Starting phenix.real_space_refine
on Wed Sep 17 05:28:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j09_61051/09_2025/9j09_61051_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j09_61051/09_2025/9j09_61051.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j09_61051/09_2025/9j09_61051_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j09_61051/09_2025/9j09_61051_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j09_61051/09_2025/9j09_61051.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j09_61051/09_2025/9j09_61051.map"
  }
  resolution = 2.95
  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=   0.068
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: 5
    Type Number    sf(0)   Gaussians
     P     149      5.49       5
     S       2      5.16       5
     C    2735      2.51       5
     N     971      2.21       5
     O    1370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 5227
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2053
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2053
          Classifications: {'peptide': 257}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 247}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "C"
      Number of atoms: 484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 484
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "D"
      Number of atoms: 250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 250
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "R"
      Number of atoms: 2440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 2440
          Classifications: {'RNA': 114}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 1, 'rna3p_pur': 58, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 7, 'rna3p': 106}
          Chain breaks: 4
  Time building chain proxies: 1.56, per 1000 atoms: 0.30
  Number of scatterers: 5227
  At special positions: 0
  Unit cell: (87.36, 97.92, 90.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     P     149     15.00
     O    1370      8.00
     N     971      7.00
     C    2735      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 73.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  484

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 2 sheets defined
      51.4% alpha, 12.5% beta
      46 base pairs and 101 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 63
      removed outlier: 3.865A  pdb=" N   ALA A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 80
      removed outlier: 4.150A  pdb=" N   LYS A  73 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLU A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS A  80 " --> pdb=" O   ASN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 86
      removed outlier: 6.906A  pdb=" N   ARG A  84 " --> pdb=" O   GLU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 97
    Processing helix  chain 'A' and resid 97 through 113
      removed outlier: 3.717A  pdb=" N   GLU A 101 " --> pdb=" O   TYR A  97 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   GLU A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 122
      removed outlier: 3.713A  pdb=" N   VAL A 121 " --> pdb=" O   ASP A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 161
      removed outlier: 3.746A  pdb=" N   GLY A 145 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A 146 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 209
    Processing helix  chain 'A' and resid 233 through 241
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18
      removed outlier: 6.709A  pdb=" N   ARG A 257 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ARG A 253 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   TYR A 259 " --> pdb=" O   VAL A 251 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL A 251 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   SER A 261 " --> pdb=" O   TYR A 249 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   TYR A 249 " --> pdb=" O   SER A 261 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU A 263 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS A 265 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LYS A 245 " --> pdb=" O   LYS A 265 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193

    104 hydrogen bonds defined for protein.
    300 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      112 hydrogen bonds
      212 hydrogen bond angles
      0 basepair planarities
      46 basepair parallelities
      101 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.54 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: 553
        1.32 -     1.44: 2385
        1.44 -     1.56: 2417
        1.56 -     1.68: 292
        1.68 -     1.80: 4
  Bond restraints: 5651
  Sorted by residual:
  bond pdb=" C   ILE A 227 "
       pdb=" O   ILE A 227 "
    ideal  model  delta    sigma   weight residual
    1.235  1.197  0.038 1.05e-02 9.07e+03 1.34e+01
  bond pdb=" O5'   U R  -3 "
       pdb=" C5'   U R  -3 "
    ideal  model  delta    sigma   weight residual
    1.420  1.466 -0.046 1.50e-02 4.44e+03 9.32e+00
  bond pdb=" O5'   G R  -6 "
       pdb=" C5'   G R  -6 "
    ideal  model  delta    sigma   weight residual
    1.420  1.458 -0.038 1.50e-02 4.44e+03 6.57e+00
  bond pdb=" N   SER A 222 "
       pdb=" CA  SER A 222 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.42e+00
  bond pdb=" P     U R  -4 "
       pdb=" O5'   U R  -4 "
    ideal  model  delta    sigma   weight residual
    1.593  1.629 -0.036 1.50e-02 4.44e+03 5.83e+00
  ... (remaining 5646 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.13: 8138
        4.13 -     8.26: 200
        8.26 -    12.40: 9
       12.40 -    16.53: 2
       16.53 -    20.66: 1
  Bond angle restraints: 8350
  Sorted by residual:
  angle pdb=" O3'   U R   4 "
        pdb=" P     C R   5 "
        pdb=" O5'   C R   5 "
      ideal   model   delta    sigma   weight residual
     104.00  124.66  -20.66 1.50e+00 4.44e-01 1.90e+02
  angle pdb=" O4'   C R   0 "
        pdb=" C1'   C R   0 "
        pdb=" C2'   C R   0 "
      ideal   model   delta    sigma   weight residual
     105.80   99.15    6.65 1.00e+00 1.00e+00 4.42e+01
  angle pdb=" C3'   U R   3 "
        pdb=" C2'   U R   3 "
        pdb=" O2'   U R   3 "
      ideal   model   delta    sigma   weight residual
     110.70  120.08   -9.38 1.50e+00 4.44e-01 3.91e+01
  angle pdb=" O2'   U R   3 "
        pdb=" C2'   U R   3 "
        pdb=" C1'   U R   3 "
      ideal   model   delta    sigma   weight residual
     108.40   99.15    9.25 1.50e+00 4.44e-01 3.80e+01
  angle pdb=" O3'   U R   3 "
        pdb=" C3'   U R   3 "
        pdb=" C2'   U R   3 "
      ideal   model   delta    sigma   weight residual
     113.70  122.85   -9.15 1.50e+00 4.44e-01 3.72e+01
  ... (remaining 8345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.25: 2826
       33.25 -    66.50: 508
       66.50 -    99.75: 52
       99.75 -   133.01: 3
      133.01 -   166.26: 1
  Dihedral angle restraints: 3390
    sinusoidal: 2634
      harmonic: 756
  Sorted by residual:
  dihedral pdb=" O4'   C R -68 "
           pdb=" C1'   C R -68 "
           pdb=" N1    C R -68 "
           pdb=" C2    C R -68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   33.74  166.26     1      1.50e+01 4.44e-03 8.41e+01
  dihedral pdb=" C5'   A R-152 "
           pdb=" C4'   A R-152 "
           pdb=" C3'   A R-152 "
           pdb=" O3'   A R-152 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  102.98   44.02     1      8.00e+00 1.56e-02 4.21e+01
  dihedral pdb=" O4'   G R-145 "
           pdb=" C2'   G R-145 "
           pdb=" C1'   G R-145 "
           pdb=" C3'   G R-145 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -17.70   42.70     1      8.00e+00 1.56e-02 3.98e+01
  ... (remaining 3387 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.143: 904
       0.143 -    0.285: 45
       0.285 -    0.428: 7
       0.428 -    0.571: 37
       0.571 -    0.714: 18
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" P    DC D -11 "
            pdb=" OP1  DC D -11 "
            pdb=" OP2  DC D -11 "
            pdb=" O5'  DC D -11 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.06   -0.71 2.00e-01 2.50e+01 1.27e+01
  chirality pdb=" P     C R   0 "
            pdb=" OP1   C R   0 "
            pdb=" OP2   C R   0 "
            pdb=" O5'   C R   0 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.10   -0.69 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" P     G R  10 "
            pdb=" OP1   G R  10 "
            pdb=" OP2   G R  10 "
            pdb=" O5'   G R  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.10   -0.69 2.00e-01 2.50e+01 1.20e+01
  ... (remaining 1008 not shown)

  Planarity restraints: 519
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG C  27 "   -0.052 2.00e-02 2.50e+03   2.14e-02 1.38e+01
        pdb=" N9   DG C  27 "    0.046 2.00e-02 2.50e+03
        pdb=" C8   DG C  27 "    0.010 2.00e-02 2.50e+03
        pdb=" N7   DG C  27 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG C  27 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DG C  27 "   -0.008 2.00e-02 2.50e+03
        pdb=" O6   DG C  27 "   -0.013 2.00e-02 2.50e+03
        pdb=" N1   DG C  27 "   -0.008 2.00e-02 2.50e+03
        pdb=" C2   DG C  27 "    0.004 2.00e-02 2.50e+03
        pdb=" N2   DG C  27 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DG C  27 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DG C  27 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG C  17 "    0.024 2.00e-02 2.50e+03   1.41e-02 5.95e+00
        pdb=" N9   DG C  17 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8   DG C  17 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DG C  17 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5   DG C  17 "    0.008 2.00e-02 2.50e+03
        pdb=" C6   DG C  17 "    0.006 2.00e-02 2.50e+03
        pdb=" O6   DG C  17 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DG C  17 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG C  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG C  17 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3   DG C  17 "    0.011 2.00e-02 2.50e+03
        pdb=" C4   DG C  17 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U R   4 "   -0.029 2.00e-02 2.50e+03   1.48e-02 4.96e+00
        pdb=" N1    U R   4 "    0.028 2.00e-02 2.50e+03
        pdb=" C2    U R   4 "    0.000 2.00e-02 2.50e+03
        pdb=" O2    U R   4 "    0.009 2.00e-02 2.50e+03
        pdb=" N3    U R   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    U R   4 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U R   4 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    U R   4 "    0.009 2.00e-02 2.50e+03
        pdb=" C6    U R   4 "    0.004 2.00e-02 2.50e+03
  ... (remaining 516 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 119
        2.61 -     3.18: 4028
        3.18 -     3.76: 9633
        3.76 -     4.33: 12155
        4.33 -     4.90: 17212
  Nonbonded interactions: 43147
  Sorted by model distance:
  nonbonded pdb=" O2'   A R -55 "
            pdb=" O4'   U R -54 "
     model   vdw
     2.040 3.040
  nonbonded pdb=" OD2 ASP A 117 "
            pdb=" OG  SER A 119 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O2'   C R -94 "
            pdb=" O4    U R -57 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O2    U R -41 "
            pdb=" N2    G R -10 "
     model   vdw
     2.335 2.496
  nonbonded pdb=" NH1 ARG A 253 "
            pdb=" O   ALA A 255 "
     model   vdw
     2.362 3.120
  ... (remaining 43142 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.380
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4548
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      :  0.008   0.047   5651  Z= 0.422
  Angle     :  1.363  20.659   8350  Z= 0.720
  Chirality :  0.144   0.714   1011
  Planarity :  0.005   0.050    519
  Dihedral  : 26.407 166.258   2906
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.20 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  :  1.98 %
    Favored  : 93.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.52), residues: 255
  helix:  1.25 (0.47), residues: 121
  sheet: -0.19 (0.83), residues: 41
  loop : -2.42 (0.57), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 217 
 TYR   0.015   0.002   TYR A 195 
 PHE   0.011   0.002   PHE A 156 
 TRP   0.012   0.001   TRP A 153 
 HIS   0.015   0.004   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00785 ( 5651)
  covalent geometry    : angle       1.36291 ( 8350)
  hydrogen bonds       : bond        0.18463 (  216)
  hydrogen bonds       : angle       9.15292 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   11 ASN cc_start: 0.7118 (p0) cc_final: 0.6893 (p0)
REVERT: A   97 TYR cc_start: 0.5966 (m-80) cc_final: 0.5723 (m-80)
REVERT: A  104 ARG cc_start: 0.4942 (ttp80) cc_final: 0.4389 (mtm110)
REVERT: A  106 GLU cc_start: 0.4706 (tt0) cc_final: 0.3879 (tp30)
REVERT: A  176 LYS cc_start: 0.7044 (mttp) cc_final: 0.6755 (mttp)
REVERT: A  181 ARG cc_start: 0.3146 (mtp180) cc_final: 0.1434 (ptp90)
REVERT: A  191 LYS cc_start: 0.6689 (tppp) cc_final: 0.4732 (pmtt)
  outliers start: 10
  outliers final: 1
  residues processed: 34
  average time/residue: 0.9100
  time to fit residues: 31.7821
Evaluate side-chains
  17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.1980
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 139 GLN
A 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4935 r_free = 0.4935 target = 0.265756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.239611 restraints weight = 4445.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.4723 rms_B_bonded: 0.71
r_work: 0.4331 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6495
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5651  Z= 0.214
  Angle     :  0.796   5.966   8350  Z= 0.420
  Chirality :  0.044   0.282   1011
  Planarity :  0.006   0.049    519
  Dihedral  : 26.709 179.649   2435
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.41 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.90 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.53), residues: 255
  helix:  1.48 (0.47), residues: 118
  sheet: -1.16 (0.77), residues: 49
  loop : -2.52 (0.59), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 181 
 TYR   0.021   0.002   TYR A 195 
 PHE   0.012   0.002   PHE A 156 
 TRP   0.016   0.002   TRP A 153 
 HIS   0.003   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 5651)
  covalent geometry    : angle       0.79629 ( 8350)
  hydrogen bonds       : bond        0.08227 (  216)
  hydrogen bonds       : angle       4.21637 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 15
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7537 (mtm110)
REVERT: A  106 GLU cc_start: 0.6883 (tt0) cc_final: 0.6613 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 19
  average time/residue: 0.7196
  time to fit residues: 14.2444
Evaluate side-chains
  14 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 13
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0870
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4949 r_free = 0.4949 target = 0.263741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.219034 restraints weight = 4292.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.4421 rms_B_bonded: 1.41
r_work: 0.3981 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.4270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067   5651  Z= 0.364
  Angle     :  1.004  12.105   8350  Z= 0.519
  Chirality :  0.054   0.352   1011
  Planarity :  0.009   0.066    519
  Dihedral  : 26.843 174.861   2435
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  : 10.20 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 10.89 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.76 (0.49), residues: 255
  helix:  0.29 (0.46), residues: 117
  sheet: -1.57 (0.74), residues: 49
  loop : -2.88 (0.54), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 181 
 TYR   0.024   0.004   TYR A 206 
 PHE   0.015   0.003   PHE A 156 
 TRP   0.019   0.003   TRP A 153 
 HIS   0.006   0.002   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00755 ( 5651)
  covalent geometry    : angle       1.00382 ( 8350)
  hydrogen bonds       : bond        0.11239 (  216)
  hydrogen bonds       : angle       4.85764 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 17
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5531 (tp)
REVERT: A  101 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6365 (pt0)
REVERT: A  133 TRP cc_start: 0.6923 (p-90) cc_final: 0.5522 (p-90)
  outliers start: 11
  outliers final: 5
  residues processed: 25
  average time/residue: 0.7080
  time to fit residues: 18.4563
Evaluate side-chains
  23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 16
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  175 LYS
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 0 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0570
   chunk 1 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5007 r_free = 0.5007 target = 0.271606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.233368 restraints weight = 4323.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.4670 rms_B_bonded: 1.20
r_work: 0.4258 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.4258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5651  Z= 0.180
  Angle     :  0.714   6.569   8350  Z= 0.381
  Chirality :  0.041   0.222   1011
  Planarity :  0.006   0.045    519
  Dihedral  : 26.252 177.303   2435
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  7.84 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.84 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.52), residues: 255
  helix:  1.15 (0.47), residues: 119
  sheet: -1.51 (0.74), residues: 49
  loop : -2.49 (0.58), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 253 
 TYR   0.018   0.002   TYR A 195 
 PHE   0.015   0.002   PHE A 156 
 TRP   0.013   0.002   TRP A 153 
 HIS   0.002   0.001   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5651)
  covalent geometry    : angle       0.71409 ( 8350)
  hydrogen bonds       : bond        0.07168 (  216)
  hydrogen bonds       : angle       4.16919 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7611 (mtp85)
  outliers start: 5
  outliers final: 2
  residues processed: 21
  average time/residue: 0.8095
  time to fit residues: 17.6610
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4974 r_free = 0.4974 target = 0.268160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.228013 restraints weight = 4363.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.4631 rms_B_bonded: 1.21
r_work: 0.4169 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.4685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5651  Z= 0.197
  Angle     :  0.720   6.749   8350  Z= 0.383
  Chirality :  0.040   0.221   1011
  Planarity :  0.006   0.039    519
  Dihedral  : 26.096 176.133   2435
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.02 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.83 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.52), residues: 255
  helix:  1.29 (0.47), residues: 119
  sheet: -1.68 (0.73), residues: 49
  loop : -2.50 (0.57), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 181 
 TYR   0.018   0.002   TYR A 195 
 PHE   0.015   0.002   PHE A 156 
 TRP   0.012   0.002   TRP A 153 
 HIS   0.005   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5651)
  covalent geometry    : angle       0.72023 ( 8350)
  hydrogen bonds       : bond        0.07454 (  216)
  hydrogen bonds       : angle       4.07480 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 17
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.6010 (tp)
REVERT: A   49 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6285 (mp0)
REVERT: A  104 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7538 (mtm110)
REVERT: A  139 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.6114 (mm-40)
  outliers start: 7
  outliers final: 2
  residues processed: 24
  average time/residue: 0.7992
  time to fit residues: 19.8524
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  139 GLN
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4939 r_free = 0.4939 target = 0.262311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.219128 restraints weight = 4290.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.4420 rms_B_bonded: 1.35
r_work: 0.3958 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.5262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069   5651  Z= 0.352
  Angle     :  0.955  11.165   8350  Z= 0.494
  Chirality :  0.052   0.326   1011
  Planarity :  0.009   0.070    519
  Dihedral  : 26.495 177.388   2435
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.20 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 17.33 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.49), residues: 255
  helix:  0.13 (0.45), residues: 120
  sheet: -2.07 (0.69), residues: 49
  loop : -2.60 (0.57), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 181 
 TYR   0.025   0.004   TYR A 206 
 PHE   0.014   0.003   PHE A 156 
 TRP   0.020   0.003   TRP A 153 
 HIS   0.005   0.002   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00734 ( 5651)
  covalent geometry    : angle       0.95547 ( 8350)
  hydrogen bonds       : bond        0.10595 (  216)
  hydrogen bonds       : angle       4.62278 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 18
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  131 ASN cc_start: 0.7925 (m-40) cc_final: 0.7539 (m-40)
  outliers start: 9
  outliers final: 6
  residues processed: 26
  average time/residue: 0.6708
  time to fit residues: 18.1346
Evaluate side-chains
  24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    0.1980
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4998 r_free = 0.4998 target = 0.270009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.229400 restraints weight = 4310.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.4642 rms_B_bonded: 1.18
r_work: 0.4216 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
moved from start:          0.5257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5651  Z= 0.178
  Angle     :  0.693   6.521   8350  Z= 0.372
  Chirality :  0.040   0.214   1011
  Planarity :  0.005   0.040    519
  Dihedral  : 26.184 175.980   2435
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.02 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.32 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.52), residues: 255
  helix:  1.18 (0.47), residues: 119
  sheet: -1.85 (0.73), residues: 49
  loop : -2.38 (0.58), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 140 
 TYR   0.016   0.002   TYR A 195 
 PHE   0.014   0.002   PHE A 156 
 TRP   0.012   0.002   TRP A 153 
 HIS   0.003   0.001   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5651)
  covalent geometry    : angle       0.69326 ( 8350)
  hydrogen bonds       : bond        0.06662 (  216)
  hydrogen bonds       : angle       4.04298 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   49 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6409 (mp0)
REVERT: A  104 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7511 (mtp85)
REVERT: A  131 ASN cc_start: 0.7694 (m-40) cc_final: 0.7331 (m-40)
  outliers start: 7
  outliers final: 3
  residues processed: 25
  average time/residue: 0.7539
  time to fit residues: 19.5400
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.266182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.244428 restraints weight = 4294.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.4790 rms_B_bonded: 0.63
r_work: 0.4492 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.4492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6473
moved from start:          0.5437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5651  Z= 0.249
  Angle     :  0.790   6.796   8350  Z= 0.416
  Chirality :  0.044   0.250   1011
  Planarity :  0.007   0.045    519
  Dihedral  : 26.236 178.129   2435
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.20 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.82 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.51), residues: 255
  helix:  1.02 (0.47), residues: 117
  sheet: -2.04 (0.72), residues: 49
  loop : -2.44 (0.56), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 181 
 TYR   0.020   0.003   TYR A 195 
 PHE   0.016   0.002   PHE A 156 
 TRP   0.015   0.002   TRP A 153 
 HIS   0.006   0.002   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 5651)
  covalent geometry    : angle       0.79006 ( 8350)
  hydrogen bonds       : bond        0.08319 (  216)
  hydrogen bonds       : angle       4.20782 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 17
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  131 ASN cc_start: 0.7520 (m-40) cc_final: 0.7289 (m-40)
  outliers start: 7
  outliers final: 4
  residues processed: 24
  average time/residue: 0.6435
  time to fit residues: 16.1369
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   chunk 36 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.268815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.238848 restraints weight = 4314.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.4749 rms_B_bonded: 0.84
r_work: 0.4238 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.5514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5651  Z= 0.197
  Angle     :  0.717   6.541   8350  Z= 0.382
  Chirality :  0.040   0.222   1011
  Planarity :  0.006   0.041    519
  Dihedral  : 26.116 176.852   2435
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.02 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.81 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.52), residues: 255
  helix:  1.25 (0.47), residues: 119
  sheet: -1.91 (0.73), residues: 49
  loop : -2.33 (0.58), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 181 
 TYR   0.017   0.002   TYR A 195 
 PHE   0.015   0.002   PHE A 156 
 TRP   0.013   0.002   TRP A 153 
 HIS   0.007   0.002   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5651)
  covalent geometry    : angle       0.71694 ( 8350)
  hydrogen bonds       : bond        0.07048 (  216)
  hydrogen bonds       : angle       4.07545 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 16
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  131 ASN cc_start: 0.7782 (m-40) cc_final: 0.7436 (m-40)
  outliers start: 5
  outliers final: 3
  residues processed: 21
  average time/residue: 0.6932
  time to fit residues: 15.1847
Evaluate side-chains
  19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 16
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4977 r_free = 0.4977 target = 0.267200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.232463 restraints weight = 4347.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.4689 rms_B_bonded: 0.96
r_work (final): 0.4689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6274
moved from start:          0.5676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5651  Z= 0.222
  Angle     :  0.755   6.763   8350  Z= 0.399
  Chirality :  0.042   0.224   1011
  Planarity :  0.006   0.041    519
  Dihedral  : 26.111 177.850   2435
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  9.41 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.81 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.52), residues: 255
  helix:  1.24 (0.48), residues: 117
  sheet: -2.03 (0.72), residues: 49
  loop : -2.35 (0.57), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 181 
 TYR   0.020   0.002   TYR A 195 
 PHE   0.016   0.002   PHE A 156 
 TRP   0.015   0.002   TRP A 153 
 HIS   0.008   0.002   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 5651)
  covalent geometry    : angle       0.75539 ( 8350)
  hydrogen bonds       : bond        0.07711 (  216)
  hydrogen bonds       : angle       4.12455 (  512)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 16
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A  131 ASN cc_start: 0.7369 (m-40) cc_final: 0.7150 (m-40)
  outliers start: 5
  outliers final: 4
  residues processed: 21
  average time/residue: 0.6081
  time to fit residues: 13.3466
Evaluate side-chains
  20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  227 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0980
   chunk 10 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5004 r_free = 0.5004 target = 0.270781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.233661 restraints weight = 4418.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.4684 rms_B_bonded: 1.05
r_work: 0.4223 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6757
moved from start:          0.5755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5651  Z= 0.174
  Angle     :  0.677   6.651   8350  Z= 0.362
  Chirality :  0.038   0.184   1011
  Planarity :  0.006   0.041    519
  Dihedral  : 25.989 175.045   2435
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.63 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.82 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.53), residues: 255
  helix:  1.50 (0.48), residues: 119
  sheet: -1.82 (0.74), residues: 49
  loop : -2.21 (0.59), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 181 
 TYR   0.016   0.002   TYR A 195 
 PHE   0.015   0.001   PHE A 156 
 TRP   0.014   0.002   TRP A 153 
 HIS   0.009   0.002   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5651)
  covalent geometry    : angle       0.67735 ( 8350)
  hydrogen bonds       : bond        0.06439 (  216)
  hydrogen bonds       : angle       3.97220 (  512)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1720.99 seconds
wall clock time: 30 minutes 10.14 seconds (1810.14 seconds total)