Starting phenix.real_space_refine
on Fri Aug 22 13:38:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h9r_34578/08_2025/8h9r_34578.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h9r_34578/08_2025/8h9r_34578.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h9r_34578/08_2025/8h9r_34578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h9r_34578/08_2025/8h9r_34578.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h9r_34578/08_2025/8h9r_34578.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h9r_34578/08_2025/8h9r_34578.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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      11      5.16       5
     C    2176      2.51       5
     N     560      2.21       5
     O     634      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3381
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "K"
      Number of atoms: 1573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1573
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 6, 'TRANS': 191}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 549
          Classifications: {'peptide': 67}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 62}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "M"
      Number of atoms: 1259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1259
          Classifications: {'peptide': 156}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
  Time building chain proxies: 1.15, per 1000 atoms: 0.34
  Number of scatterers: 3381
  At special positions: 0
  Unit cell: (91.98, 94.9, 206.59, 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      11     16.00
     O     634      8.00
     N     560      7.00
     C    2176      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 148.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  814

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 1 sheets defined
      74.6% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'K' and resid 19 through 26
    Processing helix  chain 'K' and resid 29 through 31
      No H-bonds generated for 'chain 'K' and resid 29 through 31'
    Processing helix  chain 'K' and resid 32 through 48
      removed outlier: 3.559A  pdb=" N   VAL K  36 " --> pdb=" O   THR K  32 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 54 through 121
      removed outlier: 3.792A  pdb=" N   PHE K  58 " --> pdb=" O   SER K  54 " (cutoff:3.500A)
      Proline residue:  K  76  - end of helix
    Processing helix  chain 'K' and resid 122 through 182
      removed outlier: 3.782A  pdb=" N   VAL K 182 " --> pdb=" O   GLU K 178 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 194 through 206
    Processing helix  chain 'L' and resid 41 through 55
    Processing helix  chain 'L' and resid 67 through 83
      removed outlier: 4.303A  pdb=" N   ARG L  73 " --> pdb=" O   GLN L  69 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 12 through 18
      removed outlier: 3.768A  pdb=" N   ILE M  18 " --> pdb=" O   ALA M  14 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 19 through 22
      removed outlier: 5.643A  pdb=" N   ASN M  22 " --> pdb=" O   ILE M  19 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 19 through 22'
    Processing helix  chain 'M' and resid 23 through 43
    Processing helix  chain 'M' and resid 53 through 58
    Processing helix  chain 'M' and resid 64 through 75
    Processing helix  chain 'M' and resid 85 through 123
      removed outlier: 3.753A  pdb=" N   VAL M  89 " --> pdb=" O   TYR M  85 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 126 through 130
    Processing helix  chain 'M' and resid 131 through 139
    Processing helix  chain 'M' and resid 140 through 143
    Processing helix  chain 'M' and resid 156 through 160
    Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13

    239 hydrogen bonds defined for protein.
    699 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: 0.48

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1089
        1.34 -     1.46: 745
        1.46 -     1.58: 1601
        1.58 -     1.69: 0
        1.69 -     1.81: 21
  Bond restraints: 3456
  Sorted by residual:
  bond pdb=" N   ASP L  97 "
       pdb=" CA  ASP L  97 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 8.30e-03 1.45e+04 1.64e+01
  bond pdb=" N   ARG L  48 "
       pdb=" CA  ARG L  48 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.22e+00
  bond pdb=" N   ASN M 136 "
       pdb=" CA  ASN M 136 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.17e-02 7.31e+03 5.67e+00
  bond pdb=" CA  LYS M 146 "
       pdb=" C   LYS M 146 "
    ideal  model  delta    sigma   weight residual
    1.522  1.490  0.032 1.38e-02 5.25e+03 5.36e+00
  bond pdb=" N   THR M 131 "
       pdb=" CA  THR M 131 "
    ideal  model  delta    sigma   weight residual
    1.454  1.484 -0.030 1.34e-02 5.57e+03 5.17e+00
  ... (remaining 3451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 4469
        1.73 -     3.46: 179
        3.46 -     5.19: 22
        5.19 -     6.92: 2
        6.92 -     8.65: 2
  Bond angle restraints: 4674
  Sorted by residual:
  angle pdb=" N   MET L  81 "
        pdb=" CA  MET L  81 "
        pdb=" C   MET L  81 "
      ideal   model   delta    sigma   weight residual
     113.55  104.90    8.65 1.26e+00 6.30e-01 4.71e+01
  angle pdb=" C   PHE K 125 "
        pdb=" N   ASP K 126 "
        pdb=" CA  ASP K 126 "
      ideal   model   delta    sigma   weight residual
     120.31  115.19    5.12 1.52e+00 4.33e-01 1.13e+01
  angle pdb=" CA  THR M 131 "
        pdb=" C   THR M 131 "
        pdb=" O   THR M 131 "
      ideal   model   delta    sigma   weight residual
     121.87  118.12    3.75 1.16e+00 7.43e-01 1.05e+01
  angle pdb=" N   LYS K 152 "
        pdb=" CA  LYS K 152 "
        pdb=" C   LYS K 152 "
      ideal   model   delta    sigma   weight residual
     111.28  108.29    2.99 1.09e+00 8.42e-01 7.52e+00
  angle pdb=" CA  ARG L  48 "
        pdb=" C   ARG L  48 "
        pdb=" O   ARG L  48 "
      ideal   model   delta    sigma   weight residual
     120.82  118.04    2.78 1.05e+00 9.07e-01 7.02e+00
  ... (remaining 4669 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 1850
       16.75 -    33.49: 202
       33.49 -    50.24: 46
       50.24 -    66.99: 10
       66.99 -    83.73: 5
  Dihedral angle restraints: 2113
    sinusoidal: 862
      harmonic: 1251
  Sorted by residual:
  dihedral pdb=" CA  ILE M  10 "
           pdb=" C   ILE M  10 "
           pdb=" N   ASP M  11 "
           pdb=" CA  ASP M  11 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.17   24.83     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  PHE L  93 "
           pdb=" C   PHE L  93 "
           pdb=" N   LYS L  94 "
           pdb=" CA  LYS L  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ARG K 121 "
           pdb=" C   ARG K 121 "
           pdb=" N   HIS K 122 "
           pdb=" CA  HIS K 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.49  -19.51     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 2110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 350
       0.045 -    0.090: 127
       0.090 -    0.134: 28
       0.134 -    0.179: 2
       0.179 -    0.224: 1
  Chirality restraints: 508
  Sorted by residual:
  chirality pdb=" CA  MET L  81 "
            pdb=" N   MET L  81 "
            pdb=" C   MET L  81 "
            pdb=" CB  MET L  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE M 125 "
            pdb=" N   ILE M 125 "
            pdb=" C   ILE M 125 "
            pdb=" CB  ILE M 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.46e-01
  chirality pdb=" CA  LYS K 152 "
            pdb=" N   LYS K 152 "
            pdb=" C   LYS K 152 "
            pdb=" CB  LYS K 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 505 not shown)

  Planarity restraints: 603
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU L  96 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" C   GLU L  96 "    0.034 2.00e-02 2.50e+03
        pdb=" O   GLU L  96 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASP L  97 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE K  71 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.86e+00
        pdb=" C   ILE K  71 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE K  71 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS K  72 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN L  80 "   -0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   GLN L  80 "    0.028 2.00e-02 2.50e+03
        pdb=" O   GLN L  80 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   MET L  81 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 600 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 782
        2.78 -     3.31: 3734
        3.31 -     3.84: 5690
        3.84 -     4.37: 6055
        4.37 -     4.90: 9558
  Nonbonded interactions: 25819
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS K 158 "
            pdb=" O   MET L  87 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" O   ILE M  26 "
            pdb=" OG  SER M  29 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   LEU K 136 "
            pdb=" OG1 THR K 139 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OE2 GLU K 111 "
            pdb=" NH2 ARG M 110 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   VAL L  61 "
            pdb=" OG  SER L  64 "
     model   vdw
     2.318 3.040
  ... (remaining 25814 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:             10.320
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.580
  Find NCS groups from input model:        0.020
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
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      :  0.006   0.039   3456  Z= 0.323
  Angle     :  0.793   8.648   4674  Z= 0.488
  Chirality :  0.046   0.224    508
  Planarity :  0.005   0.035    603
  Dihedral  : 15.254  83.733   1299
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.99 (0.36), residues: 413
  helix: -0.76 (0.26), residues: 277
  sheet:  None (None), residues: 0
  loop : -2.31 (0.50), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  54 
 TYR   0.015   0.002   TYR K 145 
 PHE   0.021   0.003   PHE M  69 
 TRP   0.010   0.002   TRP K 176 
 HIS   0.011   0.003   HIS K 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00609 ( 3456)
  covalent geometry    : angle       0.79255 ( 4674)
  hydrogen bonds       : bond        0.09596 (  239)
  hydrogen bonds       : angle       5.12944 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8492 (mtt180) cc_final: 0.8240 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8219 (tttt)
REVERT: K  106 ASN cc_start: 0.7972 (m-40) cc_final: 0.7596 (m-40)
REVERT: K  134 MET cc_start: 0.8654 (ttm) cc_final: 0.8360 (ttm)
REVERT: K  164 MET cc_start: 0.8939 (tpp) cc_final: 0.7063 (tpp)
REVERT: L   78 LEU cc_start: 0.9094 (tp) cc_final: 0.8834 (tt)
REVERT: L   94 LYS cc_start: 0.8979 (tmmt) cc_final: 0.8715 (tmmt)
REVERT: M   17 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8976 (mm-30)
REVERT: M   55 TYR cc_start: 0.9345 (t80) cc_final: 0.9067 (t80)
REVERT: M  111 ILE cc_start: 0.9270 (mt) cc_final: 0.9066 (mt)
REVERT: M  148 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8656 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1027
  time to fit residues: 11.6504
Evaluate side-chains
  64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0020
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0000
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
K 115 GLN
K 130 ASN
K 153 ASN
K 180 HIS
L  80 GLN
** M 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 159 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.076421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.067242 restraints weight = 19403.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.068450 restraints weight = 9972.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.069198 restraints weight = 6030.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.069688 restraints weight = 4105.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.069990 restraints weight = 3057.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3456  Z= 0.146
  Angle     :  0.640   7.146   4674  Z= 0.339
  Chirality :  0.043   0.152    508
  Planarity :  0.005   0.037    603
  Dihedral  :  4.584  21.700    452
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 13.80 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.41), residues: 413
  helix:  1.27 (0.30), residues: 290
  sheet:  None (None), residues: 0
  loop : -1.45 (0.56), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  54 
 TYR   0.023   0.002   TYR M  85 
 PHE   0.021   0.002   PHE M  15 
 TRP   0.015   0.002   TRP M  53 
 HIS   0.008   0.002   HIS K 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3456)
  covalent geometry    : angle       0.64005 ( 4674)
  hydrogen bonds       : bond        0.05090 (  239)
  hydrogen bonds       : angle       4.14691 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7933 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8087 (tttt)
REVERT: K   90 LEU cc_start: 0.8208 (tp) cc_final: 0.7946 (tt)
REVERT: K  129 ARG cc_start: 0.8749 (mtm-85) cc_final: 0.8167 (mtm-85)
REVERT: K  134 MET cc_start: 0.8674 (ttm) cc_final: 0.8455 (ttm)
REVERT: K  146 ARG cc_start: 0.8542 (tmm-80) cc_final: 0.8040 (ttt-90)
REVERT: K  164 MET cc_start: 0.8933 (tpp) cc_final: 0.8150 (tpp)
REVERT: K  167 ARG cc_start: 0.9014 (mtm180) cc_final: 0.8750 (mtm180)
REVERT: M  118 MET cc_start: 0.8358 (tpp) cc_final: 0.8111 (tpp)
  outliers start: 12
  outliers final: 7
  residues processed: 99
  average time/residue: 0.0893
  time to fit residues: 10.3376
Evaluate side-chains
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain M residue   34 ASN
Chi-restraints excluded: chain M residue   73 PHE
Chi-restraints excluded: chain M residue   80 VAL
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0770
   chunk 5 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
K 102 GLN
M  23 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.076006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.066926 restraints weight = 19479.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.068167 restraints weight = 10229.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.068948 restraints weight = 6264.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.069457 restraints weight = 4268.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.069781 restraints weight = 3156.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3456  Z= 0.141
  Angle     :  0.634   8.259   4674  Z= 0.328
  Chirality :  0.045   0.344    508
  Planarity :  0.004   0.038    603
  Dihedral  :  4.365  19.280    452
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.18 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.41), residues: 413
  helix:  1.86 (0.30), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.11 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 166 
 TYR   0.033   0.001   TYR M  85 
 PHE   0.011   0.001   PHE K  24 
 TRP   0.008   0.001   TRP M  53 
 HIS   0.011   0.002   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3456)
  covalent geometry    : angle       0.63350 ( 4674)
  hydrogen bonds       : bond        0.04935 (  239)
  hydrogen bonds       : angle       3.96356 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7960 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8104 (tttt)
REVERT: K   90 LEU cc_start: 0.8274 (tp) cc_final: 0.8057 (tt)
REVERT: K  129 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8046 (mtm-85)
REVERT: K  130 ASN cc_start: 0.8722 (m-40) cc_final: 0.8213 (m110)
REVERT: K  134 MET cc_start: 0.8656 (ttm) cc_final: 0.8418 (ttm)
REVERT: K  146 ARG cc_start: 0.8611 (tmm-80) cc_final: 0.8134 (ttt-90)
REVERT: K  164 MET cc_start: 0.8975 (tpp) cc_final: 0.7907 (tpp)
REVERT: K  167 ARG cc_start: 0.9052 (mtm180) cc_final: 0.8744 (mtm180)
REVERT: L   87 MET cc_start: 0.5931 (mmt) cc_final: 0.5602 (mmt)
  outliers start: 12
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0883
  time to fit residues: 8.7245
Evaluate side-chains
  73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  132 ILE
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain M residue   34 ASN
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   80 VAL
Chi-restraints excluded: chain M residue  131 THR
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0870
   chunk 12 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   overall best weight:    1.1762

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

Flipped N/Q/H residues before XYZ refinement:
M 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.076392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.067411 restraints weight = 19547.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.068650 restraints weight = 10213.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.069436 restraints weight = 6249.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.069934 restraints weight = 4242.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.070259 restraints weight = 3151.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3456  Z= 0.136
  Angle     :  0.616  11.628   4674  Z= 0.319
  Chirality :  0.043   0.313    508
  Planarity :  0.004   0.037    603
  Dihedral  :  4.305  17.220    452
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.15 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.41), residues: 413
  helix:  2.06 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.94 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 146 
 TYR   0.027   0.001   TYR M  85 
 PHE   0.021   0.001   PHE M  15 
 TRP   0.006   0.001   TRP K 176 
 HIS   0.009   0.002   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3456)
  covalent geometry    : angle       0.61594 ( 4674)
  hydrogen bonds       : bond        0.04788 (  239)
  hydrogen bonds       : angle       3.91836 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7876 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8116 (tttt)
REVERT: K   90 LEU cc_start: 0.8291 (tp) cc_final: 0.8075 (tt)
REVERT: K  130 ASN cc_start: 0.8693 (m-40) cc_final: 0.8208 (m110)
REVERT: K  134 MET cc_start: 0.8643 (ttm) cc_final: 0.8403 (ttm)
REVERT: K  146 ARG cc_start: 0.8593 (tmm-80) cc_final: 0.8046 (ttt-90)
REVERT: K  164 MET cc_start: 0.8983 (tpp) cc_final: 0.8021 (tpp)
REVERT: K  167 ARG cc_start: 0.9045 (mtm180) cc_final: 0.8709 (mtm180)
REVERT: L   82 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6654 (t80)
REVERT: L   87 MET cc_start: 0.5791 (mmt) cc_final: 0.5476 (mmt)
  outliers start: 12
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0796
  time to fit residues: 7.1474
Evaluate side-chains
  71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  132 ILE
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue   76 PHE
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain M residue   34 ASN
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue   80 VAL
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  131 THR
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
M 155 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.075004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.066136 restraints weight = 20650.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.067345 restraints weight = 10819.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.068108 restraints weight = 6634.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068618 restraints weight = 4505.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.068907 restraints weight = 3323.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3456  Z= 0.185
  Angle     :  0.628  13.608   4674  Z= 0.330
  Chirality :  0.041   0.137    508
  Planarity :  0.004   0.039    603
  Dihedral  :  4.440  19.474    452
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 18.59 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.41), residues: 413
  helix:  2.08 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.85 (0.56), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  48 
 TYR   0.019   0.002   TYR M  85 
 PHE   0.015   0.002   PHE K  24 
 TRP   0.006   0.001   TRP K 176 
 HIS   0.008   0.002   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 3456)
  covalent geometry    : angle       0.62835 ( 4674)
  hydrogen bonds       : bond        0.04823 (  239)
  hydrogen bonds       : angle       4.01953 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7852 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8156 (tttt)
REVERT: K  129 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8126 (mtm-85)
REVERT: K  130 ASN cc_start: 0.8758 (m-40) cc_final: 0.8253 (m110)
REVERT: K  134 MET cc_start: 0.8667 (ttm) cc_final: 0.8332 (ttm)
REVERT: K  146 ARG cc_start: 0.8627 (tmm-80) cc_final: 0.8029 (ttt-90)
REVERT: K  167 ARG cc_start: 0.9089 (mtm180) cc_final: 0.8853 (mtm180)
REVERT: L   82 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6892 (t80)
REVERT: L   87 MET cc_start: 0.5744 (mmt) cc_final: 0.5442 (mmt)
REVERT: M  130 MET cc_start: 0.8519 (ttt) cc_final: 0.8235 (tmm)
  outliers start: 16
  outliers final: 11
  residues processed: 71
  average time/residue: 0.0879
  time to fit residues: 7.4544
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  132 ILE
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue   76 PHE
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain M residue   19 ILE
Chi-restraints excluded: chain M residue   34 ASN
Chi-restraints excluded: chain M residue   73 PHE
Chi-restraints excluded: chain M residue   78 VAL
Chi-restraints excluded: chain M residue   80 VAL
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  131 THR
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
M  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.076654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.067694 restraints weight = 19821.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.068956 restraints weight = 10381.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.069746 restraints weight = 6301.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.070256 restraints weight = 4258.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.070563 restraints weight = 3162.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3456  Z= 0.124
  Angle     :  0.603  13.507   4674  Z= 0.307
  Chirality :  0.039   0.137    508
  Planarity :  0.004   0.036    603
  Dihedral  :  4.126  16.940    452
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.69 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.41), residues: 413
  helix:  2.32 (0.30), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.63 (0.57), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 167 
 TYR   0.023   0.001   TYR M  85 
 PHE   0.009   0.001   PHE K  24 
 TRP   0.007   0.001   TRP M  12 
 HIS   0.007   0.002   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3456)
  covalent geometry    : angle       0.60344 ( 4674)
  hydrogen bonds       : bond        0.04602 (  239)
  hydrogen bonds       : angle       3.78879 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7851 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8475 (mmmt) cc_final: 0.8117 (tttt)
REVERT: K   90 LEU cc_start: 0.8302 (tp) cc_final: 0.8030 (tt)
REVERT: K  130 ASN cc_start: 0.8688 (m-40) cc_final: 0.8187 (m-40)
REVERT: K  134 MET cc_start: 0.8662 (ttm) cc_final: 0.8386 (ttm)
REVERT: K  146 ARG cc_start: 0.8644 (tmm-80) cc_final: 0.8061 (ttt-90)
REVERT: L   87 MET cc_start: 0.5610 (mmt) cc_final: 0.5357 (mmt)
  outliers start: 8
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0851
  time to fit residues: 7.9614
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue   76 PHE
Chi-restraints excluded: chain M residue   34 ASN
Chi-restraints excluded: chain M residue   80 VAL
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.1980
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0030
   chunk 18 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.0194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.076848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.067847 restraints weight = 20420.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.069118 restraints weight = 10627.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.069903 restraints weight = 6466.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.070430 restraints weight = 4377.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.070737 restraints weight = 3227.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3456  Z= 0.131
  Angle     :  0.651  14.547   4674  Z= 0.326
  Chirality :  0.040   0.125    508
  Planarity :  0.004   0.037    603
  Dihedral  :  4.141  18.277    452
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 25.63 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.41), residues: 413
  helix:  2.26 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.63 (0.56), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 146 
 TYR   0.022   0.001   TYR M  85 
 PHE   0.024   0.001   PHE M  15 
 TRP   0.006   0.001   TRP M  12 
 HIS   0.006   0.002   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3456)
  covalent geometry    : angle       0.65125 ( 4674)
  hydrogen bonds       : bond        0.04646 (  239)
  hydrogen bonds       : angle       3.79404 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7852 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8107 (tttt)
REVERT: K   90 LEU cc_start: 0.8336 (tp) cc_final: 0.8110 (tt)
REVERT: K  130 ASN cc_start: 0.8674 (m-40) cc_final: 0.8194 (m-40)
REVERT: K  134 MET cc_start: 0.8697 (ttm) cc_final: 0.8353 (ttm)
REVERT: K  146 ARG cc_start: 0.8666 (tmm-80) cc_final: 0.8438 (tmm-80)
REVERT: L   82 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7257 (t80)
REVERT: L   87 MET cc_start: 0.5568 (mmt) cc_final: 0.5317 (mmt)
  outliers start: 7
  outliers final: 5
  residues processed: 69
  average time/residue: 0.0886
  time to fit residues: 7.2751
Evaluate side-chains
  73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue   76 PHE
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain M residue   66 VAL
Chi-restraints excluded: chain M residue  131 THR
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    2.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.075429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.066687 restraints weight = 20477.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.067927 restraints weight = 10660.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068652 restraints weight = 6439.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.069150 restraints weight = 4396.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.069474 restraints weight = 3262.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3456  Z= 0.187
  Angle     :  0.688  15.587   4674  Z= 0.349
  Chirality :  0.042   0.125    508
  Planarity :  0.004   0.039    603
  Dihedral  :  4.342  17.910    452
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 25.07 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.41), residues: 413
  helix:  2.15 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.63 (0.58), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  48 
 TYR   0.019   0.002   TYR M  85 
 PHE   0.016   0.002   PHE K  24 
 TRP   0.008   0.001   TRP K 176 
 HIS   0.007   0.002   HIS K 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 3456)
  covalent geometry    : angle       0.68850 ( 4674)
  hydrogen bonds       : bond        0.04726 (  239)
  hydrogen bonds       : angle       3.97441 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7842 (mtm-85)
REVERT: K  129 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8096 (mtm-85)
REVERT: K  130 ASN cc_start: 0.8705 (m-40) cc_final: 0.8224 (m-40)
REVERT: K  134 MET cc_start: 0.8698 (ttm) cc_final: 0.8274 (ttm)
REVERT: K  146 ARG cc_start: 0.8702 (tmm-80) cc_final: 0.8423 (tmm-80)
REVERT: L   82 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7299 (t80)
REVERT: L   87 MET cc_start: 0.5560 (mmt) cc_final: 0.5282 (mmt)
REVERT: M  130 MET cc_start: 0.7782 (tmm) cc_final: 0.7541 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0873
  time to fit residues: 6.8005
Evaluate side-chains
  60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  132 ILE
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue   76 PHE
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain M residue   38 THR
Chi-restraints excluded: chain M residue  131 THR
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.076443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.067587 restraints weight = 20290.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.068857 restraints weight = 10561.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.069611 restraints weight = 6388.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.070105 restraints weight = 4342.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.070436 restraints weight = 3224.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3456  Z= 0.138
  Angle     :  0.648  15.071   4674  Z= 0.323
  Chirality :  0.040   0.123    508
  Planarity :  0.004   0.037    603
  Dihedral  :  4.189  17.290    452
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 25.63 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.41), residues: 413
  helix:  2.31 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.64 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 167 
 TYR   0.021   0.001   TYR M  85 
 PHE   0.010   0.001   PHE K  24 
 TRP   0.006   0.001   TRP M  12 
 HIS   0.006   0.002   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3456)
  covalent geometry    : angle       0.64836 ( 4674)
  hydrogen bonds       : bond        0.04596 (  239)
  hydrogen bonds       : angle       3.81827 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7881 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8114 (tttt)
REVERT: K  130 ASN cc_start: 0.8720 (m-40) cc_final: 0.8185 (m-40)
REVERT: K  134 MET cc_start: 0.8723 (ttm) cc_final: 0.8347 (ttm)
REVERT: K  146 ARG cc_start: 0.8729 (tmm-80) cc_final: 0.8487 (tmm-80)
REVERT: L   87 MET cc_start: 0.5570 (mmt) cc_final: 0.5306 (mmt)
REVERT: M  130 MET cc_start: 0.7700 (tmm) cc_final: 0.7438 (tmm)
  outliers start: 4
  outliers final: 4
  residues processed: 66
  average time/residue: 0.0907
  time to fit residues: 7.0546
Evaluate side-chains
  58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue   76 PHE
Chi-restraints excluded: chain M residue  131 THR
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
K 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.076158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.067354 restraints weight = 20280.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068587 restraints weight = 10630.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.069324 restraints weight = 6486.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.069816 restraints weight = 4414.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.070148 restraints weight = 3281.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3456  Z= 0.149
  Angle     :  0.677  15.807   4674  Z= 0.336
  Chirality :  0.041   0.142    508
  Planarity :  0.004   0.038    603
  Dihedral  :  4.219  16.587    452
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 24.51 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.41), residues: 413
  helix:  2.24 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.81 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 167 
 TYR   0.021   0.001   TYR M  85 
 PHE   0.012   0.001   PHE K  24 
 TRP   0.004   0.001   TRP M  53 
 HIS   0.006   0.002   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3456)
  covalent geometry    : angle       0.67661 ( 4674)
  hydrogen bonds       : bond        0.04621 (  239)
  hydrogen bonds       : angle       3.83311 (  699)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7892 (mtm-85)
REVERT: K  129 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8092 (mtm-85)
REVERT: K  130 ASN cc_start: 0.8697 (m-40) cc_final: 0.8148 (m-40)
REVERT: K  134 MET cc_start: 0.8707 (ttm) cc_final: 0.8340 (ttm)
REVERT: K  146 ARG cc_start: 0.8714 (tmm-80) cc_final: 0.8483 (tmm-80)
REVERT: L   87 MET cc_start: 0.5555 (mmt) cc_final: 0.5299 (mmt)
REVERT: M  130 MET cc_start: 0.7720 (tmm) cc_final: 0.7454 (tmm)
  outliers start: 6
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0906
  time to fit residues: 6.4763
Evaluate side-chains
  62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  132 ILE
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue   76 PHE
Chi-restraints excluded: chain M residue   78 VAL
Chi-restraints excluded: chain M residue  131 THR
Chi-restraints excluded: chain M residue  157 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
K 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.076837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.068035 restraints weight = 20622.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.069244 restraints weight = 10886.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.069994 restraints weight = 6662.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.070477 restraints weight = 4545.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.070796 restraints weight = 3383.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3456  Z= 0.135
  Angle     :  0.661  15.603   4674  Z= 0.327
  Chirality :  0.040   0.137    508
  Planarity :  0.004   0.037    603
  Dihedral  :  4.187  16.268    452
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 24.79 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.42), residues: 413
  helix:  2.24 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.74 (0.58), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 167 
 TYR   0.024   0.001   TYR M  85 
 PHE   0.010   0.001   PHE K  24 
 TRP   0.006   0.001   TRP M  12 
 HIS   0.005   0.001   HIS K 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3456)
  covalent geometry    : angle       0.66145 ( 4674)
  hydrogen bonds       : bond        0.04571 (  239)
  hydrogen bonds       : angle       3.79448 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1301.29 seconds
wall clock time: 23 minutes 6.14 seconds (1386.14 seconds total)