Starting phenix.real_space_refine
on Tue Feb 11 00:31:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h9r_34578/02_2025/8h9r_34578.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h9r_34578/02_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_34578/02_2025/8h9r_34578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h9r_34578/02_2025/8h9r_34578.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h9r_34578/02_2025/8h9r_34578.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h9r_34578/02_2025/8h9r_34578.cif"
  }
  resolution = 3.97
  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=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.65, per 1000 atoms: 1.38
  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: 0.87
  Conformation dependent library (CDL) restraints added in 385.5 milliseconds
  

  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: 0.26
  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: 0.82

  Time building geometry restraints manager: 1.00 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:             6.110
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.660
  Find NCS groups from input model:        0.030
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.950
-------------------------------------------------------------------------------
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= 0.393
  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 (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: -1.99 (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
 TRP   0.010   0.002   TRP K 176 
 HIS   0.011   0.003   HIS K 172 
 PHE   0.021   0.003   PHE M  69 
 TYR   0.015   0.002   TYR K 145 
 ARG   0.005   0.001   ARG L  54 

*********************** 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  : 0.386 
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: 0.2306
  time to fit residues: 26.1876
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  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0980
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3595 r_free = 0.3595 target = 0.076234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.067197 restraints weight = 19923.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.068375 restraints weight = 10392.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.069113 restraints weight = 6330.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3456  Z= 0.192
  Angle     :  0.643   7.231   4674  Z= 0.340
  Chirality :  0.043   0.147    508
  Planarity :  0.005   0.037    603
  Dihedral  :  4.612  21.808    452
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 13.52 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.63 (0.41), residues: 413
  helix:  1.20 (0.30), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.43 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP M  53 
 HIS   0.008   0.002   HIS K 172 
 PHE   0.022   0.002   PHE M  15 
 TYR   0.024   0.001   TYR M  85 
 ARG   0.005   0.001   ARG L  54 

*********************** 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
  104 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7922 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8242 (tttt)
REVERT: K   90 LEU cc_start: 0.8216 (tp) cc_final: 0.7953 (tt)
REVERT: K  126 ASP cc_start: 0.7785 (p0) cc_final: 0.7456 (p0)
REVERT: K  129 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8214 (mtm-85)
REVERT: K  134 MET cc_start: 0.8674 (ttm) cc_final: 0.8465 (ttm)
REVERT: K  146 ARG cc_start: 0.8537 (tmm-80) cc_final: 0.7964 (ttt-90)
REVERT: K  164 MET cc_start: 0.8978 (tpp) cc_final: 0.8227 (tpp)
REVERT: K  167 ARG cc_start: 0.9055 (mtm180) cc_final: 0.8823 (mtm180)
REVERT: L   94 LYS cc_start: 0.8718 (tmmt) cc_final: 0.8516 (tmmt)
REVERT: M  118 MET cc_start: 0.8361 (tpp) cc_final: 0.8111 (tpp)
  outliers start: 12
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1861
  time to fit residues: 21.3738
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  : 0.403 
-------------------------------------------------------------------------------
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 12 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.075878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.066902 restraints weight = 19361.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.068097 restraints weight = 10185.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.068845 restraints weight = 6247.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2796

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= 0.194
  Angle     :  0.639   8.429   4674  Z= 0.333
  Chirality :  0.045   0.343    508
  Planarity :  0.004   0.039    603
  Dihedral  :  4.408  19.731    452
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 17.46 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.38 (0.41), residues: 413
  helix:  1.77 (0.30), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.16 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP M  53 
 HIS   0.011   0.002   HIS K 158 
 PHE   0.013   0.001   PHE K  24 
 TYR   0.032   0.001   TYR M  85 
 ARG   0.003   0.000   ARG L  54 

*********************** 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
  87 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7924 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8244 (tttt)
REVERT: K   90 LEU cc_start: 0.8282 (tp) cc_final: 0.8062 (tt)
REVERT: K  129 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8191 (mtm-85)
REVERT: K  130 ASN cc_start: 0.8728 (m-40) cc_final: 0.8256 (m110)
REVERT: K  134 MET cc_start: 0.8684 (ttm) cc_final: 0.8432 (ttm)
REVERT: K  146 ARG cc_start: 0.8603 (tmm-80) cc_final: 0.8105 (ttt-90)
REVERT: K  164 MET cc_start: 0.9032 (tpp) cc_final: 0.8608 (tpp)
REVERT: K  167 ARG cc_start: 0.9112 (mtm180) cc_final: 0.8811 (mtm180)
REVERT: L   94 LYS cc_start: 0.8707 (tmmt) cc_final: 0.8496 (tmmt)
REVERT: M   60 VAL cc_start: 0.7914 (t) cc_final: 0.7710 (p)
  outliers start: 14
  outliers final: 10
  residues processed: 79
  average time/residue: 0.1969
  time to fit residues: 18.3089
Evaluate side-chains
  74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   50 ILE
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  132 ILE
Chi-restraints excluded: chain L residue   45 ASP
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  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 33 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.075252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.066247 restraints weight = 20119.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.067496 restraints weight = 10523.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.068239 restraints weight = 6396.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3456  Z= 0.240
  Angle     :  0.643  12.190   4674  Z= 0.334
  Chirality :  0.044   0.315    508
  Planarity :  0.004   0.039    603
  Dihedral  :  4.491  18.329    452
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 18.31 %
    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 (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:  1.59 (0.41), residues: 413
  helix:  1.91 (0.30), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.02 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K 176 
 HIS   0.009   0.002   HIS K 158 
 PHE   0.018   0.002   PHE M  15 
 TYR   0.029   0.002   TYR M  85 
 ARG   0.003   0.000   ARG K 146 

*********************** 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
  83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.437 
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: 0.8180 (mtt180) cc_final: 0.7856 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8186 (tttt)
REVERT: K  126 ASP cc_start: 0.7886 (p0) cc_final: 0.7433 (p0)
REVERT: K  130 ASN cc_start: 0.8730 (m-40) cc_final: 0.8247 (m110)
REVERT: K  134 MET cc_start: 0.8675 (ttm) cc_final: 0.8430 (ttm)
REVERT: K  146 ARG cc_start: 0.8566 (tmm-80) cc_final: 0.7979 (ttt-90)
REVERT: K  164 MET cc_start: 0.9027 (tpp) cc_final: 0.8092 (tpp)
REVERT: K  167 ARG cc_start: 0.9075 (mtm180) cc_final: 0.8743 (mtm180)
REVERT: L   82 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6720 (t80)
REVERT: L   87 MET cc_start: 0.6049 (mmt) cc_final: 0.5730 (mmt)
REVERT: M   60 VAL cc_start: 0.7938 (t) cc_final: 0.7695 (p)
  outliers start: 17
  outliers final: 12
  residues processed: 75
  average time/residue: 0.1825
  time to fit residues: 16.1702
Evaluate side-chains
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   50 ILE
Chi-restraints excluded: chain K residue  108 ILE
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   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
Chi-restraints excluded: chain M residue  160 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
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 = 0.3580 r_free = 0.3580 target = 0.075758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.066796 restraints weight = 20137.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.068044 restraints weight = 10478.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.068803 restraints weight = 6348.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.3075

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= 0.212
  Angle     :  0.628  14.835   4674  Z= 0.323
  Chirality :  0.043   0.313    508
  Planarity :  0.004   0.038    603
  Dihedral  :  4.381  19.537    452
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 20.56 %
    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 (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:  1.87 (0.41), residues: 413
  helix:  2.04 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.72 (0.56), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K 176 
 HIS   0.007   0.002   HIS K 158 
 PHE   0.013   0.001   PHE K  24 
 TYR   0.023   0.001   TYR M  85 
 ARG   0.002   0.000   ARG L  48 

*********************** 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
  82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7837 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8194 (tttt)
REVERT: K  130 ASN cc_start: 0.8693 (m-40) cc_final: 0.8232 (m110)
REVERT: K  134 MET cc_start: 0.8671 (ttm) cc_final: 0.8302 (ttm)
REVERT: K  146 ARG cc_start: 0.8631 (tmm-80) cc_final: 0.8055 (ttt-90)
REVERT: K  164 MET cc_start: 0.9043 (tpp) cc_final: 0.8114 (tpp)
REVERT: K  167 ARG cc_start: 0.9089 (mtm180) cc_final: 0.8801 (mtm180)
REVERT: L   82 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6907 (t80)
REVERT: L   87 MET cc_start: 0.5886 (mmt) cc_final: 0.5561 (mmt)
REVERT: L   94 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8350 (tmtt)
  outliers start: 12
  outliers final: 11
  residues processed: 76
  average time/residue: 0.1884
  time to fit residues: 16.8532
Evaluate side-chains
  74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   50 ILE
Chi-restraints excluded: chain K residue  108 ILE
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   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
Chi-restraints excluded: chain M residue  160 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0010
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.9388

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.076583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.067539 restraints weight = 20296.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.068800 restraints weight = 10552.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.069581 restraints weight = 6395.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3456  Z= 0.175
  Angle     :  0.601  13.360   4674  Z= 0.303
  Chirality :  0.042   0.340    508
  Planarity :  0.004   0.037    603
  Dihedral  :  4.199  18.073    452
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 22.25 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.09 (0.41), residues: 413
  helix:  2.21 (0.29), residues: 287
  sheet:  None (None), residues: 0
  loop : -0.59 (0.55), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP M  12 
 HIS   0.006   0.002   HIS K 172 
 PHE   0.023   0.001   PHE M  15 
 TYR   0.024   0.001   TYR M  85 
 ARG   0.002   0.000   ARG K 146 

*********************** 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
  83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7849 (mtm-85)
REVERT: K   48 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8183 (tttt)
REVERT: K  109 ASP cc_start: 0.8684 (m-30) cc_final: 0.8454 (p0)
REVERT: K  129 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8051 (mtm-85)
REVERT: K  130 ASN cc_start: 0.8667 (m-40) cc_final: 0.8244 (m110)
REVERT: K  134 MET cc_start: 0.8689 (ttm) cc_final: 0.8409 (ttm)
REVERT: K  146 ARG cc_start: 0.8634 (tmm-80) cc_final: 0.8054 (ttt-90)
REVERT: K  164 MET cc_start: 0.9061 (tpp) cc_final: 0.8156 (tpp)
REVERT: K  167 ARG cc_start: 0.9111 (mtm180) cc_final: 0.8862 (mtm180)
REVERT: L   82 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7042 (t80)
REVERT: L   87 MET cc_start: 0.5750 (mmt) cc_final: 0.5462 (mmt)
REVERT: M   82 GLU cc_start: 0.7881 (pp20) cc_final: 0.7607 (pp20)
REVERT: M  130 MET cc_start: 0.7781 (tmm) cc_final: 0.7453 (tmm)
REVERT: M  155 GLN cc_start: 0.8385 (pt0) cc_final: 0.8131 (pt0)
  outliers start: 10
  outliers final: 6
  residues processed: 78
  average time/residue: 0.1857
  time to fit residues: 17.2421
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  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  179 LYS
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   89 VAL
Chi-restraints excluded: chain M residue  131 THR
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 15 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.075053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.066154 restraints weight = 20659.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.067393 restraints weight = 10716.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.068162 restraints weight = 6482.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3456  Z= 0.234
  Angle     :  0.614  14.388   4674  Z= 0.318
  Chirality :  0.040   0.119    508
  Planarity :  0.004   0.038    603
  Dihedral  :  4.301  18.986    452
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 22.54 %
    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 (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:  1.99 (0.41), residues: 413
  helix:  2.17 (0.29), residues: 287
  sheet:  None (None), residues: 0
  loop : -0.73 (0.55), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K 176 
 HIS   0.006   0.002   HIS K 172 
 PHE   0.014   0.002   PHE K  24 
 TYR   0.019   0.002   TYR M  85 
 ARG   0.003   0.001   ARG L  48 

*********************** 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
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7854 (mtm-85)
REVERT: K  129 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8163 (mtm-85)
REVERT: K  130 ASN cc_start: 0.8693 (m-40) cc_final: 0.8304 (m110)
REVERT: K  134 MET cc_start: 0.8716 (ttm) cc_final: 0.8364 (ttm)
REVERT: K  146 ARG cc_start: 0.8675 (tmm-80) cc_final: 0.8384 (tmm-80)
REVERT: K  164 MET cc_start: 0.9097 (tpp) cc_final: 0.7993 (tpp)
REVERT: K  167 ARG cc_start: 0.9099 (mtm180) cc_final: 0.8853 (mtm180)
REVERT: L   82 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7283 (t80)
REVERT: L   87 MET cc_start: 0.5693 (mmt) cc_final: 0.5375 (mmt)
REVERT: M   82 GLU cc_start: 0.7873 (pp20) cc_final: 0.7595 (pp20)
  outliers start: 14
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1905
  time to fit residues: 16.0290
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   50 ILE
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 0 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.7158

-------------------------------------------------------------------------------
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 = 0.076755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.067942 restraints weight = 20397.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.069183 restraints weight = 10597.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.069940 restraints weight = 6438.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3456  Z= 0.158
  Angle     :  0.598  13.910   4674  Z= 0.301
  Chirality :  0.039   0.125    508
  Planarity :  0.004   0.036    603
  Dihedral  :  4.031  17.367    452
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 26.20 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.35 (0.42), residues: 413
  helix:  2.44 (0.30), residues: 287
  sheet:  None (None), residues: 0
  loop : -0.57 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP M  12 
 HIS   0.005   0.002   HIS K 172 
 PHE   0.008   0.001   PHE K  24 
 TYR   0.022   0.001   TYR M  85 
 ARG   0.001   0.000   ARG K 166 

*********************** 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
  74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7878 (mtm-85)
REVERT: K   90 LEU cc_start: 0.8610 (tt) cc_final: 0.8178 (mm)
REVERT: K  129 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.8098 (mtm-85)
REVERT: K  130 ASN cc_start: 0.8685 (m-40) cc_final: 0.8240 (m110)
REVERT: K  134 MET cc_start: 0.8713 (ttm) cc_final: 0.8409 (ttm)
REVERT: K  146 ARG cc_start: 0.8702 (tmm-80) cc_final: 0.8480 (tmm-80)
REVERT: K  164 MET cc_start: 0.9089 (tpp) cc_final: 0.8160 (tpp)
REVERT: K  167 ARG cc_start: 0.9157 (mtm180) cc_final: 0.8905 (mtm180)
REVERT: L   87 MET cc_start: 0.5638 (mmt) cc_final: 0.5367 (mmt)
REVERT: M   37 LEU cc_start: 0.9569 (mt) cc_final: 0.8843 (mp)
REVERT: M   82 GLU cc_start: 0.7851 (pp20) cc_final: 0.7600 (pp20)
REVERT: M  130 MET cc_start: 0.7645 (tmm) cc_final: 0.7412 (tmm)
  outliers start: 3
  outliers final: 3
  residues processed: 73
  average time/residue: 0.1863
  time to fit residues: 16.0838
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
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  157 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0010
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.5792

-------------------------------------------------------------------------------
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 = 0.3589 r_free = 0.3589 target = 0.076093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.067221 restraints weight = 20381.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.068455 restraints weight = 10690.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.069211 restraints weight = 6484.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3832

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= 0.196
  Angle     :  0.651  15.058   4674  Z= 0.317
  Chirality :  0.040   0.125    508
  Planarity :  0.004   0.037    603
  Dihedral  :  4.072  17.521    452
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 25.63 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.29 (0.41), residues: 413
  helix:  2.38 (0.29), residues: 287
  sheet:  None (None), residues: 0
  loop : -0.56 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K 176 
 HIS   0.004   0.001   HIS K 158 
 PHE   0.023   0.002   PHE M  15 
 TYR   0.020   0.001   TYR M  85 
 ARG   0.003   0.000   ARG K 141 

*********************** 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
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7923 (mtm-85)
REVERT: K   90 LEU cc_start: 0.8640 (tt) cc_final: 0.8277 (mm)
REVERT: K  130 ASN cc_start: 0.8670 (m-40) cc_final: 0.8236 (m110)
REVERT: K  134 MET cc_start: 0.8676 (ttm) cc_final: 0.8330 (ttm)
REVERT: K  146 ARG cc_start: 0.8718 (tmm-80) cc_final: 0.8499 (tmm-80)
REVERT: K  164 MET cc_start: 0.9082 (tpp) cc_final: 0.7930 (tpp)
REVERT: K  167 ARG cc_start: 0.9119 (mtm180) cc_final: 0.8859 (mtm180)
REVERT: L   87 MET cc_start: 0.5661 (mmt) cc_final: 0.5378 (mmt)
REVERT: M   37 LEU cc_start: 0.9585 (mt) cc_final: 0.9034 (mp)
REVERT: M   82 GLU cc_start: 0.7823 (pp20) cc_final: 0.7601 (pp20)
REVERT: M  130 MET cc_start: 0.7711 (tmm) cc_final: 0.7445 (tmm)
  outliers start: 5
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1936
  time to fit residues: 17.0284
Evaluate side-chains
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
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   19 ILE
Chi-restraints excluded: chain M residue   80 VAL
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 16 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0000
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
M  74 ASN
M 155 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.077303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.068420 restraints weight = 20079.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.069653 restraints weight = 10426.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.070350 restraints weight = 6321.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3456  Z= 0.165
  Angle     :  0.661  14.778   4674  Z= 0.320
  Chirality :  0.039   0.125    508
  Planarity :  0.004   0.036    603
  Dihedral  :  3.922  17.199    452
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 26.48 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.36 (0.41), residues: 413
  helix:  2.45 (0.30), residues: 287
  sheet:  None (None), residues: 0
  loop : -0.58 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP M  12 
 HIS   0.004   0.001   HIS K 158 
 PHE   0.008   0.001   PHE L 100 
 TYR   0.023   0.001   TYR M  85 
 ARG   0.002   0.000   ARG K 141 

********************** 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
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   13 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7857 (mtm-85)
REVERT: K   90 LEU cc_start: 0.8594 (tt) cc_final: 0.8225 (mm)
REVERT: K  130 ASN cc_start: 0.8639 (m-40) cc_final: 0.8192 (m110)
REVERT: K  134 MET cc_start: 0.8638 (ttm) cc_final: 0.8396 (ttm)
REVERT: K  146 ARG cc_start: 0.8713 (tmm-80) cc_final: 0.8511 (tmm-80)
REVERT: K  164 MET cc_start: 0.9019 (tpp) cc_final: 0.7894 (tpp)
REVERT: K  167 ARG cc_start: 0.9102 (mtm180) cc_final: 0.8831 (mtm180)
REVERT: L   87 MET cc_start: 0.5597 (mmt) cc_final: 0.5355 (mmt)
REVERT: M   37 LEU cc_start: 0.9582 (mt) cc_final: 0.8837 (mp)
REVERT: M  130 MET cc_start: 0.7601 (tmm) cc_final: 0.7354 (tmm)
  outliers start: 6
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1703
  time to fit residues: 15.3562
Evaluate side-chains
  65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
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   66 VAL
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 9 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.077327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.068272 restraints weight = 20575.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.069515 restraints weight = 10860.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.070279 restraints weight = 6658.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3456  Z= 0.181
  Angle     :  0.692  15.302   4674  Z= 0.334
  Chirality :  0.039   0.132    508
  Planarity :  0.004   0.037    603
  Dihedral  :  3.937  17.259    452
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 27.89 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  2.31 (0.41), residues: 413
  helix:  2.43 (0.29), residues: 287
  sheet:  None (None), residues: 0
  loop : -0.66 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP M  12 
 HIS   0.004   0.001   HIS K 158 
 PHE   0.008   0.001   PHE L 100 
 TYR   0.025   0.001   TYR M  85 
 ARG   0.002   0.000   ARG K 141 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2347.93 seconds
wall clock time: 42 minutes 28.06 seconds (2548.06 seconds total)