Starting phenix.real_space_refine
on Fri Aug 22 13:35:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h9g_34566/08_2025/8h9g_34566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h9g_34566/08_2025/8h9g_34566.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h9g_34566/08_2025/8h9g_34566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h9g_34566/08_2025/8h9g_34566.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h9g_34566/08_2025/8h9g_34566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h9g_34566/08_2025/8h9g_34566.map"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
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 20 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: 1.19, per 1000 atoms: 0.35
  Number of scatterers: 3381
  At special positions: 0
  Unit cell: (79.57, 101.47, 205.86, 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: 0.24
  Conformation dependent library (CDL) restraints added in 135.3 milliseconds
  
  Enol-peptide restraints added in 953.7 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:
      15 helices and 1 sheets defined
      72.7% 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 30
      Proline residue:  K  27  - end of helix
    Processing helix  chain 'K' and resid 32 through 48
    Processing helix  chain 'K' and resid 54 through 121
      removed outlier: 3.970A  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
    Processing helix  chain 'K' and resid 194 through 206
      removed outlier: 4.074A  pdb=" N   LEU K 201 " --> pdb=" O   CYS K 197 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 41 through 55
    Processing helix  chain 'L' and resid 67 through 83
      removed outlier: 4.409A  pdb=" N   ARG L  73 " --> pdb=" O   GLN L  69 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 12 through 18
      removed outlier: 3.761A  pdb=" N   ILE M  18 " --> pdb=" O   ALA M  14 " (cutoff:3.500A)
    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: 3.810A  pdb=" N   VAL M  89 " --> pdb=" O   TYR M  85 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 126 through 130
      removed outlier: 3.735A  pdb=" N   MET M 130 " --> pdb=" O   PHE M 127 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 131 through 139
      removed outlier: 3.538A  pdb=" N   LEU M 135 " --> pdb=" O   THR M 131 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 140 through 143
      removed outlier: 3.517A  pdb=" N   LYS M 143 " --> pdb=" O   PRO M 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 140 through 143'
    Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13

    236 hydrogen bonds defined for protein.
    702 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: 0.35

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1086
        1.34 -     1.46: 576
        1.46 -     1.57: 1773
        1.57 -     1.69: 0
        1.69 -     1.81: 21
  Bond restraints: 3456
  Sorted by residual:
  bond pdb=" CB  PRO M 153 "
       pdb=" CG  PRO M 153 "
    ideal  model  delta    sigma   weight residual
    1.506  1.437  0.069 3.90e-02 6.57e+02 3.09e+00
  bond pdb=" CG1 ILE M  10 "
       pdb=" CD1 ILE M  10 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.44e+00
  bond pdb=" N   SER K 184 "
       pdb=" CA  SER K 184 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.90e-02 2.77e+03 2.26e+00
  bond pdb=" CB  VAL K 118 "
       pdb=" CG2 VAL K 118 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  bond pdb=" N   HIS K 122 "
       pdb=" CA  HIS K 122 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.35e-02 5.49e+03 1.43e+00
  ... (remaining 3451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 4325
        1.34 -     2.68: 284
        2.68 -     4.02: 54
        4.02 -     5.36: 8
        5.36 -     6.70: 3
  Bond angle restraints: 4674
  Sorted by residual:
  angle pdb=" N   ILE L 103 "
        pdb=" CA  ILE L 103 "
        pdb=" C   ILE L 103 "
      ideal   model   delta    sigma   weight residual
     113.42  107.77    5.65 1.17e+00 7.31e-01 2.34e+01
  angle pdb=" CA  ILE L 103 "
        pdb=" C   ILE L 103 "
        pdb=" N   GLU L 104 "
      ideal   model   delta    sigma   weight residual
     118.90  115.40    3.50 9.40e-01 1.13e+00 1.38e+01
  angle pdb=" C   PHE K 125 "
        pdb=" N   ASP K 126 "
        pdb=" CA  ASP K 126 "
      ideal   model   delta    sigma   weight residual
     120.72  115.25    5.47 1.67e+00 3.59e-01 1.07e+01
  angle pdb=" N   ARG K 121 "
        pdb=" CA  ARG K 121 "
        pdb=" C   ARG K 121 "
      ideal   model   delta    sigma   weight residual
     111.75  115.83   -4.08 1.28e+00 6.10e-01 1.02e+01
  angle pdb=" C   ILE K 174 "
        pdb=" N   ASN K 175 "
        pdb=" CA  ASN K 175 "
      ideal   model   delta    sigma   weight residual
     120.68  116.19    4.49 1.70e+00 3.46e-01 6.96e+00
  ... (remaining 4669 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.69: 1855
       16.69 -    33.37: 206
       33.37 -    50.06: 40
       50.06 -    66.75: 9
       66.75 -    83.43: 3
  Dihedral angle restraints: 2113
    sinusoidal: 862
      harmonic: 1251
  Sorted by residual:
  dihedral pdb=" CA  PHE L 100 "
           pdb=" C   PHE L 100 "
           pdb=" N   GLU L 101 "
           pdb=" CA  GLU L 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.81  -20.19     0      5.00e+00 4.00e-02 1.63e+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 -161.13  -18.87     0      5.00e+00 4.00e-02 1.42e+01
  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  162.25   17.75     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 2110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 262
       0.034 -    0.067: 169
       0.067 -    0.101: 58
       0.101 -    0.135: 15
       0.135 -    0.169: 4
  Chirality restraints: 508
  Sorted by residual:
  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    2.60   -0.17 2.00e-01 2.50e+01 7.11e-01
  chirality pdb=" CA  ILE L 103 "
            pdb=" N   ILE L 103 "
            pdb=" C   ILE L 103 "
            pdb=" CB  ILE L 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CB  VAL K 177 "
            pdb=" CA  VAL K 177 "
            pdb=" CG1 VAL K 177 "
            pdb=" CG2 VAL K 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.69e-01
  ... (remaining 505 not shown)

  Planarity restraints: 603
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE K  71 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.93e+00
        pdb=" C   ILE K  71 "    0.030 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=" C   LEU M  44 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO M  45 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO M  45 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO M  45 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE M  69 "    0.012 2.00e-02 2.50e+03   1.22e-02 2.60e+00
        pdb=" CG  PHE M  69 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE M  69 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE M  69 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE M  69 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE M  69 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE M  69 "    0.003 2.00e-02 2.50e+03
  ... (remaining 600 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 925
        2.80 -     3.33: 3321
        3.33 -     3.85: 5378
        3.85 -     4.38: 5777
        4.38 -     4.90: 9940
  Nonbonded interactions: 25341
  Sorted by model distance:
  nonbonded pdb=" OG1 THR L  56 "
            pdb=" O   GLY L  59 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" NH1 ARG K 121 "
            pdb=" O   ILE M  18 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" NH2 ARG K 143 "
            pdb=" O   GLU L  96 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" NH1 ARG K 154 "
            pdb=" O   THR L  89 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" O   GLU M  35 "
            pdb=" OG1 THR M  38 "
     model   vdw
     2.326 3.040
  ... (remaining 25336 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.000
  Find NCS groups from input model:        0.010
  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:5.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.069   3456  Z= 0.325
  Angle     :  0.770   6.703   4674  Z= 0.449
  Chirality :  0.048   0.169    508
  Planarity :  0.005   0.042    603
  Dihedral  : 14.927  83.433   1299
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  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: -2.39 (0.34), residues: 413
  helix: -1.14 (0.25), residues: 283
  sheet:  None (None), residues: 0
  loop : -2.34 (0.50), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG M  40 
 TYR   0.014   0.002   TYR K  51 
 PHE   0.028   0.003   PHE M  69 
 TRP   0.009   0.002   TRP M 103 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00770 ( 3456)
  covalent geometry    : angle       0.77015 ( 4674)
  hydrogen bonds       : bond        0.10907 (  236)
  hydrogen bonds       : angle       5.15326 (  702)

*********************** 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
  66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.106 
Fit side-chains
REVERT: K   98 GLN cc_start: 0.7378 (mm110) cc_final: 0.7164 (mt0)
REVERT: K  150 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6701 (mm-30)
REVERT: K  165 MET cc_start: 0.7818 (tpp) cc_final: 0.7109 (mmp)
REVERT: K  173 MET cc_start: 0.6700 (tpp) cc_final: 0.6448 (tpt)
REVERT: L   40 GLN cc_start: 0.6025 (pt0) cc_final: 0.5796 (pt0)
REVERT: L   96 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7909 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.5736
  time to fit residues: 38.8981
Evaluate side-chains
  50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
K  88 GLN
K  98 GLN
K 115 GLN
K 130 ASN
K 175 ASN
K 183 GLN
M 136 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.175537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140811 restraints weight = 5036.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.18
r_work: 0.3572 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3456  Z= 0.148
  Angle     :  0.596   9.662   4674  Z= 0.322
  Chirality :  0.041   0.150    508
  Planarity :  0.005   0.043    603
  Dihedral  :  5.397  55.054    452
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.49 %
    Favored  : 81.97 %
  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:  0.28 (0.41), residues: 413
  helix:  0.97 (0.29), residues: 286
  sheet:  None (None), residues: 0
  loop : -1.59 (0.59), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  48 
 TYR   0.009   0.001   TYR K 157 
 PHE   0.010   0.001   PHE M  15 
 TRP   0.011   0.001   TRP M  53 
 HIS   0.004   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3456)
  covalent geometry    : angle       0.59561 ( 4674)
  hydrogen bonds       : bond        0.05649 (  236)
  hydrogen bonds       : angle       4.19982 (  702)

*********************** 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
  63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.144 
Fit side-chains
REVERT: K   19 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7026 (tt0)
REVERT: K   98 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7053 (mt0)
REVERT: K  150 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6931 (mp0)
REVERT: K  165 MET cc_start: 0.7729 (tpp) cc_final: 0.6953 (mmp)
REVERT: L   40 GLN cc_start: 0.5815 (pt0) cc_final: 0.5540 (pt0)
REVERT: L   96 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8286 (mt-10)
  outliers start: 9
  outliers final: 4
  residues processed: 58
  average time/residue: 0.4595
  time to fit residues: 27.6263
Evaluate side-chains
  53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain M residue  112 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0770
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.8942

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

Flipped N/Q/H residues before XYZ refinement:
M  23 GLN
M 136 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.176657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.141971 restraints weight = 5031.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.20
r_work: 0.3581 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3456  Z= 0.145
  Angle     :  0.571   8.637   4674  Z= 0.308
  Chirality :  0.041   0.152    508
  Planarity :  0.005   0.043    603
  Dihedral  :  5.065  53.466    452
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 16.90 %
    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 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:  1.18 (0.42), residues: 413
  helix:  1.73 (0.30), residues: 282
  sheet:  None (None), residues: 0
  loop : -1.38 (0.58), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K 166 
 TYR   0.008   0.001   TYR M  55 
 PHE   0.010   0.001   PHE K 125 
 TRP   0.006   0.001   TRP M  33 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3456)
  covalent geometry    : angle       0.57101 ( 4674)
  hydrogen bonds       : bond        0.05334 (  236)
  hydrogen bonds       : angle       4.08020 (  702)

*********************** 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
  66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.104 
Fit side-chains
REVERT: K   98 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7026 (mt0)
REVERT: K  150 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6896 (mp0)
REVERT: K  154 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6738 (mmm-85)
REVERT: K  165 MET cc_start: 0.7737 (tpp) cc_final: 0.7084 (mmp)
REVERT: L   96 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8347 (mt-10)
REVERT: M  141 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6906 (pm20)
  outliers start: 16
  outliers final: 6
  residues processed: 64
  average time/residue: 0.5571
  time to fit residues: 36.6416
Evaluate side-chains
  53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  154 ARG
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain L residue   56 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  141 GLU
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:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 21 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.4135 r_free = 0.4135 target = 0.174306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.139503 restraints weight = 5004.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.17
r_work: 0.3553 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3456  Z= 0.194
  Angle     :  0.590   9.059   4674  Z= 0.319
  Chirality :  0.042   0.159    508
  Planarity :  0.005   0.041    603
  Dihedral  :  5.216  56.604    452
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 18.03 %
    Favored  : 77.18 %
  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:  1.38 (0.42), residues: 413
  helix:  1.85 (0.30), residues: 282
  sheet:  None (None), residues: 0
  loop : -1.22 (0.59), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 166 
 TYR   0.012   0.001   TYR M  56 
 PHE   0.015   0.002   PHE K 125 
 TRP   0.005   0.001   TRP M  33 
 HIS   0.002   0.001   HIS K 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 3456)
  covalent geometry    : angle       0.58954 ( 4674)
  hydrogen bonds       : bond        0.05613 (  236)
  hydrogen bonds       : angle       4.17380 (  702)

*********************** 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
  64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.156 
Fit side-chains
REVERT: K    7 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8264 (tp30)
REVERT: K   98 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7099 (mt0)
REVERT: K  104 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7865 (mp)
REVERT: K  150 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6951 (mp0)
REVERT: K  165 MET cc_start: 0.7746 (tpp) cc_final: 0.7024 (mmp)
REVERT: L   96 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: M  128 ASP cc_start: 0.8624 (p0) cc_final: 0.8390 (p0)
REVERT: M  141 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6935 (pm20)
  outliers start: 17
  outliers final: 7
  residues processed: 61
  average time/residue: 0.5108
  time to fit residues: 32.1971
Evaluate side-chains
  56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 GLU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  147 VAL
Chi-restraints excluded: chain K residue  164 MET
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   56 THR
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  141 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
L  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.177283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.142573 restraints weight = 5038.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.21
r_work: 0.3589 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3484 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3456  Z= 0.131
  Angle     :  0.550   8.044   4674  Z= 0.295
  Chirality :  0.039   0.143    508
  Planarity :  0.005   0.042    603
  Dihedral  :  4.896  53.191    452
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 20.85 %
    Favored  : 75.21 %
  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:  1.74 (0.43), residues: 413
  helix:  2.21 (0.30), residues: 284
  sheet:  None (None), residues: 0
  loop : -1.35 (0.59), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 166 
 TYR   0.009   0.001   TYR M  56 
 PHE   0.009   0.001   PHE M  15 
 TRP   0.006   0.001   TRP M  33 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 3456)
  covalent geometry    : angle       0.54992 ( 4674)
  hydrogen bonds       : bond        0.05124 (  236)
  hydrogen bonds       : angle       3.97484 (  702)

*********************** 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
  61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.147 
Fit side-chains
REVERT: K    7 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8198 (tp30)
REVERT: K  150 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6972 (mp0)
REVERT: K  154 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6685 (mmm-85)
REVERT: K  165 MET cc_start: 0.7722 (tpp) cc_final: 0.6916 (mmp)
REVERT: K  174 ILE cc_start: 0.4850 (tt) cc_final: 0.4097 (pp)
REVERT: L   48 ARG cc_start: 0.7443 (ppt170) cc_final: 0.7129 (ppt170)
REVERT: L   96 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8346 (mt-10)
REVERT: M  141 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6819 (pm20)
  outliers start: 14
  outliers final: 5
  residues processed: 58
  average time/residue: 0.5846
  time to fit residues: 34.9388
Evaluate side-chains
  50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 GLU
Chi-restraints excluded: chain K residue  147 VAL
Chi-restraints excluded: chain K residue  154 ARG
Chi-restraints excluded: chain K residue  164 MET
Chi-restraints excluded: chain L residue   56 THR
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  141 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0370
   chunk 27 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0040
   chunk 14 optimal weight:    0.6980
   chunk 29 optimal weight:    9.9990
   overall best weight:    0.4470

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

Flipped N/Q/H residues before XYZ refinement:
L  40 GLN
M  22 ASN
M 136 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.178677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.143956 restraints weight = 4946.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 2.22
r_work: 0.3617 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3513 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3456  Z= 0.125
  Angle     :  0.554   9.968   4674  Z= 0.295
  Chirality :  0.038   0.145    508
  Planarity :  0.005   0.041    603
  Dihedral  :  4.685  49.600    452
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.00 %
    Favored  : 74.65 %
  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:  2.09 (0.43), residues: 413
  helix:  2.44 (0.30), residues: 284
  sheet:  None (None), residues: 0
  loop : -1.12 (0.59), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 166 
 TYR   0.008   0.001   TYR M  56 
 PHE   0.008   0.001   PHE M  15 
 TRP   0.005   0.001   TRP M  33 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3456)
  covalent geometry    : angle       0.55376 ( 4674)
  hydrogen bonds       : bond        0.04900 (  236)
  hydrogen bonds       : angle       3.87007 (  702)

*********************** 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
  69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.118 
Fit side-chains
REVERT: K    7 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8192 (tp30)
REVERT: K  104 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7849 (mp)
REVERT: K  150 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6926 (mp0)
REVERT: K  154 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6745 (mmm-85)
REVERT: K  165 MET cc_start: 0.7777 (tpp) cc_final: 0.6980 (mmp)
REVERT: K  174 ILE cc_start: 0.4918 (tt) cc_final: 0.4190 (pp)
REVERT: L   48 ARG cc_start: 0.7457 (ppt170) cc_final: 0.7144 (ppt170)
REVERT: L   96 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8291 (mt-10)
REVERT: M  141 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6833 (pm20)
  outliers start: 19
  outliers final: 7
  residues processed: 65
  average time/residue: 0.5667
  time to fit residues: 37.9230
Evaluate side-chains
  57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 GLU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  147 VAL
Chi-restraints excluded: chain K residue  154 ARG
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   56 THR
Chi-restraints excluded: chain M residue   51 ILE
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  141 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0370
   chunk 9 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0060
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.4874

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

Flipped N/Q/H residues before XYZ refinement:
K 175 ASN
L  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.179316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.144761 restraints weight = 5089.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 2.25
r_work: 0.3626 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   3456  Z= 0.121
  Angle     :  0.543   8.964   4674  Z= 0.288
  Chirality :  0.038   0.146    508
  Planarity :  0.005   0.040    603
  Dihedral  :  4.525  47.923    452
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.97 %
    Favored  : 74.08 %
  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:  2.22 (0.43), residues: 413
  helix:  2.54 (0.30), residues: 287
  sheet:  None (None), residues: 0
  loop : -1.17 (0.59), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 166 
 TYR   0.007   0.001   TYR M  56 
 PHE   0.010   0.001   PHE L  82 
 TRP   0.005   0.001   TRP M  12 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 3456)
  covalent geometry    : angle       0.54292 ( 4674)
  hydrogen bonds       : bond        0.04823 (  236)
  hydrogen bonds       : angle       3.76995 (  702)

*********************** 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
  63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: K    7 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8231 (tp30)
REVERT: K  104 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7852 (mp)
REVERT: K  165 MET cc_start: 0.7801 (tpp) cc_final: 0.7060 (mmp)
REVERT: K  174 ILE cc_start: 0.4872 (tt) cc_final: 0.4173 (pp)
REVERT: L   48 ARG cc_start: 0.7480 (ppt170) cc_final: 0.7223 (ppt170)
REVERT: L   96 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8264 (mt-10)
REVERT: M  118 MET cc_start: 0.7448 (tpp) cc_final: 0.7159 (tpp)
REVERT: M  141 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7349 (pm20)
  outliers start: 14
  outliers final: 7
  residues processed: 61
  average time/residue: 0.5815
  time to fit residues: 36.5279
Evaluate side-chains
  56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue    7 GLU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  147 VAL
Chi-restraints excluded: chain K residue  175 ASN
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   56 THR
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  141 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** K 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.176792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.141974 restraints weight = 5018.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.20
r_work: 0.3582 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3456  Z= 0.163
  Angle     :  0.601  10.018   4674  Z= 0.315
  Chirality :  0.040   0.151    508
  Planarity :  0.005   0.040    603
  Dihedral  :  4.713  53.192    452
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 23.38 %
    Favored  : 72.68 %
  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:  2.26 (0.43), residues: 413
  helix:  2.56 (0.30), residues: 284
  sheet:  None (None), residues: 0
  loop : -1.05 (0.60), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 166 
 TYR   0.007   0.001   TYR K 148 
 PHE   0.012   0.001   PHE K 125 
 TRP   0.013   0.001   TRP K 176 
 HIS   0.002   0.001   HIS K 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3456)
  covalent geometry    : angle       0.60062 ( 4674)
  hydrogen bonds       : bond        0.05082 (  236)
  hydrogen bonds       : angle       3.86823 (  702)

*********************** 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
  58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.155 
Fit side-chains
REVERT: K  104 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7849 (mp)
REVERT: K  150 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7008 (mp0)
REVERT: K  165 MET cc_start: 0.7832 (tpp) cc_final: 0.7094 (mmp)
REVERT: K  174 ILE cc_start: 0.5020 (tt) cc_final: 0.4310 (pp)
REVERT: L   48 ARG cc_start: 0.7499 (ppt170) cc_final: 0.7242 (ppt170)
REVERT: L   96 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8275 (mt-10)
REVERT: M   82 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.3996 (pm20)
REVERT: M  128 ASP cc_start: 0.8955 (p0) cc_final: 0.8667 (p0)
REVERT: M  141 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6932 (pm20)
  outliers start: 14
  outliers final: 7
  residues processed: 56
  average time/residue: 0.5275
  time to fit residues: 30.5405
Evaluate side-chains
  54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  147 VAL
Chi-restraints excluded: chain K residue  175 ASN
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain L residue   45 ASP
Chi-restraints excluded: chain M residue   82 GLU
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  141 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0670
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0270
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
K 175 ASN
L  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.179313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.144556 restraints weight = 5029.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.24
r_work: 0.3617 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3456  Z= 0.124
  Angle     :  0.558  10.154   4674  Z= 0.292
  Chirality :  0.038   0.145    508
  Planarity :  0.005   0.039    603
  Dihedral  :  4.523  50.562    452
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 23.10 %
    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 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:  2.37 (0.43), residues: 413
  helix:  2.64 (0.30), residues: 287
  sheet:  None (None), residues: 0
  loop : -1.08 (0.59), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 166 
 TYR   0.007   0.001   TYR M  56 
 PHE   0.008   0.001   PHE M  15 
 TRP   0.005   0.001   TRP M  12 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 3456)
  covalent geometry    : angle       0.55788 ( 4674)
  hydrogen bonds       : bond        0.04802 (  236)
  hydrogen bonds       : angle       3.75591 (  702)

*********************** 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
  61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.129 
Fit side-chains
REVERT: K  104 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7843 (mp)
REVERT: K  150 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7007 (mp0)
REVERT: K  165 MET cc_start: 0.7812 (tpp) cc_final: 0.7097 (mmp)
REVERT: K  174 ILE cc_start: 0.4957 (tt) cc_final: 0.4254 (pp)
REVERT: L   48 ARG cc_start: 0.7500 (ppt170) cc_final: 0.7245 (ppt170)
REVERT: L   96 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8274 (mt-10)
REVERT: M  128 ASP cc_start: 0.8935 (p0) cc_final: 0.8652 (p0)
REVERT: M  141 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6833 (pm20)
  outliers start: 14
  outliers final: 7
  residues processed: 59
  average time/residue: 0.5341
  time to fit residues: 32.5070
Evaluate side-chains
  56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   25 LEU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  147 VAL
Chi-restraints excluded: chain K residue  175 ASN
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  141 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 32 optimal weight:   20.0000
   chunk 25 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 39 optimal weight:    0.3980
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** K 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  40 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 = 0.4190 r_free = 0.4190 target = 0.179260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.144465 restraints weight = 4992.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.21
r_work: 0.3618 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3456  Z= 0.125
  Angle     :  0.562  10.403   4674  Z= 0.297
  Chirality :  0.038   0.159    508
  Planarity :  0.005   0.042    603
  Dihedral  :  4.501  50.004    452
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 23.66 %
    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 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:  2.49 (0.43), residues: 413
  helix:  2.74 (0.30), residues: 284
  sheet:  None (None), residues: 0
  loop : -0.99 (0.60), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K 129 
 TYR   0.007   0.001   TYR M  56 
 PHE   0.008   0.001   PHE K 125 
 TRP   0.005   0.001   TRP M  12 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3456)
  covalent geometry    : angle       0.56249 ( 4674)
  hydrogen bonds       : bond        0.04822 (  236)
  hydrogen bonds       : angle       3.73826 (  702)

********************** 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
  56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.138 
Fit side-chains
REVERT: K  104 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7834 (mp)
REVERT: K  150 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7012 (mp0)
REVERT: K  165 MET cc_start: 0.7830 (tpp) cc_final: 0.7046 (mmp)
REVERT: K  174 ILE cc_start: 0.4974 (tt) cc_final: 0.4301 (pp)
REVERT: L   48 ARG cc_start: 0.7515 (ppt170) cc_final: 0.7264 (ppt170)
REVERT: L   96 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8264 (mt-10)
REVERT: M  128 ASP cc_start: 0.8925 (p0) cc_final: 0.8634 (p0)
REVERT: M  141 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6828 (pm20)
  outliers start: 12
  outliers final: 6
  residues processed: 55
  average time/residue: 0.5134
  time to fit residues: 29.2221
Evaluate side-chains
  53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   25 LEU
Chi-restraints excluded: chain K residue  104 ILE
Chi-restraints excluded: chain K residue  147 VAL
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Chi-restraints excluded: chain M residue  141 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    0.2980
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
K 172 HIS
L  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.178857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143939 restraints weight = 5060.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.22
r_work: 0.3609 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3456  Z= 0.132
  Angle     :  0.565  10.082   4674  Z= 0.299
  Chirality :  0.038   0.158    508
  Planarity :  0.005   0.039    603
  Dihedral  :  4.532  51.138    452
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 24.23 %
    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:  2.40 (0.43), residues: 413
  helix:  2.66 (0.30), residues: 287
  sheet:  None (None), residues: 0
  loop : -1.05 (0.59), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 129 
 TYR   0.006   0.001   TYR M  56 
 PHE   0.009   0.001   PHE K 125 
 TRP   0.006   0.001   TRP K 176 
 HIS   0.003   0.001   HIS K 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3456)
  covalent geometry    : angle       0.56507 ( 4674)
  hydrogen bonds       : bond        0.04888 (  236)
  hydrogen bonds       : angle       3.77090 (  702)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2459.65 seconds
wall clock time: 42 minutes 35.36 seconds (2555.36 seconds total)