Starting phenix.real_space_refine
on Tue Mar  3 13:21:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xlt_33286/03_2026/7xlt_33286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xlt_33286/03_2026/7xlt_33286.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xlt_33286/03_2026/7xlt_33286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xlt_33286/03_2026/7xlt_33286.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xlt_33286/03_2026/7xlt_33286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xlt_33286/03_2026/7xlt_33286.map"
  }
  resolution = 4.4
  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=  -0.001 sd=   0.046
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      78      5.49       5
     S      14      5.16       5
     C    2869      2.51       5
     N     845      2.21       5
     O    1179      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4985
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1635
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 11, 'TRANS': 203}
    Chain: "L"
      Number of atoms: 1676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1676
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 11, 'TRANS': 204}
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 801
          Classifications: {'DNA': 40}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 39}
    Chain: "B"
      Number of atoms: 873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 873
          Classifications: {'RNA': 40}
          Modifications used: {'5*END': 1, 'rna3p_pur': 32, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 39}
  Time building chain proxies: 1.28, per 1000 atoms: 0.26
  Number of scatterers: 4985
  At special positions: 0
  Unit cell: (125.465, 106.918, 93.826, 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      14     16.00
     P      78     15.00
     O    1179      8.00
     N     845      7.00
     C    2869      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 146 " - pdb=" SG  CYS H 201 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 139 " - pdb=" SG  CYS L 199 " distance=2.04

  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: 0.44
  Conformation dependent library (CDL) restraints added in 221.1 milliseconds
  

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  796

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 9 sheets defined
      5.6% alpha, 36.0% beta
      41 base pairs and 55 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.606A  pdb=" N   ASP H  90 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'H' and resid 176 through 180
    Processing helix  chain 'H' and resid 192 through 194
      No H-bonds generated for 'chain 'H' and resid 192 through 194'
    Processing helix  chain 'L' and resid 126 through 131
    Processing helix  chain 'L' and resid 188 through 192
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.340A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   VAL H  33 " --> pdb=" O   ASP H  99 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   MET H  34 " --> pdb=" O   PHE H  50 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   PHE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.340A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TYR H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 129
      removed outlier: 3.988A  pdb=" N   SER H 186 " --> pdb=" O   HIS H 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 50 through 53
      removed outlier: 5.817A  pdb=" N   LEU L  51 " --> pdb=" O   LEU L  42 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   LEU L  42 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR L 107 " --> pdb=" O   TYR L  91 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   CYS L  93 " --> pdb=" O   GLY L 105 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   GLY L 105 " --> pdb=" O   CYS L  93 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 119 through 123
    Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 155

    108 hydrogen bonds defined for protein.
    264 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      102 hydrogen bonds
      200 hydrogen bond angles
      0 basepair planarities
      41 basepair parallelities
      55 stacking parallelities
  Total time for adding SS restraints: 0.72

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1253
        1.34 -     1.46: 1731
        1.46 -     1.58: 2107
        1.58 -     1.70: 156
        1.70 -     1.82: 19
  Bond restraints: 5266
  Sorted by residual:
  bond pdb=" CA  VAL L  99 "
       pdb=" CB  VAL L  99 "
    ideal  model  delta    sigma   weight residual
    1.534  1.551 -0.017 6.80e-03 2.16e+04 6.17e+00
  bond pdb=" C   GLU H 154 "
       pdb=" N   PRO H 155 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 5.02e+00
  bond pdb=" C   VAL L  99 "
       pdb=" N   PRO L 100 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 5.00e+00
  bond pdb=" CA  VAL L  99 "
       pdb=" C   VAL L  99 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 8.80e-03 1.29e+04 4.68e+00
  bond pdb=" O5'   C B  10 "
       pdb=" C5'   C B  10 "
    ideal  model  delta    sigma   weight residual
    1.420  1.452 -0.032 1.50e-02 4.44e+03 4.65e+00
  ... (remaining 5261 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 7219
        2.07 -     4.14: 247
        4.14 -     6.21: 41
        6.21 -     8.29: 10
        8.29 -    10.36: 3
  Bond angle restraints: 7520
  Sorted by residual:
  angle pdb=" C   HIS L  98 "
        pdb=" N   VAL L  99 "
        pdb=" CA  VAL L  99 "
      ideal   model   delta    sigma   weight residual
     120.24  123.82   -3.58 6.30e-01 2.52e+00 3.22e+01
  angle pdb=" C   PRO H 153 "
        pdb=" N   GLU H 154 "
        pdb=" CA  GLU H 154 "
      ideal   model   delta    sigma   weight residual
     120.09  125.72   -5.63 1.25e+00 6.40e-01 2.03e+01
  angle pdb=" CA  VAL L  99 "
        pdb=" C   VAL L  99 "
        pdb=" N   PRO L 100 "
      ideal   model   delta    sigma   weight residual
     121.00  123.99   -2.99 8.30e-01 1.45e+00 1.30e+01
  angle pdb=" CA  GLU H  82 "
        pdb=" CB  GLU H  82 "
        pdb=" CG  GLU H  82 "
      ideal   model   delta    sigma   weight residual
     114.10  121.30   -7.20 2.00e+00 2.50e-01 1.30e+01
  angle pdb=" CB  MET L 180 "
        pdb=" CG  MET L 180 "
        pdb=" SD  MET L 180 "
      ideal   model   delta    sigma   weight residual
     112.70  123.06  -10.36 3.00e+00 1.11e-01 1.19e+01
  ... (remaining 7515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.74: 2374
       15.74 -    31.49: 398
       31.49 -    47.23: 133
       47.23 -    62.97: 53
       62.97 -    78.72: 33
  Dihedral angle restraints: 2991
    sinusoidal: 1743
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CA  ASN L  58 "
           pdb=" C   ASN L  58 "
           pdb=" N   ARG L  59 "
           pdb=" CA  ARG L  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.04  -24.96     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  VAL H 156 "
           pdb=" C   VAL H 156 "
           pdb=" N   THR H 157 "
           pdb=" CA  THR H 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.62  -24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  TYR H  80 "
           pdb=" C   TYR H  80 "
           pdb=" N   MET H  81 "
           pdb=" CA  MET H  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.33   22.67     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 2988 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 807
       0.086 -    0.172: 59
       0.172 -    0.258: 4
       0.258 -    0.344: 3
       0.344 -    0.430: 1
  Chirality restraints: 874
  Sorted by residual:
  chirality pdb=" P     C B  37 "
            pdb=" OP1   C B  37 "
            pdb=" OP2   C B  37 "
            pdb=" O5'   C B  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.84   -0.43 2.00e-01 2.50e+01 4.62e+00
  chirality pdb=" CB  ILE L 155 "
            pdb=" CA  ILE L 155 "
            pdb=" CG1 ILE L 155 "
            pdb=" CG2 ILE L 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" P     C B  10 "
            pdb=" OP1   C B  10 "
            pdb=" OP2   C B  10 "
            pdb=" O5'   C B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.71   -0.30 2.00e-01 2.50e+01 2.30e+00
  ... (remaining 871 not shown)

  Planarity restraints: 662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR L   7 "   -0.036 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO L   8 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 108 "    0.016 2.00e-02 2.50e+03   1.50e-02 4.50e+00
        pdb=" CG  TYR H 108 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 108 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 108 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 108 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 108 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H 108 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP H 107 "   -0.009 2.00e-02 2.50e+03   1.92e-02 3.70e+00
        pdb=" CG  ASP H 107 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASP H 107 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP H 107 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 659 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1322
        2.81 -     3.33: 3795
        3.33 -     3.86: 9088
        3.86 -     4.38: 9680
        4.38 -     4.90: 15108
  Nonbonded interactions: 38993
  Sorted by model distance:
  nonbonded pdb=" O   GLY H   8 "
            pdb=" OG1 THR H 113 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OG  SER H 141 "
            pdb=" O   VAL H 189 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OG  SER L  57 "
            pdb=" O   GLY L  69 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG  SER L  25 "
            pdb=" O   GLN L  27 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" NH1 ARG L  66 "
            pdb=" OE2 GLU L  84 "
     model   vdw
     2.369 3.120
  ... (remaining 38988 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:             0.370
  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:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.570
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5953
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5270  Z= 0.214
  Angle     :  0.888  10.357   7528  Z= 0.482
  Chirality :  0.050   0.430    874
  Planarity :  0.006   0.055    662
  Dihedral  : 18.802  78.716   2183
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 34.30 %
    Favored  : 64.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.39), residues: 427
  helix: -3.85 (0.81), residues: 12
  sheet:  0.01 (0.39), residues: 188
  loop : -2.75 (0.37), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  66 
 TYR   0.037   0.002   TYR H 108 
 PHE   0.024   0.002   PHE L  94 
 TRP   0.024   0.003   TRP L 168 
 HIS   0.012   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 5266)
  covalent geometry    : angle       0.88698 ( 7520)
  SS BOND              : bond        0.00513 (    4)
  SS BOND              : angle       1.39737 (    8)
  hydrogen bonds       : bond        0.10362 (  206)
  hydrogen bonds       : angle       7.41819 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  107 THR cc_start: 0.6878 (m) cc_final: 0.6515 (m)
REVERT: L  171 GLN cc_start: 0.6884 (tp40) cc_final: 0.6116 (tp-100)
  outliers start: 3
  outliers final: 1
  residues processed: 71
  average time/residue: 0.0786
  time to fit residues: 7.1593
Evaluate side-chains
  62 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
L  43 GLN
** L 166 ASN ** 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 = 0.4565 r_free = 0.4565 target = 0.146226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.117032 restraints weight = 34291.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.118534 restraints weight = 22297.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.120310 restraints weight = 16569.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.120942 restraints weight = 13508.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.121418 restraints weight = 11911.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5270  Z= 0.187
  Angle     :  0.696   8.544   7528  Z= 0.372
  Chirality :  0.038   0.159    874
  Planarity :  0.005   0.054    662
  Dihedral  : 16.419  73.718   1436
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.39), residues: 427
  helix: -3.79 (0.69), residues: 18
  sheet: -0.03 (0.39), residues: 178
  loop : -2.53 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  82 
 TYR   0.015   0.002   TYR H  27 
 PHE   0.027   0.003   PHE H 106 
 TRP   0.013   0.003   TRP H 105 
 HIS   0.009   0.002   HIS H 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 5266)
  covalent geometry    : angle       0.69477 ( 7520)
  SS BOND              : bond        0.00557 (    4)
  SS BOND              : angle       1.32610 (    8)
  hydrogen bonds       : bond        0.05404 (  206)
  hydrogen bonds       : angle       6.48748 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: H   20 MET cc_start: 0.8091 (tpp) cc_final: 0.7519 (tpt)
REVERT: L   60 PHE cc_start: 0.6326 (t80) cc_final: 0.6085 (t80)
REVERT: L   61 SER cc_start: 0.8780 (m) cc_final: 0.8553 (p)
REVERT: L   78 LEU cc_start: 0.9055 (tt) cc_final: 0.8444 (tt)
REVERT: L   92 TYR cc_start: 0.7959 (m-10) cc_final: 0.7619 (m-80)
REVERT: L  102 THR cc_start: 0.7952 (m) cc_final: 0.7657 (m)
REVERT: L  142 ASN cc_start: 0.8254 (t0) cc_final: 0.7971 (m-40)
REVERT: L  180 MET cc_start: 0.7296 (mmm) cc_final: 0.6382 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0762
  time to fit residues: 6.7720
Evaluate side-chains
  52 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 48 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    5.9388

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 202 ASN
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 129 GLN
** L 166 ASN ** 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 = 0.4438 r_free = 0.4438 target = 0.133603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.107431 restraints weight = 33334.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.106561 restraints weight = 25399.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.107059 restraints weight = 19112.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.107296 restraints weight = 16616.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.107415 restraints weight = 14485.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072   5270  Z= 0.303
  Angle     :  0.839   9.533   7528  Z= 0.446
  Chirality :  0.043   0.187    874
  Planarity :  0.007   0.074    662
  Dihedral  : 16.997  74.250   1436
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 29.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.80 %
    Favored  : 93.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.39), residues: 427
  helix: -3.64 (0.66), residues: 19
  sheet: -0.27 (0.40), residues: 169
  loop : -2.74 (0.36), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  59 
 TYR   0.028   0.003   TYR L  91 
 PHE   0.021   0.003   PHE L  76 
 TRP   0.019   0.004   TRP L  40 
 HIS   0.011   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00663 ( 5266)
  covalent geometry    : angle       0.83767 ( 7520)
  SS BOND              : bond        0.00655 (    4)
  SS BOND              : angle       1.57925 (    8)
  hydrogen bonds       : bond        0.08261 (  206)
  hydrogen bonds       : angle       7.45217 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   92 TYR cc_start: 0.8073 (m-10) cc_final: 0.7466 (m-10)
REVERT: L  149 ILE cc_start: 0.6563 (mm) cc_final: 0.6229 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0676
  time to fit residues: 4.5776
Evaluate side-chains
  42 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0570
   chunk 14 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   overall best weight:    5.0106

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.133515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.102921 restraints weight = 33109.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.104451 restraints weight = 22211.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.105653 restraints weight = 16736.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.106198 restraints weight = 13845.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.106887 restraints weight = 12337.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5270  Z= 0.257
  Angle     :  0.770   8.968   7528  Z= 0.413
  Chirality :  0.041   0.178    874
  Planarity :  0.006   0.054    662
  Dihedral  : 17.182  74.188   1436
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 28.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.65 (0.40), residues: 427
  helix: -3.00 (0.82), residues: 19
  sheet: -0.48 (0.39), residues: 179
  loop : -2.83 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  98 
 TYR   0.021   0.003   TYR L 191 
 PHE   0.030   0.003   PHE L  76 
 TRP   0.012   0.002   TRP H 109 
 HIS   0.003   0.001   HIS L  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 5266)
  covalent geometry    : angle       0.76786 ( 7520)
  SS BOND              : bond        0.00580 (    4)
  SS BOND              : angle       1.89043 (    8)
  hydrogen bonds       : bond        0.07162 (  206)
  hydrogen bonds       : angle       7.24736 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.143 
Fit side-chains
REVERT: H   36 TRP cc_start: 0.7763 (m100) cc_final: 0.7390 (m100)
REVERT: H   45 LEU cc_start: 0.8841 (mt) cc_final: 0.8573 (mt)
REVERT: H   74 LYS cc_start: 0.7663 (tptt) cc_final: 0.7441 (tppt)
REVERT: L   50 LYS cc_start: 0.7401 (mmpt) cc_final: 0.6825 (mmmt)
REVERT: L   92 TYR cc_start: 0.8031 (m-80) cc_final: 0.7722 (m-10)
REVERT: L  149 ILE cc_start: 0.6374 (mm) cc_final: 0.6096 (mm)
REVERT: L  181 SER cc_start: 0.8205 (t) cc_final: 0.7434 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0672
  time to fit residues: 4.3990
Evaluate side-chains
  44 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 46 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.137912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.107375 restraints weight = 32170.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.109452 restraints weight = 20362.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.110536 restraints weight = 14824.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.111815 restraints weight = 12006.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.112018 restraints weight = 10458.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5270  Z= 0.161
  Angle     :  0.683   9.580   7528  Z= 0.365
  Chirality :  0.038   0.156    874
  Planarity :  0.005   0.044    662
  Dihedral  : 16.961  73.849   1436
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 19.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.40), residues: 427
  helix: -3.40 (0.88), residues: 19
  sheet: -0.24 (0.40), residues: 169
  loop : -2.71 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG L 193 
 TYR   0.020   0.002   TYR H  27 
 PHE   0.018   0.002   PHE L  76 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5266)
  covalent geometry    : angle       0.68189 ( 7520)
  SS BOND              : bond        0.00513 (    4)
  SS BOND              : angle       1.27595 (    8)
  hydrogen bonds       : bond        0.05294 (  206)
  hydrogen bonds       : angle       6.70267 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: L   50 LYS cc_start: 0.7373 (mmpt) cc_final: 0.6932 (mmmt)
REVERT: L   92 TYR cc_start: 0.7952 (m-80) cc_final: 0.7549 (m-10)
REVERT: L  149 ILE cc_start: 0.6108 (mm) cc_final: 0.5763 (mm)
REVERT: L  181 SER cc_start: 0.8060 (t) cc_final: 0.7297 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0754
  time to fit residues: 5.4857
Evaluate side-chains
  49 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 49 optimal weight:   30.0000
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.137734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.107833 restraints weight = 33333.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.109302 restraints weight = 21698.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.110375 restraints weight = 15907.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.111443 restraints weight = 12845.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.111806 restraints weight = 11192.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.4422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5270  Z= 0.156
  Angle     :  0.658   8.022   7528  Z= 0.354
  Chirality :  0.038   0.163    874
  Planarity :  0.005   0.050    662
  Dihedral  : 16.828  73.813   1436
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.41), residues: 427
  helix: -3.08 (0.96), residues: 19
  sheet: -0.29 (0.40), residues: 177
  loop : -2.53 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  98 
 TYR   0.019   0.002   TYR H  27 
 PHE   0.019   0.002   PHE L  76 
 TRP   0.012   0.002   TRP H 105 
 HIS   0.013   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5266)
  covalent geometry    : angle       0.65714 ( 7520)
  SS BOND              : bond        0.00530 (    4)
  SS BOND              : angle       1.34417 (    8)
  hydrogen bonds       : bond        0.05295 (  206)
  hydrogen bonds       : angle       6.44463 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.152 
Fit side-chains
REVERT: H  107 ASP cc_start: 0.6518 (p0) cc_final: 0.5699 (p0)
REVERT: L    4 MET cc_start: 0.8420 (tmm) cc_final: 0.8147 (tmm)
REVERT: L   58 ASN cc_start: 0.6432 (t0) cc_final: 0.6207 (t0)
REVERT: L  149 ILE cc_start: 0.6272 (mm) cc_final: 0.6025 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0669
  time to fit residues: 4.7870
Evaluate side-chains
  46 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.136196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.105767 restraints weight = 32889.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.107803 restraints weight = 21075.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.108748 restraints weight = 15384.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.109560 restraints weight = 12554.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.109852 restraints weight = 11011.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.4716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5270  Z= 0.180
  Angle     :  0.687   7.605   7528  Z= 0.369
  Chirality :  0.039   0.254    874
  Planarity :  0.005   0.048    662
  Dihedral  : 16.818  73.914   1436
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 21.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.41), residues: 427
  helix: -2.84 (1.04), residues: 19
  sheet: -0.28 (0.40), residues: 173
  loop : -2.56 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 104 
 TYR   0.018   0.002   TYR H  27 
 PHE   0.019   0.002   PHE H 106 
 TRP   0.024   0.002   TRP L 168 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 5266)
  covalent geometry    : angle       0.68642 ( 7520)
  SS BOND              : bond        0.00486 (    4)
  SS BOND              : angle       1.32285 (    8)
  hydrogen bonds       : bond        0.05747 (  206)
  hydrogen bonds       : angle       6.45908 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: H  107 ASP cc_start: 0.5873 (p0) cc_final: 0.5604 (p0)
REVERT: L    4 MET cc_start: 0.8487 (tmm) cc_final: 0.8188 (tmm)
REVERT: L   58 ASN cc_start: 0.6516 (t0) cc_final: 0.6307 (t0)
REVERT: L  149 ILE cc_start: 0.6150 (mm) cc_final: 0.5906 (mm)
REVERT: L  180 MET cc_start: 0.7845 (mmp) cc_final: 0.7235 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0630
  time to fit residues: 4.3845
Evaluate side-chains
  46 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 46 optimal weight:   30.0000
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0970
   chunk 19 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.139997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.110812 restraints weight = 32736.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.112550 restraints weight = 21230.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.113547 restraints weight = 15541.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.114597 restraints weight = 12581.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.114953 restraints weight = 11056.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5270  Z= 0.132
  Angle     :  0.636   6.969   7528  Z= 0.340
  Chirality :  0.037   0.222    874
  Planarity :  0.004   0.050    662
  Dihedral  : 16.624  73.720   1436
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.40), residues: 427
  helix: -2.81 (1.01), residues: 19
  sheet: -0.22 (0.40), residues: 168
  loop : -2.46 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 104 
 TYR   0.013   0.002   TYR H  27 
 PHE   0.021   0.002   PHE L  60 
 TRP   0.029   0.002   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5266)
  covalent geometry    : angle       0.63546 ( 7520)
  SS BOND              : bond        0.00619 (    4)
  SS BOND              : angle       1.15961 (    8)
  hydrogen bonds       : bond        0.04653 (  206)
  hydrogen bonds       : angle       5.88316 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: H  107 ASP cc_start: 0.6367 (p0) cc_final: 0.5814 (p0)
REVERT: L    4 MET cc_start: 0.8438 (tmm) cc_final: 0.8023 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0590
  time to fit residues: 4.6701
Evaluate side-chains
  48 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    0.7980
   chunk 12 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.134069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.103116 restraints weight = 32542.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.104908 restraints weight = 21468.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.105843 restraints weight = 15995.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.106130 restraints weight = 13162.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.107442 restraints weight = 11895.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5270  Z= 0.213
  Angle     :  0.709   7.706   7528  Z= 0.378
  Chirality :  0.040   0.234    874
  Planarity :  0.005   0.049    662
  Dihedral  : 16.750  73.992   1436
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 24.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.40), residues: 427
  helix: -3.13 (0.86), residues: 18
  sheet: -0.43 (0.41), residues: 168
  loop : -2.50 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H 104 
 TYR   0.016   0.002   TYR H 100 
 PHE   0.025   0.002   PHE L  76 
 TRP   0.042   0.004   TRP H  36 
 HIS   0.014   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 5266)
  covalent geometry    : angle       0.70702 ( 7520)
  SS BOND              : bond        0.00706 (    4)
  SS BOND              : angle       1.71075 (    8)
  hydrogen bonds       : bond        0.06332 (  206)
  hydrogen bonds       : angle       6.51199 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.150 
Fit side-chains
REVERT: H   74 LYS cc_start: 0.7660 (tptt) cc_final: 0.7409 (tppt)
REVERT: H  107 ASP cc_start: 0.6478 (p0) cc_final: 0.6104 (p0)
REVERT: L    4 MET cc_start: 0.8522 (tmm) cc_final: 0.8204 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0684
  time to fit residues: 4.5417
Evaluate side-chains
  45 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 42 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 47 optimal weight:   10.9990
   chunk 49 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.135296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.104834 restraints weight = 33707.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.106325 restraints weight = 22240.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.107407 restraints weight = 16859.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.108333 restraints weight = 13863.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.108743 restraints weight = 12233.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5270  Z= 0.185
  Angle     :  0.695   7.833   7528  Z= 0.372
  Chirality :  0.040   0.238    874
  Planarity :  0.005   0.049    662
  Dihedral  : 16.815  73.940   1436
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 22.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.40), residues: 427
  helix: -3.81 (0.62), residues: 19
  sheet: -0.61 (0.42), residues: 157
  loop : -2.46 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H 104 
 TYR   0.015   0.002   TYR L  91 
 PHE   0.023   0.002   PHE L  76 
 TRP   0.041   0.004   TRP H  36 
 HIS   0.008   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 5266)
  covalent geometry    : angle       0.69310 ( 7520)
  SS BOND              : bond        0.00532 (    4)
  SS BOND              : angle       1.59236 (    8)
  hydrogen bonds       : bond        0.05688 (  206)
  hydrogen bonds       : angle       6.41911 (  464)

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

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

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  854 Ramachandran restraints generated.
    427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: H   74 LYS cc_start: 0.7600 (tptt) cc_final: 0.7337 (tppt)
REVERT: H  105 TRP cc_start: 0.7828 (p-90) cc_final: 0.7607 (p-90)
REVERT: H  107 ASP cc_start: 0.6555 (p0) cc_final: 0.6187 (p0)
REVERT: L    4 MET cc_start: 0.8512 (tmm) cc_final: 0.8190 (tmm)
REVERT: L  149 ILE cc_start: 0.6149 (mm) cc_final: 0.5817 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0695
  time to fit residues: 4.9095
Evaluate side-chains
  48 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.140861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.111815 restraints weight = 34344.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.113323 restraints weight = 22556.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.114659 restraints weight = 16576.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.115304 restraints weight = 13493.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.115578 restraints weight = 11894.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.5028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5270  Z= 0.129
  Angle     :  0.637   7.021   7528  Z= 0.340
  Chirality :  0.037   0.220    874
  Planarity :  0.004   0.047    662
  Dihedral  : 16.494  73.673   1436
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.47 (0.39), residues: 427
  helix: -3.63 (0.56), residues: 18
  sheet: -0.66 (0.40), residues: 168
  loop : -2.28 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  59 
 TYR   0.013   0.002   TYR L 197 
 PHE   0.015   0.002   PHE L  76 
 TRP   0.033   0.003   TRP H  36 
 HIS   0.003   0.001   HIS L 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5266)
  covalent geometry    : angle       0.63661 ( 7520)
  SS BOND              : bond        0.00532 (    4)
  SS BOND              : angle       1.12726 (    8)
  hydrogen bonds       : bond        0.04391 (  206)
  hydrogen bonds       : angle       5.77691 (  464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1163.88 seconds
wall clock time: 20 minutes 44.40 seconds (1244.40 seconds total)