.516  1.446  0.070 2.50e-02 1.60e+03 7.74e+00
  bond pdb=" CB  ARG C 406 "
       pdb=" CG  ARG C 406 "
    ideal  model  delta    sigma   weight residual
    1.520  1.438  0.082 3.00e-02 1.11e+03 7.49e+00
  bond pdb=" CE3 TRP C 402 "
       pdb=" CZ3 TRP C 402 "
    ideal  model  delta    sigma   weight residual
    1.382  1.303  0.079 3.00e-02 1.11e+03 6.89e+00
  ... (remaining 23424 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 34100
        2.49 -     4.99: 1454
        4.99 -     7.48: 192
        7.48 -     9.97: 37
        9.97 -    12.47: 9
  Bond angle restraints: 35792
  Sorted by residual:
  angle pdb=" C3'   A A 481 "
        pdb=" O3'   A A 481 "
        pdb=" P     U A 482 "
      ideal   model   delta    sigma   weight residual
     120.20  128.24   -8.04 1.50e+00 4.44e-01 2.87e+01
  angle pdb=" C3'   U A 545 "
        pdb=" O3'   U A 545 "
        pdb=" P     C A 546 "
      ideal   model   delta    sigma   weight residual
     120.20  127.78   -7.58 1.50e+00 4.44e-01 2.55e+01
  angle pdb=" C3'   A A 462 "
        pdb=" O3'   A A 462 "
        pdb=" P     U A 463 "
      ideal   model   delta    sigma   weight residual
     120.20  127.58   -7.38 1.50e+00 4.44e-01 2.42e+01
  angle pdb=" O3'   A A  12 "
        pdb=" C3'   A A  12 "
        pdb=" C2'   A A  12 "
      ideal   model   delta    sigma   weight residual
     113.70  120.85   -7.15 1.50e+00 4.44e-01 2.27e+01
  angle pdb=" C3'   C A 666 "
        pdb=" O3'   C A 666 "
        pdb=" P     A A 667 "
      ideal   model   delta    sigma   weight residual
     120.20  127.31   -7.11 1.50e+00 4.44e-01 2.24e+01
  ... (remaining 35787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 12656
       35.58 -    71.16: 2052
       71.16 -   106.74: 274
      106.74 -   142.33: 8
      142.33 -   177.91: 10
  Dihedral angle restraints: 15000
    sinusoidal: 13802
      harmonic: 1198
  Sorted by residual:
  dihedral pdb=" O4'   U A 258 "
           pdb=" C1'   U A 258 "
           pdb=" N1    U A 258 "
           pdb=" C2    U A 258 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   49.91 -177.91     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U A 839 "
           pdb=" C1'   U A 839 "
           pdb=" N1    U A 839 "
           pdb=" C2    U A 839 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   45.05 -173.05     1      1.70e+01 3.46e-03 6.62e+01
  dihedral pdb=" CA  TYR C 273 "
           pdb=" C   TYR C 273 "
           pdb=" N   ALA C 274 "
           pdb=" CA  ALA C 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.17  -39.83     0      5.00e+00 4.00e-02 6.35e+01
  ... (remaining 14997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 4117
       0.088 -    0.175: 475
       0.175 -    0.263: 40
       0.263 -    0.351: 8
       0.351 -    0.439: 4
  Chirality restraints: 4644
  Sorted by residual:
  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      2.44    2.00    0.44 2.00e-01 2.50e+01 4.81e+00
  chirality pdb=" C3'   G A   8 "
            pdb=" C4'   G A   8 "
            pdb=" O3'   G A   8 "
            pdb=" C2'   G A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.10   -0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" C3'   G A 832 "
            pdb=" C4'   G A 832 "
            pdb=" O3'   G A 832 "
            pdb=" C2'   G A 832 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.11   -0.37 2.00e-01 2.50e+01 3.40e+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:             5.910
  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:          0.540
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     27.850
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
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      :  0.010   0.099  23429  Z= 0.525
  Angle     :  1.213  12.467  35792  Z= 0.589
  Chirality :  0.058   0.439   4644
  Planarity :  0.008   0.087   1417
  Dihedral  : 25.555 177.907  14224
  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 aren 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
  covalent geometry    : bond        0.01024 (23429)
  covalent geometry    : angle       1.21290 (35792)
  hydrogen bonds       : bond        0.14282 (  888)
  hydrogen bonds       : angle       4.69836 ( 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  : 0.355 
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: 0.2271
  time to fit residues: 32.9680
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  : 0.348 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
C  32 ASN
C 202 HIS
C 269 ASN
C 341 ASN
C 346 HIS
** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 407 HIS
C 417 ASN
C 455 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.123230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.096448 restraints weight = 58493.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.098169 restraints weight = 40238.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.098159 restraints weight = 26348.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.098490 restraints weight = 23637.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.098464 restraints weight = 22643.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  23429  Z= 0.174
  Angle     :  0.701   8.688  35792  Z= 0.352
  Chirality :  0.035   0.269   4644
  Planarity :  0.006   0.050   1417
  Dihedral  : 25.959 179.609  13361
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 10.14 %
    Favored  : 86.76 %
  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 aren not related in a simple way.
  whole: -3.16 (0.38), residues: 408
  helix: -1.41 (0.32), residues: 216
  sheet: -1.49 (0.83), residues: 34
  loop : -3.13 (0.46), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 357 
 TYR   0.020   0.002   TYR C  66 
 PHE   0.030   0.002   PHE C 231 
 TRP   0.040   0.004   TRP C 396 
 HIS   0.007   0.002   HIS C 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (23429)
  covalent geometry    : angle       0.70068 (35792)
  hydrogen bonds       : bond        0.07146 (  888)
  hydrogen bonds       : angle       3.00207 ( 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
  81 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.348 
Fit side-chains
REVERT: C  231 PHE cc_start: 0.8161 (p90) cc_final: 0.7744 (p90)
  outliers start: 11
  outliers final: 6
  residues processed: 77
  average time/residue: 0.2195
  time to fit residues: 24.0046
Evaluate side-chains
  59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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  117 VAL
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:    6.9990
   chunk 56 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 116 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 67 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 266 GLN
C 269 ASN
C 346 HIS
** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 417 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.116267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.088190 restraints weight = 58579.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.089524 restraints weight = 37439.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.089811 restraints weight = 23543.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.090016 restraints weight = 21494.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.090089 restraints weight = 19371.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.114  23429  Z= 0.491
  Angle     :  0.974  11.232  35792  Z= 0.480
  Chirality :  0.048   0.350   4644
  Planarity :  0.007   0.078   1417
  Dihedral  : 26.110 178.907  13361
  Min Nonbonded Distance : 1.739

Molprobity Statistics.
  All-atom Clashscore : 18.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 12.68 %
    Favored  : 80.56 %
  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 aren not related in a simple way.
  whole: -3.21 (0.37), residues: 408
  helix: -1.31 (0.32), residues: 216
  sheet: -0.97 (0.85), residues: 32
  loop : -3.52 (0.44), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 327 
 TYR   0.018   0.003   TYR C 445 
 PHE   0.027   0.003   PHE C 231 
 TRP   0.026   0.004   TRP C 433 
 HIS   0.013   0.003   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00958 (23429)
  covalent geometry    : angle       0.97405 (35792)
  hydrogen bonds       : bond        0.09783 (  888)
  hydrogen bonds       : angle       3.45260 ( 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
  68 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 44
  time to evaluate  : 0.355 
Fit side-chains
  outliers start: 24
  outliers final: 16
  residues processed: 60
  average time/residue: 0.2271
  time to fit residues: 19.3451
Evaluate side-chains
  54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
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  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  184 CYS
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  276 ASP
Chi-restraints excluded: chain C residue  291 THR
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:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 95 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
C  39 GLN
C 269 ASN
C 341 ASN
** C 382 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 = 0.3955 r_free = 0.3955 target = 0.123290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.095655 restraints weight = 58509.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.097015 restraints weight = 34860.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.097469 restraints weight = 21777.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.097774 restraints weight = 20176.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.097676 restraints weight = 17872.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  23429  Z= 0.159
  Angle     :  0.667   7.901  35792  Z= 0.332
  Chirality :  0.034   0.274   4644
  Planarity :  0.005   0.041   1417
  Dihedral  : 25.796 178.385  13361
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.18 %
    Favored  : 79.44 %
  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 aren not related in a simple way.
  whole: -2.21 (0.41), residues: 408
  helix: -0.29 (0.35), residues: 217
  sheet: -0.69 (0.84), residues: 32
  loop : -3.37 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 327 
 TYR   0.010   0.002   TYR C  66 
 PHE   0.020   0.002   PHE C 231 
 TRP   0.020   0.002   TRP C 402 
 HIS   0.005   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (23429)
  covalent geometry    : angle       0.66737 (35792)
  hydrogen bonds       : bond        0.06879 (  888)
  hydrogen bonds       : angle       2.74296 ( 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
  68 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: C   39 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6376 (mm-40)
REVERT: C   50 ARG cc_start: 0.8202 (mmp-170) cc_final: 0.7852 (mmp-170)
REVERT: C   70 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8007 (mm)
REVERT: C  149 PRO cc_start: 0.8829 (Cg_endo) cc_final: 0.8602 (Cg_exo)
REVERT: C  231 PHE cc_start: 0.8188 (p90) cc_final: 0.7542 (p90)
REVERT: C  246 MET cc_start: 0.8180 (tpp) cc_final: 0.7941 (ttm)
  outliers start: 12
  outliers final: 6
  residues processed: 65
  average time/residue: 0.1796
  time to fit residues: 17.7508
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   39 GLN
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  299 LYS
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:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 119 optimal weight:    0.3980
   chunk 90 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 115 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 341 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.123152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.095261 restraints weight = 58480.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.096577 restraints weight = 35668.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.097071 restraints weight = 22617.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.097420 restraints weight = 20211.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.097286 restraints weight = 17737.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  23429  Z= 0.172
  Angle     :  0.647   8.531  35792  Z= 0.324
  Chirality :  0.033   0.267   4644
  Planarity :  0.005   0.041   1417
  Dihedral  : 25.705 179.238  13361
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.87 %
    Favored  : 77.75 %
  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 aren not related in a simple way.
  whole: -1.81 (0.42), residues: 408
  helix:  0.14 (0.36), residues: 214
  sheet: -0.93 (0.78), residues: 32
  loop : -3.19 (0.48), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 327 
 TYR   0.012   0.002   TYR C 187 
 PHE   0.018   0.002   PHE C 231 
 TRP   0.020   0.002   TRP C 402 
 HIS   0.005   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (23429)
  covalent geometry    : angle       0.64653 (35792)
  hydrogen bonds       : bond        0.06453 (  888)
  hydrogen bonds       : angle       2.71764 ( 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
  64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: C   34 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8126 (tp30)
REVERT: C   70 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8071 (mm)
  outliers start: 12
  outliers final: 7
  residues processed: 62
  average time/residue: 0.1847
  time to fit residues: 17.3284
Evaluate side-chains
  54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  117 VAL
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  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:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 120 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 269 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.118158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.090167 restraints weight = 57835.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.091476 restraints weight = 35261.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.091586 restraints weight = 24199.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.091962 restraints weight = 22549.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.091873 restraints weight = 21426.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.093  23429  Z= 0.369
  Angle     :  0.823   9.438  35792  Z= 0.407
  Chirality :  0.041   0.282   4644
  Planarity :  0.006   0.059   1417
  Dihedral  : 25.852 178.962  13361
  Min Nonbonded Distance : 1.766

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 20.00 %
    Favored  : 74.93 %
  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 aren not related in a simple way.
  whole: -2.17 (0.41), residues: 408
  helix: -0.18 (0.35), residues: 214
  sheet: -0.67 (0.84), residues: 32
  loop : -3.43 (0.46), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 456 
 TYR   0.021   0.003   TYR C 329 
 PHE   0.015   0.002   PHE C 321 
 TRP   0.030   0.003   TRP C 402 
 HIS   0.008   0.003   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00716 (23429)
  covalent geometry    : angle       0.82286 (35792)
  hydrogen bonds       : bond        0.08322 (  888)
  hydrogen bonds       : angle       3.07698 ( 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
  57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.364 
Fit side-chains
REVERT: C   34 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: C   70 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8373 (mm)
  outliers start: 18
  outliers final: 11
  residues processed: 54
  average time/residue: 0.1835
  time to fit residues: 15.1065
Evaluate side-chains
  51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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  117 VAL
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  315 ILE
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:    8.9990
   chunk 71 optimal weight:    8.9990
   chunk 96 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 92 optimal weight:    0.0270
   chunk 14 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 60 optimal weight:   20.0000
   chunk 94 optimal weight:    0.4980
   chunk 43 optimal weight:   20.0000
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.5044

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

Flipped N/Q/H residues before XYZ refinement:
C  63 HIS
C 269 ASN
** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.122778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.095811 restraints weight = 58757.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.096261 restraints weight = 49325.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.096637 restraints weight = 31755.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.096965 restraints weight = 27907.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.097106 restraints weight = 25560.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  23429  Z= 0.180
  Angle     :  0.654   8.339  35792  Z= 0.326
  Chirality :  0.033   0.271   4644
  Planarity :  0.005   0.044   1417
  Dihedral  : 25.681 179.126  13361
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 21.13 %
    Favored  : 74.37 %
  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 aren not related in a simple way.
  whole: -1.68 (0.42), residues: 408
  helix:  0.31 (0.36), residues: 214
  sheet: -0.66 (0.83), residues: 32
  loop : -3.29 (0.48), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 137 
 TYR   0.010   0.002   TYR C 143 
 PHE   0.017   0.002   PHE C 231 
 TRP   0.024   0.002   TRP C 402 
 HIS   0.005   0.002   HIS C 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (23429)
  covalent geometry    : angle       0.65398 (35792)
  hydrogen bonds       : bond        0.06724 (  888)
  hydrogen bonds       : angle       2.66185 ( 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: 16
    poor density    : 50
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   34 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8093 (mm-30)
REVERT: C   70 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8101 (mm)
REVERT: C  139 MET cc_start: 0.7043 (mmp) cc_final: 0.6578 (mmp)
REVERT: C  246 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7655 (mtm)
  outliers start: 16
  outliers final: 10
  residues processed: 62
  average time/residue: 0.1571
  time to fit residues: 14.8648
Evaluate side-chains
  57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  117 VAL
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  211 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  268 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 105 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 100 optimal weight:    0.6980
   chunk 48 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
C 269 ASN
** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 417 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.121089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.093567 restraints weight = 58508.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.094513 restraints weight = 43927.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.095243 restraints weight = 27176.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.095364 restraints weight = 23237.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.095355 restraints weight = 21659.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  23429  Z= 0.257
  Angle     :  0.707   8.983  35792  Z= 0.352
  Chirality :  0.036   0.268   4644
  Planarity :  0.005   0.049   1417
  Dihedral  : 25.707 178.999  13361
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 21.41 %
    Favored  : 74.37 %
  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 aren not related in a simple way.
  whole: -1.83 (0.41), residues: 408
  helix:  0.21 (0.35), residues: 218
  sheet: -0.69 (0.83), residues: 32
  loop : -3.49 (0.46), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 413 
 TYR   0.013   0.002   TYR C 329 
 PHE   0.011   0.002   PHE C 197 
 TRP   0.022   0.002   TRP C 433 
 HIS   0.006   0.002   HIS C 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (23429)
  covalent geometry    : angle       0.70674 (35792)
  hydrogen bonds       : bond        0.07170 (  888)
  hydrogen bonds       : angle       2.80830 ( 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  : 0.283 
Fit side-chains
REVERT: C   34 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8104 (mm-30)
REVERT: C   70 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8217 (mm)
REVERT: C  246 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7760 (mtm)
  outliers start: 15
  outliers final: 10
  residues processed: 57
  average time/residue: 0.1707
  time to fit residues: 14.7050
Evaluate side-chains
  56 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  117 VAL
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  268 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 90 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 115 optimal weight:    0.8980
   overall best weight:    3.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.118834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.090754 restraints weight = 57522.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.091937 restraints weight = 35553.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.091815 restraints weight = 25354.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.092258 restraints weight = 25311.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.092169 restraints weight = 21875.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.090  23429  Z= 0.314
  Angle     :  0.776   9.008  35792  Z= 0.386
  Chirality :  0.039   0.279   4644
  Planarity :  0.006   0.053   1417
  Dihedral  : 25.806 178.897  13361
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 20.00 %
    Favored  : 74.93 %
  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 aren not related in a simple way.
  whole: -2.01 (0.41), residues: 408
  helix:  0.06 (0.35), residues: 215
  sheet: -0.74 (0.85), residues: 32
  loop : -3.50 (0.45), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 137 
 TYR   0.017   0.002   TYR C 329 
 PHE   0.013   0.002   PHE C 197 
 TRP   0.024   0.003   TRP C 433 
 HIS   0.007   0.002   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 (23429)
  covalent geometry    : angle       0.77629 (35792)
  hydrogen bonds       : bond        0.07949 (  888)
  hydrogen bonds       : angle       3.00631 ( 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: 18
    poor density    : 45
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   34 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8232 (mm-30)
REVERT: C   70 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8345 (mm)
REVERT: C  246 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7802 (mtm)
  outliers start: 18
  outliers final: 13
  residues processed: 60
  average time/residue: 0.1525
  time to fit residues: 14.3800
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  117 VAL
Chi-restraints excluded: chain C residue  133 THR
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  382 GLN
Chi-restraints excluded: chain C residue  415 THR
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:    7.9990
   chunk 92 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 116 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    3.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.119337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.091701 restraints weight = 59097.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.093133 restraints weight = 37885.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.092989 restraints weight = 24536.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.093318 restraints weight = 25149.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.093383 restraints weight = 21598.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.092  23429  Z= 0.332
  Angle     :  0.794   8.932  35792  Z= 0.393
  Chirality :  0.039   0.281   4644
  Planarity :  0.006   0.056   1417
  Dihedral  : 25.825 178.771  13361
  Min Nonbonded Distance : 1.775

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 20.85 %
    Favored  : 74.37 %
  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 aren not related in a simple way.
  whole: -2.17 (0.41), residues: 408
  helix: -0.10 (0.35), residues: 215
  sheet: -0.59 (0.91), residues: 32
  loop : -3.59 (0.45), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 137 
 TYR   0.016   0.003   TYR C 329 
 PHE   0.013   0.002   PHE C 197 
 TRP   0.025   0.003   TRP C 433 
 HIS   0.007   0.002   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 (23429)
  covalent geometry    : angle       0.79375 (35792)
  hydrogen bonds       : bond        0.08170 (  888)
  hydrogen bonds       : angle       3.06288 ( 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
  64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: C   34 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8132 (mm-30)
REVERT: C   70 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8361 (mm)
REVERT: C  192 ASP cc_start: 0.6908 (m-30) cc_final: 0.6454 (m-30)
REVERT: C  246 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7887 (mtm)
  outliers start: 17
  outliers final: 15
  residues processed: 61
  average time/residue: 0.1704
  time to fit residues: 15.7870
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  : 0.317 
-------------------------------------------------------------------------------
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  184 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  224 PHE
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  379 HIS
Chi-restraints excluded: chain C residue  382 GLN
Chi-restraints excluded: chain C residue  415 THR
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:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 65 optimal weight:   20.0000
   chunk 76 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   chunk 45 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.123099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.096508 restraints weight = 58529.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.096706 restraints weight = 42458.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.097359 restraints weight = 31141.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.097461 restraints weight = 26575.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.097564 restraints weight = 24309.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  23429  Z= 0.183
  Angle     :  0.651   8.363  35792  Z= 0.325
  Chirality :  0.033   0.268   4644
  Planarity :  0.005   0.064   1417
  Dihedral  : 25.669 178.507  13361
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 21.41 %
    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 aren not related in a simple way.
  whole: -1.70 (0.42), residues: 408
  helix:  0.29 (0.36), residues: 218
  sheet: -0.86 (0.90), residues: 32
  loop : -3.33 (0.48), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  33 
 TYR   0.014   0.002   TYR C 143 
 PHE   0.014   0.002   PHE C 231 
 TRP   0.024   0.002   TRP C  59 
 HIS   0.005   0.001   HIS C 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (23429)
  covalent geometry    : angle       0.65074 (35792)
  hydrogen bonds       : bond        0.06681 (  888)
  hydrogen bonds       : angle       2.66929 ( 1725)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2981.91 seconds
wall clock time: 52 minutes 48.72 seconds (3168.72 seconds total)