Starting phenix.real_space_refine
on Wed Jun  4 17:54:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5f_37290/06_2025/8w5f_37290.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5f_37290/06_2025/8w5f_37290.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5f_37290/06_2025/8w5f_37290.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5f_37290/06_2025/8w5f_37290.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5f_37290/06_2025/8w5f_37290.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5f_37290/06_2025/8w5f_37290.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.010 sd=   0.194
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: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    2326      2.51       5
     N     637      2.21       5
     O     727      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3700
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 790
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 950
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "c"
      Number of atoms: 980
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 980
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 8, 'TRANS': 122}
    Chain: "C"
      Number of atoms: 980
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 980
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 8, 'TRANS': 122}
  Time building chain proxies: 2.99, per 1000 atoms: 0.81
  Number of scatterers: 3700
  At special positions: 0
  Unit cell: (88.4, 66.64, 81.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     727      8.00
     N     637      7.00
     C    2326      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  41 " - pdb=" SG  CYS L 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03

  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: 0.90
  Conformation dependent library (CDL) restraints added in 467.8 milliseconds
  

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  898

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 6 sheets defined
      10.9% alpha, 26.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'c' and resid 101 through 116
      removed outlier: 3.645A  pdb=" N   ARG c 109 " --> pdb=" O   ARG c 105 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   THR c 110 " --> pdb=" O   ALA c 106 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 118 through 127
      removed outlier: 3.630A  pdb=" N   GLN c 127 " --> pdb=" O   ASP c 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 117
      removed outlier: 3.613A  pdb=" N   ARG C 105 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 127
      removed outlier: 4.037A  pdb=" N   ASP C 123 " --> pdb=" O   PRO C 119 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 23 through 24
      removed outlier: 3.514A  pdb=" N   VAL L  37 " --> pdb=" O   ILE L  93 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   TYR L  89 " --> pdb=" O   CYS L  41 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 51 through 52
    Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 24
    Processing sheet with id=AA4, first strand: chain 'H' and resid 29 through 30
      removed outlier: 6.837A  pdb=" N   GLU H  29 " --> pdb=" O   THR H 139 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'H' and resid 77 through 79
      removed outlier: 3.542A  pdb=" N   GLY H  68 " --> pdb=" O   TRP H  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'c' and resid 6 through 11
      removed outlier: 6.180A  pdb=" N   GLN c  17 " --> pdb=" O   ASN c  10 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   CYS c  74 " --> pdb=" O   VAL c  84 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   VAL c  84 " --> pdb=" O   CYS c  74 " (cutoff:3.500A)
      removed outlier: 8.553A  pdb=" N   GLN c  87 " --> pdb=" O   THR C  97 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   THR C  97 " --> pdb=" O   GLN c  87 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASP c  91 " --> pdb=" O   THR C  93 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   VAL C  84 " --> pdb=" O   CYS C  74 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   CYS C  74 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG C  86 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR C  62 " --> pdb=" O   PHE C  96 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG C  47 " --> pdb=" O   GLN C  69 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   SER C  34 " --> pdb=" O   ARG C  24 " (cutoff:3.500A)

    123 hydrogen bonds defined for protein.
    327 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.89

  Time building geometry restraints manager: 1.10 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: 1211
        1.34 -     1.46: 773
        1.46 -     1.58: 1779
        1.58 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 3775
  Sorted by residual:
  bond pdb=" C   SER L  25 "
       pdb=" N   PRO L  26 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.040 2.34e-02 1.83e+03 2.93e+00
  bond pdb=" CB  PRO c  28 "
       pdb=" CG  PRO c  28 "
    ideal  model  delta    sigma   weight residual
    1.492  1.550 -0.058 5.00e-02 4.00e+02 1.34e+00
  bond pdb=" CA  GLU H 108 "
       pdb=" CB  GLU H 108 "
    ideal  model  delta    sigma   weight residual
    1.524  1.536 -0.012 1.30e-02 5.92e+03 8.58e-01
  bond pdb=" N   LYS H  32 "
       pdb=" CA  LYS H  32 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.41e-02 5.03e+03 8.39e-01
  bond pdb=" N   PRO H  26 "
       pdb=" CA  PRO H  26 "
    ideal  model  delta    sigma   weight residual
    1.469  1.480 -0.012 1.28e-02 6.10e+03 8.11e-01
  ... (remaining 3770 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 5054
        2.77 -     5.55: 73
        5.55 -     8.32: 9
        8.32 -    11.09: 1
       11.09 -    13.86: 1
  Bond angle restraints: 5138
  Sorted by residual:
  angle pdb=" C   VAL H  31 "
        pdb=" N   LYS H  32 "
        pdb=" CA  LYS H  32 "
      ideal   model   delta    sigma   weight residual
     121.80  135.66  -13.86 2.44e+00 1.68e-01 3.23e+01
  angle pdb=" C   SER L  30 "
        pdb=" N   VAL L  31 "
        pdb=" CA  VAL L  31 "
      ideal   model   delta    sigma   weight residual
     121.97  128.98   -7.01 1.80e+00 3.09e-01 1.52e+01
  angle pdb=" C   SER L  98 "
        pdb=" N   GLU L  99 "
        pdb=" CA  GLU L  99 "
      ideal   model   delta    sigma   weight residual
     121.54  128.92   -7.38 1.91e+00 2.74e-01 1.49e+01
  angle pdb=" N   PRO H  26 "
        pdb=" CA  PRO H  26 "
        pdb=" C   PRO H  26 "
      ideal   model   delta    sigma   weight residual
     112.47  120.34   -7.87 2.06e+00 2.36e-01 1.46e+01
  angle pdb=" C   GLY c  12 "
        pdb=" N   LYS c  13 "
        pdb=" CA  LYS c  13 "
      ideal   model   delta    sigma   weight residual
     121.54  128.11   -6.57 1.91e+00 2.74e-01 1.18e+01
  ... (remaining 5133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.75: 1998
       15.75 -    31.50: 216
       31.50 -    47.25: 35
       47.25 -    63.00: 8
       63.00 -    78.75: 3
  Dihedral angle restraints: 2260
    sinusoidal: 858
      harmonic: 1402
  Sorted by residual:
  dihedral pdb=" CA  SER L  25 "
           pdb=" C   SER L  25 "
           pdb=" N   PRO L  26 "
           pdb=" CA  PRO L  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.47  -42.53     0      5.00e+00 4.00e-02 7.24e+01
  dihedral pdb=" CA  ILE c  11 "
           pdb=" C   ILE c  11 "
           pdb=" N   GLY c  12 "
           pdb=" CA  GLY c  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -138.43  -41.57     0      5.00e+00 4.00e-02 6.91e+01
  dihedral pdb=" CA  TRP L 114 "
           pdb=" C   TRP L 114 "
           pdb=" N   THR L 115 "
           pdb=" CA  THR L 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.95  -23.05     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 2257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 454
       0.052 -    0.103: 102
       0.103 -    0.154: 30
       0.154 -    0.206: 1
       0.206 -    0.257: 1
  Chirality restraints: 588
  Sorted by residual:
  chirality pdb=" CA  PRO H  26 "
            pdb=" N   PRO H  26 "
            pdb=" C   PRO H  26 "
            pdb=" CB  PRO H  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  ASN H  74 "
            pdb=" N   ASN H  74 "
            pdb=" C   ASN H  74 "
            pdb=" CB  ASN H  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.15e-01
  chirality pdb=" CA  THR L 112 "
            pdb=" N   THR L 112 "
            pdb=" C   THR L 112 "
            pdb=" CB  THR L 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 585 not shown)

  Planarity restraints: 665
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  25 "    0.065 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO H  26 "   -0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO H  26 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO H  26 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  25 "   -0.059 5.00e-02 4.00e+02   9.03e-02 1.30e+01
        pdb=" N   PRO L  26 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO L  26 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO L  26 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN H  25 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.86e+00
        pdb=" C   GLN H  25 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   GLN H  25 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO H  26 "    0.013 2.00e-02 2.50e+03
  ... (remaining 662 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1130
        2.82 -     3.34: 3163
        3.34 -     3.86: 5529
        3.86 -     4.38: 6386
        4.38 -     4.90: 11858
  Nonbonded interactions: 28066
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS H  86 "
            pdb=" O   SER H 104 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NH1 ARG L  79 "
            pdb=" OD2 ASP L 100 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" N   THR H 106 "
            pdb=" OD2 ASP H 109 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" O   ASN C  70 "
            pdb=" ND2 ASN C  70 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" OE2 GLU H  65 "
            pdb=" NZ  LYS H  82 "
     model   vdw
     2.371 3.120
  ... (remaining 28061 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'c'
}

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:             0.520
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.270
  Find NCS groups from input model:        0.080
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
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   0.058   3777  Z= 0.169
  Angle     :  0.822  13.864   5142  Z= 0.433
  Chirality :  0.048   0.257    588
  Planarity :  0.007   0.100    665
  Dihedral  : 13.392  78.749   1356
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  1.47 %
    Allowed  :  9.85 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.49 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.36), residues: 477
  helix: -1.02 (0.75), residues: 44
  sheet: -1.42 (0.38), residues: 190
  loop : -2.68 (0.35), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 132 
 HIS   0.003   0.001   HIS L  55 
 PHE   0.008   0.001   PHE L 116 
 TYR   0.012   0.001   TYR L  54 
 ARG   0.003   0.000   ARG H 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18694 (  123)
  hydrogen bonds       : angle       8.03197 (  327)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.65307 (    4)
  covalent geometry    : bond        0.00383 ( 3775)
  covalent geometry    : angle       0.82229 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.390 
Fit side-chains
REVERT: L   54 TYR cc_start: 0.9216 (m-80) cc_final: 0.8931 (m-80)
REVERT: C   27 ASN cc_start: 0.8485 (t0) cc_final: 0.8012 (t0)
REVERT: C   30 ASN cc_start: 0.9021 (p0) cc_final: 0.8619 (p0)
REVERT: C   60 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8020 (pttp)
  outliers start: 1
  outliers final: 1
  residues processed: 93
  average time/residue: 0.1693
  time to fit residues: 18.9935
Evaluate side-chains
  93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    0.3980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  54 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.124698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.097998 restraints weight = 4961.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.30
r_work: 0.3005 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3777  Z= 0.152
  Angle     :  0.765  11.202   5142  Z= 0.394
  Chirality :  0.048   0.242    588
  Planarity :  0.006   0.084    665
  Dihedral  :  5.987  38.439    525
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  1.47 %
    Allowed  :  9.85 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.12 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.37), residues: 477
  helix: -0.34 (0.76), residues: 46
  sheet: -1.13 (0.39), residues: 190
  loop : -2.66 (0.35), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  66 
 HIS   0.003   0.001   HIS L  55 
 PHE   0.008   0.001   PHE L 116 
 TYR   0.010   0.001   TYR L  48 
 ARG   0.003   0.001   ARG L  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  123)
  hydrogen bonds       : angle       5.50423 (  327)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       0.82026 (    4)
  covalent geometry    : bond        0.00346 ( 3775)
  covalent geometry    : angle       0.76469 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.370 
Fit side-chains
REVERT: L   92 LYS cc_start: 0.9076 (ptmm) cc_final: 0.8585 (ttpt)
REVERT: H   65 GLU cc_start: 0.8947 (tp30) cc_final: 0.8731 (tp30)
REVERT: H  109 ASP cc_start: 0.7902 (m-30) cc_final: 0.7564 (m-30)
REVERT: C   27 ASN cc_start: 0.8729 (t0) cc_final: 0.8260 (t0)
REVERT: C   30 ASN cc_start: 0.9103 (p0) cc_final: 0.8650 (p0)
REVERT: C   60 LYS cc_start: 0.8831 (mtmt) cc_final: 0.7526 (pttp)
REVERT: C   70 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.9027 (p0)
  outliers start: 5
  outliers final: 2
  residues processed: 107
  average time/residue: 0.1599
  time to fit residues: 20.7025
Evaluate side-chains
  103 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain C residue   70 ASN
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 8 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0010
   chunk 14 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.5992

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  87 GLN
C  10 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.124739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.098111 restraints weight = 4953.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.31
r_work: 0.3003 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3777  Z= 0.144
  Angle     :  0.743  10.069   5142  Z= 0.376
  Chirality :  0.047   0.268    588
  Planarity :  0.007   0.118    665
  Dihedral  :  5.712  35.763    525
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  1.47 %
    Allowed  :  9.43 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.58 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.37), residues: 477
  helix:  0.05 (0.79), residues: 46
  sheet: -0.79 (0.39), residues: 187
  loop : -2.49 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 132 
 HIS   0.002   0.001   HIS L  55 
 PHE   0.008   0.001   PHE L 116 
 TYR   0.010   0.001   TYR L  48 
 ARG   0.002   0.000   ARG H 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03901 (  123)
  hydrogen bonds       : angle       5.15143 (  327)
  SS BOND              : bond        0.00234 (    2)
  SS BOND              : angle       0.67684 (    4)
  covalent geometry    : bond        0.00328 ( 3775)
  covalent geometry    : angle       0.74317 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.448 
Fit side-chains
REVERT: L   92 LYS cc_start: 0.9058 (ptmm) cc_final: 0.8554 (ttpt)
REVERT: H  109 ASP cc_start: 0.7852 (m-30) cc_final: 0.7487 (m-30)
REVERT: c  123 ASP cc_start: 0.8537 (m-30) cc_final: 0.8327 (m-30)
REVERT: C   13 LYS cc_start: 0.8821 (tptt) cc_final: 0.8525 (tppt)
REVERT: C   27 ASN cc_start: 0.8713 (t0) cc_final: 0.8279 (t0)
REVERT: C   30 ASN cc_start: 0.9100 (p0) cc_final: 0.8682 (p0)
REVERT: C   70 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8984 (p0)
  outliers start: 13
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1747
  time to fit residues: 23.0318
Evaluate side-chains
  111 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   60 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue  121 LEU
Chi-restraints excluded: chain C residue   70 ASN
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  125 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0270
   chunk 11 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 10 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.0840

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  69 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.126075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.099391 restraints weight = 4926.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.31
r_work: 0.3025 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3777  Z= 0.128
  Angle     :  0.705   9.239   5142  Z= 0.359
  Chirality :  0.046   0.247    588
  Planarity :  0.006   0.094    665
  Dihedral  :  5.398  32.208    525
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  1.26 %
    Allowed  :  8.81 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 14.57 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.38), residues: 477
  helix: -0.14 (0.77), residues: 48
  sheet: -0.62 (0.39), residues: 187
  loop : -2.38 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  66 
 HIS   0.001   0.001   HIS L  55 
 PHE   0.008   0.001   PHE L 116 
 TYR   0.009   0.001   TYR L  48 
 ARG   0.003   0.000   ARG H 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  123)
  hydrogen bonds       : angle       4.90690 (  327)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.56316 (    4)
  covalent geometry    : bond        0.00290 ( 3775)
  covalent geometry    : angle       0.70515 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: L   45 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7152 (mp0)
REVERT: H   65 GLU cc_start: 0.8861 (tp30) cc_final: 0.8634 (tp30)
REVERT: H   86 LYS cc_start: 0.9035 (tppp) cc_final: 0.8825 (tptm)
REVERT: H  109 ASP cc_start: 0.7875 (m-30) cc_final: 0.7474 (m-30)
REVERT: C   13 LYS cc_start: 0.8765 (tptt) cc_final: 0.8461 (tppt)
REVERT: C   27 ASN cc_start: 0.8684 (t0) cc_final: 0.8260 (t0)
REVERT: C   30 ASN cc_start: 0.9104 (p0) cc_final: 0.8723 (p0)
REVERT: C   45 GLU cc_start: 0.8594 (pt0) cc_final: 0.8389 (pt0)
REVERT: C   70 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8918 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 119
  average time/residue: 0.1613
  time to fit residues: 23.3091
Evaluate side-chains
  113 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   60 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain c residue   11 ILE
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue   70 ASN
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  125 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.119586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.093002 restraints weight = 5140.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.28
r_work: 0.2922 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3777  Z= 0.235
  Angle     :  0.805   9.522   5142  Z= 0.414
  Chirality :  0.051   0.238    588
  Planarity :  0.006   0.086    665
  Dihedral  :  5.935  39.995    525
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 11.95 %
    Favored  : 87.00 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.04 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.38), residues: 477
  helix: -0.23 (0.76), residues: 50
  sheet: -0.72 (0.39), residues: 187
  loop : -2.42 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H 132 
 HIS   0.003   0.001   HIS L  55 
 PHE   0.012   0.002   PHE c  94 
 TYR   0.012   0.002   TYR c  89 
 ARG   0.005   0.001   ARG H 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04561 (  123)
  hydrogen bonds       : angle       5.13091 (  327)
  SS BOND              : bond        0.00299 (    2)
  SS BOND              : angle       0.85995 (    4)
  covalent geometry    : bond        0.00570 ( 3775)
  covalent geometry    : angle       0.80493 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.425 
Fit side-chains
REVERT: L   25 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7510 (p)
REVERT: L   92 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8638 (ttpt)
REVERT: H   65 GLU cc_start: 0.8942 (tp30) cc_final: 0.8717 (tp30)
REVERT: H  109 ASP cc_start: 0.7946 (m-30) cc_final: 0.7485 (m-30)
REVERT: c  127 GLN cc_start: 0.9009 (mp10) cc_final: 0.8558 (mp10)
REVERT: C   13 LYS cc_start: 0.8808 (tptt) cc_final: 0.8534 (tppt)
REVERT: C   27 ASN cc_start: 0.8726 (t0) cc_final: 0.8278 (t0)
REVERT: C   30 ASN cc_start: 0.9124 (p0) cc_final: 0.8697 (p0)
REVERT: C   45 GLU cc_start: 0.8646 (pt0) cc_final: 0.8377 (pt0)
  outliers start: 18
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1651
  time to fit residues: 21.3129
Evaluate side-chains
  111 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   25 SER
Chi-restraints excluded: chain L residue   31 VAL
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   58 GLN
Chi-restraints excluded: chain L residue   60 ILE
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue   97 GLN
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 14 optimal weight:   10.0000
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.124339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.097591 restraints weight = 5013.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 2.31
r_work: 0.3009 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3777  Z= 0.131
  Angle     :  0.711   8.450   5142  Z= 0.363
  Chirality :  0.046   0.242    588
  Planarity :  0.005   0.079    665
  Dihedral  :  5.411  34.162    523
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  :  8.39 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 17.78 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.38), residues: 477
  helix: -0.13 (0.75), residues: 50
  sheet: -0.43 (0.41), residues: 179
  loop : -2.39 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  66 
 HIS   0.001   0.001   HIS L  55 
 PHE   0.007   0.001   PHE L  80 
 TYR   0.010   0.001   TYR L  48 
 ARG   0.002   0.000   ARG H 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  123)
  hydrogen bonds       : angle       4.83468 (  327)
  SS BOND              : bond        0.00199 (    2)
  SS BOND              : angle       0.59570 (    4)
  covalent geometry    : bond        0.00302 ( 3775)
  covalent geometry    : angle       0.71074 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.393 
Fit side-chains
REVERT: L   92 LYS cc_start: 0.9015 (ptmm) cc_final: 0.8523 (ttpt)
REVERT: L   97 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7996 (mt0)
REVERT: H   86 LYS cc_start: 0.8996 (tppp) cc_final: 0.8689 (tptm)
REVERT: H  109 ASP cc_start: 0.7908 (m-30) cc_final: 0.7459 (m-30)
REVERT: c  123 ASP cc_start: 0.8434 (m-30) cc_final: 0.8233 (m-30)
REVERT: C   27 ASN cc_start: 0.8679 (t0) cc_final: 0.8258 (t0)
REVERT: C   30 ASN cc_start: 0.9069 (p0) cc_final: 0.8689 (p0)
REVERT: C   45 GLU cc_start: 0.8671 (pt0) cc_final: 0.8415 (pt0)
REVERT: C   70 ASN cc_start: 0.9215 (p0) cc_final: 0.8908 (p0)
  outliers start: 19
  outliers final: 13
  residues processed: 112
  average time/residue: 0.1661
  time to fit residues: 22.5481
Evaluate side-chains
  113 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   31 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   60 ILE
Chi-restraints excluded: chain L residue   97 GLN
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  139 THR
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 36 optimal weight:    0.0770
   chunk 16 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0370
   chunk 31 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.5216

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.128593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.101836 restraints weight = 4952.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.30
r_work: 0.3059 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3777  Z= 0.117
  Angle     :  0.687   9.319   5142  Z= 0.350
  Chirality :  0.045   0.237    588
  Planarity :  0.005   0.076    665
  Dihedral  :  5.010  28.723    523
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  9.43 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 18.27 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.39), residues: 477
  helix:  0.17 (0.75), residues: 50
  sheet: -0.23 (0.40), residues: 184
  loop : -2.23 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  66 
 HIS   0.001   0.000   HIS H  54 
 PHE   0.008   0.001   PHE L 116 
 TYR   0.015   0.001   TYR H 122 
 ARG   0.001   0.000   ARG L  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02902 (  123)
  hydrogen bonds       : angle       4.57595 (  327)
  SS BOND              : bond        0.00130 (    2)
  SS BOND              : angle       0.39997 (    4)
  covalent geometry    : bond        0.00264 ( 3775)
  covalent geometry    : angle       0.68719 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.448 
Fit side-chains
REVERT: L   45 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6977 (mp0)
REVERT: L   92 LYS cc_start: 0.8999 (ptmm) cc_final: 0.8596 (ttpt)
REVERT: H   86 LYS cc_start: 0.9012 (tppp) cc_final: 0.8555 (tptm)
REVERT: H  109 ASP cc_start: 0.7844 (m-30) cc_final: 0.7297 (m-30)
REVERT: c   16 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8304 (mtmt)
REVERT: c   63 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8402 (mttm)
REVERT: c  123 ASP cc_start: 0.8427 (m-30) cc_final: 0.8177 (m-30)
REVERT: C   27 ASN cc_start: 0.8619 (t0) cc_final: 0.8228 (t0)
REVERT: C   30 ASN cc_start: 0.8976 (p0) cc_final: 0.8700 (p0)
REVERT: C   45 GLU cc_start: 0.8597 (pt0) cc_final: 0.8344 (pt0)
REVERT: C   70 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8688 (p0)
  outliers start: 19
  outliers final: 13
  residues processed: 124
  average time/residue: 0.1662
  time to fit residues: 24.9813
Evaluate side-chains
  119 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   31 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   60 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain c residue   46 LYS
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   70 ASN
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  125 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    8.9990
   chunk 30 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0010
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.128946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.102147 restraints weight = 5030.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.31
r_work: 0.3074 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3777  Z= 0.120
  Angle     :  0.684   8.917   5142  Z= 0.351
  Chirality :  0.047   0.236    588
  Planarity :  0.005   0.074    665
  Dihedral  :  4.908  28.552    523
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  8.39 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.00 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.39), residues: 477
  helix:  0.31 (0.74), residues: 50
  sheet: -0.12 (0.41), residues: 185
  loop : -2.13 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  66 
 HIS   0.002   0.001   HIS H  54 
 PHE   0.007   0.001   PHE L 116 
 TYR   0.010   0.001   TYR H  46 
 ARG   0.001   0.000   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02949 (  123)
  hydrogen bonds       : angle       4.52757 (  327)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       0.43525 (    4)
  covalent geometry    : bond        0.00269 ( 3775)
  covalent geometry    : angle       0.68373 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: L   45 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6959 (mp0)
REVERT: L   92 LYS cc_start: 0.9010 (ptmm) cc_final: 0.8604 (ttpt)
REVERT: H   86 LYS cc_start: 0.8989 (tppp) cc_final: 0.8525 (tptm)
REVERT: H  109 ASP cc_start: 0.7795 (m-30) cc_final: 0.7250 (m-30)
REVERT: c   16 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8175 (mtmt)
REVERT: c   61 ASN cc_start: 0.8692 (p0) cc_final: 0.8345 (p0)
REVERT: c   63 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8427 (mttm)
REVERT: C   27 ASN cc_start: 0.8654 (t0) cc_final: 0.8269 (t0)
REVERT: C   30 ASN cc_start: 0.8924 (p0) cc_final: 0.8676 (p0)
REVERT: C   45 GLU cc_start: 0.8626 (pt0) cc_final: 0.8338 (pt0)
REVERT: C   70 ASN cc_start: 0.9032 (p0) cc_final: 0.8726 (p0)
  outliers start: 15
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1790
  time to fit residues: 23.5361
Evaluate side-chains
  116 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   31 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   60 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain c residue   11 ILE
Chi-restraints excluded: chain c residue   46 LYS
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  125 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  71 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 = 0.3462 r_free = 0.3462 target = 0.123415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.097052 restraints weight = 4969.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.25
r_work: 0.2997 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3777  Z= 0.164
  Angle     :  0.740   9.817   5142  Z= 0.383
  Chirality :  0.049   0.230    588
  Planarity :  0.005   0.074    665
  Dihedral  :  5.324  34.474    523
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 10.48 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 20.00 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.39), residues: 477
  helix:  0.15 (0.75), residues: 50
  sheet: -0.12 (0.40), residues: 184
  loop : -2.10 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 132 
 HIS   0.003   0.001   HIS H  54 
 PHE   0.010   0.001   PHE c  94 
 TYR   0.015   0.002   TYR H 122 
 ARG   0.009   0.001   ARG L  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  123)
  hydrogen bonds       : angle       4.75818 (  327)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.64942 (    4)
  covalent geometry    : bond        0.00390 ( 3775)
  covalent geometry    : angle       0.73977 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.443 
Fit side-chains
REVERT: L   45 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7001 (mp0)
REVERT: L   92 LYS cc_start: 0.9026 (ptmm) cc_final: 0.8541 (ttpt)
REVERT: H   86 LYS cc_start: 0.9013 (tppp) cc_final: 0.8655 (tptm)
REVERT: H  109 ASP cc_start: 0.7922 (m-30) cc_final: 0.7456 (m-30)
REVERT: c   16 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8386 (mtmt)
REVERT: C   27 ASN cc_start: 0.8655 (t0) cc_final: 0.8224 (t0)
REVERT: C   30 ASN cc_start: 0.9058 (p0) cc_final: 0.8659 (p0)
REVERT: C   70 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8990 (p0)
  outliers start: 18
  outliers final: 14
  residues processed: 107
  average time/residue: 0.1735
  time to fit residues: 22.4045
Evaluate side-chains
  110 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   31 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   60 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  139 THR
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   70 ASN
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  120 LEU
Chi-restraints excluded: chain C residue  125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0870
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0470
   chunk 8 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    0.8058

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  71 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 = 0.3510 r_free = 0.3510 target = 0.127241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.100912 restraints weight = 4886.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.22
r_work: 0.3056 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   3777  Z= 0.121
  Angle     :  0.693   9.612   5142  Z= 0.357
  Chirality :  0.047   0.237    588
  Planarity :  0.005   0.071    665
  Dihedral  :  5.085  30.869    523
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  9.01 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 20.49 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.39), residues: 477
  helix:  0.22 (0.74), residues: 50
  sheet:  0.08 (0.42), residues: 176
  loop : -2.03 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 132 
 HIS   0.003   0.001   HIS H  54 
 PHE   0.006   0.001   PHE L 116 
 TYR   0.017   0.001   TYR H 122 
 ARG   0.008   0.000   ARG L  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03042 (  123)
  hydrogen bonds       : angle       4.55169 (  327)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.45027 (    4)
  covalent geometry    : bond        0.00274 ( 3775)
  covalent geometry    : angle       0.69342 ( 5138)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.415 
Fit side-chains
REVERT: L   83 SER cc_start: 0.8940 (t) cc_final: 0.8549 (p)
REVERT: L   92 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8628 (ttpt)
REVERT: H   86 LYS cc_start: 0.8998 (tppp) cc_final: 0.8721 (tptm)
REVERT: H  109 ASP cc_start: 0.7871 (m-30) cc_final: 0.7369 (m-30)
REVERT: c   14 ASP cc_start: 0.8491 (p0) cc_final: 0.8108 (p0)
REVERT: c   16 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8291 (mtmm)
REVERT: c   63 LYS cc_start: 0.8896 (mtpp) cc_final: 0.8402 (mttm)
REVERT: C   27 ASN cc_start: 0.8628 (t0) cc_final: 0.8230 (t0)
REVERT: C   30 ASN cc_start: 0.8978 (p0) cc_final: 0.8695 (p0)
REVERT: C   70 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8727 (p0)
  outliers start: 16
  outliers final: 15
  residues processed: 104
  average time/residue: 0.1531
  time to fit residues: 19.4962
Evaluate side-chains
  113 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   31 VAL
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   39 LEU
Chi-restraints excluded: chain L residue   60 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  139 THR
Chi-restraints excluded: chain c residue   68 ILE
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue  120 LEU
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   70 ASN
Chi-restraints excluded: chain C residue   92 VAL
Chi-restraints excluded: chain C residue  120 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 8 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** H  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  71 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 = 0.3485 r_free = 0.3485 target = 0.125435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.098922 restraints weight = 5032.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.25
r_work: 0.3023 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3777  Z= 0.139
  Angle     :  0.716   9.370   5142  Z= 0.368
  Chirality :  0.048   0.231    588
  Planarity :  0.005   0.072    665
  Dihedral  :  5.141  32.396    523
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  9.64 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 20.49 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.39), residues: 477
  helix:  0.21 (0.75), residues: 50
  sheet:  0.12 (0.41), residues: 176
  loop : -2.03 (0.39), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 132 
 HIS   0.003   0.001   HIS H  54 
 PHE   0.008   0.001   PHE c  94 
 TYR   0.017   0.001   TYR H 122 
 ARG   0.008   0.000   ARG L  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  123)
  hydrogen bonds       : angle       4.63707 (  327)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.48530 (    4)
  covalent geometry    : bond        0.00326 ( 3775)
  covalent geometry    : angle       0.71624 ( 5138)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2311.43 seconds
wall clock time: 40 minutes 22.38 seconds (2422.38 seconds total)