Starting phenix.real_space_refine
on Wed Jul 23 13:30:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h9k_34570/07_2025/8h9k_34570.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h9k_34570/07_2025/8h9k_34570.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h9k_34570/07_2025/8h9k_34570.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h9k_34570/07_2025/8h9k_34570.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h9k_34570/07_2025/8h9k_34570.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h9k_34570/07_2025/8h9k_34570.cif"
  }
  resolution = 3.51
  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=   0.011
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 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.57, per 1000 atoms: 1.65
  Number of scatterers: 3381
  At special positions: 0
  Unit cell: (56.21, 102.93, 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: 0.85
  Conformation dependent library (CDL) restraints added in 404.4 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:
      14 helices and 1 sheets defined
      71.5% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  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 120
      removed outlier: 3.836A  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
    Processing helix  chain 'L' and resid 41 through 55
      removed outlier: 3.884A  pdb=" N   ARG L  48 " --> pdb=" O   VAL L  44 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLU L  49 " --> pdb=" O   ASP L  45 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 67 through 83
      removed outlier: 4.146A  pdb=" N   ARG L  73 " --> pdb=" O   GLN L  69 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 12 through 18
      removed outlier: 3.706A  pdb=" N   ILE M  18 " --> pdb=" O   ALA M  14 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 23 through 44
      removed outlier: 3.800A  pdb=" N   LEU M  44 " --> pdb=" O   ARG M  40 " (cutoff:3.500A)
    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: 3.786A  pdb=" N   VAL M  89 " --> pdb=" O   TYR M  85 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 131 through 139
    Processing helix  chain 'M' and resid 140 through 143
    Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13

    235 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:
        1.22 -     1.34: 1090
        1.34 -     1.46: 550
        1.46 -     1.57: 1795
        1.57 -     1.69: 0
        1.69 -     1.81: 21
  Bond restraints: 3456
  Sorted by residual:
  bond pdb=" N   GLU K 178 "
       pdb=" CA  GLU K 178 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.031 1.20e-02 6.94e+03 6.84e+00
  bond pdb=" C   PHE M 139 "
       pdb=" N   PRO M 140 "
    ideal  model  delta    sigma   weight residual
    1.336  1.310  0.026 1.08e-02 8.57e+03 5.77e+00
  bond pdb=" N   LEU K  16 "
       pdb=" CA  LEU K  16 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 1.27e-02 6.20e+03 4.84e+00
  bond pdb=" CB  PRO M 153 "
       pdb=" CG  PRO M 153 "
    ideal  model  delta    sigma   weight residual
    1.506  1.451  0.055 3.90e-02 6.57e+02 2.02e+00
  bond pdb=" CB  GLN M 155 "
       pdb=" CG  GLN M 155 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.50e+00
  ... (remaining 3451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 4044
        1.20 -     2.40: 487
        2.40 -     3.60: 107
        3.60 -     4.80: 27
        4.80 -     6.00: 9
  Bond angle restraints: 4674
  Sorted by residual:
  angle pdb=" N   ALA L  85 "
        pdb=" CA  ALA L  85 "
        pdb=" C   ALA L  85 "
      ideal   model   delta    sigma   weight residual
     108.45  113.46   -5.01 1.26e+00 6.30e-01 1.58e+01
  angle pdb=" C   PHE M 127 "
        pdb=" N   ASP M 128 "
        pdb=" CA  ASP M 128 "
      ideal   model   delta    sigma   weight residual
     122.38  116.38    6.00 1.81e+00 3.05e-01 1.10e+01
  angle pdb=" N   SER L  65 "
        pdb=" CA  SER L  65 "
        pdb=" C   SER L  65 "
      ideal   model   delta    sigma   weight residual
     113.38  109.56    3.82 1.17e+00 7.31e-01 1.07e+01
  angle pdb=" N   GLU K 178 "
        pdb=" CA  GLU K 178 "
        pdb=" C   GLU K 178 "
      ideal   model   delta    sigma   weight residual
     111.14  107.77    3.37 1.08e+00 8.57e-01 9.76e+00
  angle pdb=" N   ASP M  11 "
        pdb=" CA  ASP M  11 "
        pdb=" C   ASP M  11 "
      ideal   model   delta    sigma   weight residual
     110.48  106.10    4.38 1.48e+00 4.57e-01 8.75e+00
  ... (remaining 4669 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 1861
       16.81 -    33.61: 194
       33.61 -    50.42: 41
       50.42 -    67.23: 11
       67.23 -    84.03: 6
  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 -160.43  -19.57     0      5.00e+00 4.00e-02 1.53e+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 -160.70  -19.30     0      5.00e+00 4.00e-02 1.49e+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  161.50   18.50     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 318
       0.043 -    0.086: 144
       0.086 -    0.128: 39
       0.128 -    0.171: 4
       0.171 -    0.214: 3
  Chirality restraints: 508
  Sorted by residual:
  chirality pdb=" CB  VAL L  61 "
            pdb=" CA  VAL L  61 "
            pdb=" CG1 VAL L  61 "
            pdb=" CG2 VAL L  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.14e+00
  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   -2.45   -0.18 2.00e-01 2.50e+01 8.47e-01
  chirality pdb=" CA  ASP K 156 "
            pdb=" N   ASP K 156 "
            pdb=" C   ASP K 156 "
            pdb=" CB  ASP K 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.04e-01
  ... (remaining 505 not shown)

  Planarity restraints: 603
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE L  82 "   -0.009 2.00e-02 2.50e+03   1.30e-02 2.98e+00
        pdb=" CG  PHE L  82 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE L  82 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE L  82 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE L  82 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE L  82 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE L  82 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU M  44 "   -0.027 5.00e-02 4.00e+02   4.14e-02 2.75e+00
        pdb=" N   PRO M  45 "    0.072 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=" CA  ILE K 159 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.60e+00
        pdb=" C   ILE K 159 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ILE K 159 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER K 160 "    0.009 2.00e-02 2.50e+03
  ... (remaining 600 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 232
        2.72 -     3.26: 3567
        3.26 -     3.81: 5391
        3.81 -     4.35: 6115
        4.35 -     4.90: 10122
  Nonbonded interactions: 25427
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG K 154 "
            pdb=" O   THR L  89 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" OG1 THR L  56 "
            pdb=" O   GLY L  59 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NE2 GLN K 162 "
            pdb=" O   ASN M  59 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" NH1 ARG K 121 "
            pdb=" O   ILE M  18 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" O   GLU M 102 "
            pdb=" OG  SER M 105 "
     model   vdw
     2.313 3.040
  ... (remaining 25422 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:             291.870
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.970
  Find NCS groups from input model:        0.040
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  311.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
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   0.055   3456  Z= 0.278
  Angle     :  0.906   5.996   4674  Z= 0.564
  Chirality :  0.051   0.214    508
  Planarity :  0.005   0.041    603
  Dihedral  : 15.467  84.035   1299
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.34 (0.35), residues: 413
  helix: -1.04 (0.25), residues: 286
  sheet:  None (None), residues: 0
  loop : -2.52 (0.52), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP M  53 
 HIS   0.005   0.001   HIS K 172 
 PHE   0.030   0.003   PHE L  82 
 TYR   0.016   0.002   TYR K 145 
 ARG   0.004   0.001   ARG M  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15448 (  235)
  hydrogen bonds       : angle       5.69329 (  699)
  covalent geometry    : bond        0.00598 ( 3456)
  covalent geometry    : angle       0.90641 ( 4674)

*********************** 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
  122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7749 (tttt)
REVERT: K   77 PHE cc_start: 0.8620 (t80) cc_final: 0.8265 (t80)
REVERT: K  118 VAL cc_start: 0.8101 (p) cc_final: 0.7842 (p)
REVERT: K  143 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6898 (mtm-85)
REVERT: K  146 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7505 (ttt180)
REVERT: K  169 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7861 (tt0)
REVERT: L   50 TYR cc_start: 0.3521 (t80) cc_final: 0.3049 (t80)
REVERT: M  111 ILE cc_start: 0.8375 (mt) cc_final: 0.8143 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2983
  time to fit residues: 42.0194
Evaluate side-chains
  78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 103 HIS
K 115 GLN
L  68 GLN
M 136 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.131667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.112711 restraints weight = 8906.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.112925 restraints weight = 4401.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.114745 restraints weight = 2516.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3456  Z= 0.154
  Angle     :  0.614   5.201   4674  Z= 0.337
  Chirality :  0.043   0.177    508
  Planarity :  0.005   0.042    603
  Dihedral  :  5.303  55.832    452
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 13.52 %
    Favored  : 82.54 %
  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:  0.48 (0.41), residues: 413
  helix:  1.29 (0.29), residues: 291
  sheet:  None (None), residues: 0
  loop : -2.12 (0.54), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP M  53 
 HIS   0.004   0.001   HIS K 103 
 PHE   0.011   0.001   PHE L  93 
 TYR   0.016   0.001   TYR K 148 
 ARG   0.003   0.001   ARG K 154 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05492 (  235)
  hydrogen bonds       : angle       4.24868 (  699)
  covalent geometry    : bond        0.00319 ( 3456)
  covalent geometry    : angle       0.61398 ( 4674)

*********************** 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: 14
    poor density    : 90
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7854 (mmmt) cc_final: 0.7556 (tptt)
REVERT: K  118 VAL cc_start: 0.8314 (p) cc_final: 0.8036 (p)
REVERT: K  143 ARG cc_start: 0.7177 (mtt180) cc_final: 0.6884 (mtm-85)
REVERT: K  145 TYR cc_start: 0.7324 (t80) cc_final: 0.7025 (t80)
REVERT: K  146 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7431 (ttt180)
REVERT: K  163 ASN cc_start: 0.8498 (t0) cc_final: 0.7914 (m-40)
REVERT: K  169 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7757 (tt0)
REVERT: L   68 GLN cc_start: 0.7606 (tp-100) cc_final: 0.7281 (tp-100)
REVERT: L   87 MET cc_start: 0.7879 (mpp) cc_final: 0.7351 (mpp)
REVERT: M  118 MET cc_start: 0.7837 (tmm) cc_final: 0.7605 (tpp)
  outliers start: 14
  outliers final: 11
  residues processed: 98
  average time/residue: 0.3247
  time to fit residues: 37.0211
Evaluate side-chains
  86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  113 SER
Chi-restraints excluded: chain K residue  126 ASP
Chi-restraints excluded: chain K residue  129 ARG
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain L residue   82 PHE
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   51 ILE
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue  104 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 12 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 3 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:
K 115 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.131270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.111825 restraints weight = 8840.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.113085 restraints weight = 4487.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.113926 restraints weight = 2398.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3456  Z= 0.133
  Angle     :  0.557   5.023   4674  Z= 0.304
  Chirality :  0.041   0.156    508
  Planarity :  0.004   0.043    603
  Dihedral  :  5.041  53.750    452
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.93 %
    Favored  : 81.13 %
  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:  1.45 (0.42), residues: 413
  helix:  2.00 (0.30), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.70 (0.57), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP M  53 
 HIS   0.006   0.001   HIS K 180 
 PHE   0.009   0.001   PHE L 100 
 TYR   0.013   0.001   TYR M  85 
 ARG   0.001   0.000   ARG M 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05003 (  235)
  hydrogen bonds       : angle       4.02672 (  699)
  covalent geometry    : bond        0.00272 ( 3456)
  covalent geometry    : angle       0.55724 ( 4674)

*********************** 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
  100 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7544 (tptm)
REVERT: K  114 GLN cc_start: 0.8084 (mm110) cc_final: 0.7863 (mm-40)
REVERT: K  118 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8012 (p)
REVERT: K  145 TYR cc_start: 0.7494 (t80) cc_final: 0.7166 (t80)
REVERT: K  146 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7515 (ttt180)
REVERT: K  150 GLU cc_start: 0.8283 (tt0) cc_final: 0.8016 (tt0)
REVERT: K  156 ASP cc_start: 0.8387 (p0) cc_final: 0.7527 (p0)
REVERT: K  163 ASN cc_start: 0.8498 (t0) cc_final: 0.7949 (m-40)
REVERT: K  164 MET cc_start: 0.7379 (ttm) cc_final: 0.7113 (ttm)
REVERT: L   77 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8579 (mttt)
REVERT: L   87 MET cc_start: 0.7948 (mpp) cc_final: 0.7545 (mmm)
REVERT: M  118 MET cc_start: 0.7869 (tmm) cc_final: 0.7607 (tpp)
  outliers start: 14
  outliers final: 11
  residues processed: 97
  average time/residue: 0.2579
  time to fit residues: 28.7727
Evaluate side-chains
  87 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   85 LEU
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  126 ASP
Chi-restraints excluded: chain K residue  129 ARG
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   51 ILE
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
K 128 GLN
M  21 GLN
M  23 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.129248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.107777 restraints weight = 9044.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.109734 restraints weight = 4391.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.110896 restraints weight = 2585.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3456  Z= 0.186
  Angle     :  0.624   9.178   4674  Z= 0.337
  Chirality :  0.044   0.172    508
  Planarity :  0.005   0.046    603
  Dihedral  :  5.197  59.239    452
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 16.62 %
    Favored  : 78.31 %
  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:  1.60 (0.41), residues: 413
  helix:  2.10 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.53 (0.57), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP M  53 
 HIS   0.004   0.001   HIS K 172 
 PHE   0.013   0.002   PHE L  82 
 TYR   0.009   0.001   TYR L  50 
 ARG   0.003   0.001   ARG K 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05022 (  235)
  hydrogen bonds       : angle       4.19539 (  699)
  covalent geometry    : bond        0.00411 ( 3456)
  covalent geometry    : angle       0.62415 ( 4674)

*********************** 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
  95 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7611 (tptm)
REVERT: K   85 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8075 (tt)
REVERT: K  114 GLN cc_start: 0.8108 (mm110) cc_final: 0.7836 (mm-40)
REVERT: K  118 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7787 (p)
REVERT: K  145 TYR cc_start: 0.7563 (t80) cc_final: 0.7225 (t80)
REVERT: K  146 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7538 (ttt180)
REVERT: K  150 GLU cc_start: 0.8354 (tt0) cc_final: 0.8073 (tt0)
REVERT: K  156 ASP cc_start: 0.8399 (p0) cc_final: 0.7951 (p0)
REVERT: L   77 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8613 (mttt)
REVERT: L   87 MET cc_start: 0.8010 (mpp) cc_final: 0.7655 (mmm)
REVERT: M  118 MET cc_start: 0.7975 (tmm) cc_final: 0.7655 (tpp)
  outliers start: 18
  outliers final: 11
  residues processed: 89
  average time/residue: 0.1957
  time to fit residues: 20.4182
Evaluate side-chains
  82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   85 LEU
Chi-restraints excluded: chain K residue  113 SER
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  126 ASP
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   51 ILE
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue   80 VAL
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 23 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 162 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.129671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.110094 restraints weight = 9040.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.111475 restraints weight = 4335.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.112517 restraints weight = 2328.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.4219

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= 0.153
  Angle     :  0.602   7.819   4674  Z= 0.323
  Chirality :  0.043   0.185    508
  Planarity :  0.005   0.044    603
  Dihedral  :  5.175  60.157    452
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 18.31 %
    Favored  : 76.62 %
  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:  1.94 (0.41), residues: 413
  helix:  2.31 (0.29), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.26 (0.57), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP M  53 
 HIS   0.003   0.001   HIS K 172 
 PHE   0.024   0.002   PHE L  82 
 TYR   0.008   0.001   TYR K 148 
 ARG   0.007   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04904 (  235)
  hydrogen bonds       : angle       4.09213 (  699)
  covalent geometry    : bond        0.00328 ( 3456)
  covalent geometry    : angle       0.60198 ( 4674)

*********************** 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
  93 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7582 (tptm)
REVERT: K  114 GLN cc_start: 0.8019 (mm110) cc_final: 0.7807 (mm-40)
REVERT: K  118 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7712 (p)
REVERT: K  145 TYR cc_start: 0.7589 (t80) cc_final: 0.7295 (t80)
REVERT: K  146 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7513 (ttt180)
REVERT: K  150 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8035 (tt0)
REVERT: K  156 ASP cc_start: 0.8409 (p0) cc_final: 0.8152 (p0)
REVERT: L   77 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8505 (mttt)
REVERT: L   87 MET cc_start: 0.7855 (mpp) cc_final: 0.7606 (mmm)
REVERT: M   19 ILE cc_start: 0.8983 (mm) cc_final: 0.8618 (tp)
REVERT: M  118 MET cc_start: 0.7995 (tmm) cc_final: 0.7648 (tpp)
  outliers start: 18
  outliers final: 12
  residues processed: 88
  average time/residue: 0.2137
  time to fit residues: 22.0134
Evaluate side-chains
  82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   85 LEU
Chi-restraints excluded: chain K residue  113 SER
Chi-restraints excluded: chain K residue  118 VAL
Chi-restraints excluded: chain K residue  126 ASP
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   51 ILE
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** M  21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.130163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.108870 restraints weight = 9309.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.110894 restraints weight = 4387.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.112154 restraints weight = 2516.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3456  Z= 0.139
  Angle     :  0.613   9.356   4674  Z= 0.327
  Chirality :  0.042   0.175    508
  Planarity :  0.005   0.043    603
  Dihedral  :  5.058  59.312    452
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.87 %
    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 (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:  2.25 (0.42), residues: 413
  helix:  2.49 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -1.04 (0.59), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP M  53 
 HIS   0.003   0.001   HIS K 172 
 PHE   0.022   0.002   PHE L  82 
 TYR   0.010   0.001   TYR M  85 
 ARG   0.004   0.001   ARG M  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04824 (  235)
  hydrogen bonds       : angle       4.03630 (  699)
  covalent geometry    : bond        0.00288 ( 3456)
  covalent geometry    : angle       0.61329 ( 4674)

*********************** 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
  88 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7568 (tptm)
REVERT: K  134 MET cc_start: 0.8374 (ttm) cc_final: 0.7992 (ttm)
REVERT: K  145 TYR cc_start: 0.7629 (t80) cc_final: 0.7346 (t80)
REVERT: K  146 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7523 (ttt180)
REVERT: K  150 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8067 (tt0)
REVERT: L   60 PRO cc_start: 0.6776 (Cg_endo) cc_final: 0.6522 (Cg_exo)
REVERT: L   87 MET cc_start: 0.7833 (mpp) cc_final: 0.7523 (mmm)
REVERT: M   19 ILE cc_start: 0.8906 (mm) cc_final: 0.8648 (tp)
REVERT: M  118 MET cc_start: 0.8056 (tmm) cc_final: 0.7711 (tpp)
  outliers start: 14
  outliers final: 13
  residues processed: 84
  average time/residue: 0.2265
  time to fit residues: 22.7259
Evaluate side-chains
  83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   85 LEU
Chi-restraints excluded: chain K residue  113 SER
Chi-restraints excluded: chain K residue  126 ASP
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain L residue  102 VAL
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   51 ILE
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   chunk 6 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4023 r_free = 0.4023 target = 0.131135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.110030 restraints weight = 9065.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.112074 restraints weight = 4237.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.113277 restraints weight = 2438.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.4660

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= 0.134
  Angle     :  0.606  10.289   4674  Z= 0.324
  Chirality :  0.041   0.181    508
  Planarity :  0.004   0.042    603
  Dihedral  :  4.942  57.600    452
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 18.31 %
    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 (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:  2.57 (0.42), residues: 413
  helix:  2.59 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.51 (0.64), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP M  33 
 HIS   0.001   0.000   HIS K 172 
 PHE   0.020   0.001   PHE L  82 
 TYR   0.012   0.001   TYR M  85 
 ARG   0.003   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04714 (  235)
  hydrogen bonds       : angle       3.91583 (  699)
  covalent geometry    : bond        0.00273 ( 3456)
  covalent geometry    : angle       0.60602 ( 4674)

*********************** 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
  91 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7542 (tptm)
REVERT: K  134 MET cc_start: 0.8351 (ttm) cc_final: 0.7951 (ttm)
REVERT: K  145 TYR cc_start: 0.7617 (t80) cc_final: 0.7353 (t80)
REVERT: K  146 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7541 (ttt180)
REVERT: K  150 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8048 (tt0)
REVERT: K  163 ASN cc_start: 0.8506 (t0) cc_final: 0.7864 (t0)
REVERT: K  164 MET cc_start: 0.6588 (tmm) cc_final: 0.5438 (tmm)
REVERT: L   60 PRO cc_start: 0.6806 (Cg_endo) cc_final: 0.6548 (Cg_exo)
REVERT: M   19 ILE cc_start: 0.9012 (mm) cc_final: 0.8762 (tp)
REVERT: M  118 MET cc_start: 0.8088 (tmm) cc_final: 0.7723 (tpp)
  outliers start: 16
  outliers final: 11
  residues processed: 86
  average time/residue: 0.2781
  time to fit residues: 29.1161
Evaluate side-chains
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   85 LEU
Chi-restraints excluded: chain K residue  113 SER
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   51 ILE
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    8.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.129312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.110215 restraints weight = 9043.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.111630 restraints weight = 4649.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.112578 restraints weight = 2444.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.4873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3456  Z= 0.167
  Angle     :  0.672  10.173   4674  Z= 0.355
  Chirality :  0.043   0.194    508
  Planarity :  0.005   0.042    603
  Dihedral  :  5.124  60.757    452
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.85 %
    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:  2.51 (0.42), residues: 413
  helix:  2.63 (0.29), residues: 285
  sheet:  None (None), residues: 0
  loop : -0.63 (0.62), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP M  53 
 HIS   0.002   0.001   HIS K 172 
 PHE   0.012   0.002   PHE L 100 
 TYR   0.020   0.001   TYR K 148 
 ARG   0.005   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04917 (  235)
  hydrogen bonds       : angle       4.00764 (  699)
  covalent geometry    : bond        0.00360 ( 3456)
  covalent geometry    : angle       0.67185 ( 4674)

*********************** 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
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7557 (tttm)
REVERT: K   85 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8086 (tt)
REVERT: K  134 MET cc_start: 0.8372 (ttm) cc_final: 0.8049 (ttm)
REVERT: K  145 TYR cc_start: 0.7583 (t80) cc_final: 0.7350 (t80)
REVERT: K  146 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7571 (ttt180)
REVERT: K  150 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8054 (tt0)
REVERT: L   55 GLN cc_start: 0.6820 (pp30) cc_final: 0.6512 (pm20)
REVERT: L   60 PRO cc_start: 0.6628 (Cg_endo) cc_final: 0.6367 (Cg_exo)
REVERT: M   19 ILE cc_start: 0.9037 (mm) cc_final: 0.8809 (tp)
REVERT: M   94 LYS cc_start: 0.8737 (mttm) cc_final: 0.8364 (mttp)
REVERT: M  118 MET cc_start: 0.8078 (tmm) cc_final: 0.7722 (tpp)
  outliers start: 11
  outliers final: 9
  residues processed: 78
  average time/residue: 0.2341
  time to fit residues: 21.8324
Evaluate side-chains
  77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   85 LEU
Chi-restraints excluded: chain K residue  113 SER
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0770
   chunk 28 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.8742

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.130426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.111438 restraints weight = 8866.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.112909 restraints weight = 4319.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.113914 restraints weight = 2318.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.5051

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= 0.140
  Angle     :  0.649   8.846   4674  Z= 0.341
  Chirality :  0.041   0.162    508
  Planarity :  0.004   0.041    603
  Dihedral  :  5.028  59.835    452
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.00 %
    Favored  : 76.34 %
  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:  2.66 (0.42), residues: 413
  helix:  2.73 (0.29), residues: 283
  sheet:  None (None), residues: 0
  loop : -0.48 (0.61), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP M  33 
 HIS   0.003   0.001   HIS K 158 
 PHE   0.012   0.001   PHE L 100 
 TYR   0.019   0.001   TYR K 148 
 ARG   0.004   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04711 (  235)
  hydrogen bonds       : angle       3.82594 (  699)
  covalent geometry    : bond        0.00292 ( 3456)
  covalent geometry    : angle       0.64895 ( 4674)

*********************** 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
  89 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7503 (tttm)
REVERT: K  134 MET cc_start: 0.8351 (ttm) cc_final: 0.7958 (ttm)
REVERT: K  145 TYR cc_start: 0.7596 (t80) cc_final: 0.7363 (t80)
REVERT: K  146 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7671 (ttt180)
REVERT: K  150 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8088 (tt0)
REVERT: L   55 GLN cc_start: 0.6764 (pp30) cc_final: 0.6384 (pm20)
REVERT: L   60 PRO cc_start: 0.6632 (Cg_endo) cc_final: 0.6380 (Cg_exo)
REVERT: M   19 ILE cc_start: 0.9047 (mm) cc_final: 0.8837 (tp)
REVERT: M   94 LYS cc_start: 0.8736 (mttm) cc_final: 0.8357 (mttp)
REVERT: M  118 MET cc_start: 0.8117 (tmm) cc_final: 0.7742 (tpp)
  outliers start: 13
  outliers final: 11
  residues processed: 84
  average time/residue: 0.3048
  time to fit residues: 31.1975
Evaluate side-chains
  81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   85 LEU
Chi-restraints excluded: chain K residue  113 SER
Chi-restraints excluded: chain K residue  163 ASN
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 27 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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 = 0.3973 r_free = 0.3973 target = 0.127499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.108997 restraints weight = 9077.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.109749 restraints weight = 5677.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.110564 restraints weight = 4185.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.5158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   3456  Z= 0.223
  Angle     :  0.752   9.479   4674  Z= 0.390
  Chirality :  0.046   0.225    508
  Planarity :  0.005   0.040    603
  Dihedral  :  5.475  67.734    452
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.13 %
    Favored  : 75.77 %
  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:  2.37 (0.42), residues: 413
  helix:  2.41 (0.29), residues: 284
  sheet:  None (None), residues: 0
  loop : -0.35 (0.63), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP M  53 
 HIS   0.002   0.001   HIS M 154 
 PHE   0.013   0.002   PHE K  58 
 TYR   0.016   0.002   TYR K 148 
 ARG   0.005   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05043 (  235)
  hydrogen bonds       : angle       4.21337 (  699)
  covalent geometry    : bond        0.00510 ( 3456)
  covalent geometry    : angle       0.75177 ( 4674)

********************** 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
  76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   48 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7649 (tttm)
REVERT: K  134 MET cc_start: 0.8314 (ttm) cc_final: 0.8042 (ttm)
REVERT: K  145 TYR cc_start: 0.7558 (t80) cc_final: 0.7339 (t80)
REVERT: L   55 GLN cc_start: 0.6782 (pp30) cc_final: 0.6237 (pm20)
REVERT: M   94 LYS cc_start: 0.8720 (mttm) cc_final: 0.8346 (mttp)
REVERT: M  118 MET cc_start: 0.8116 (tmm) cc_final: 0.7735 (tpp)
  outliers start: 11
  outliers final: 11
  residues processed: 74
  average time/residue: 0.2411
  time to fit residues: 21.3509
Evaluate side-chains
  70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   85 LEU
Chi-restraints excluded: chain K residue  113 SER
Chi-restraints excluded: chain K residue  174 ILE
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain L residue   97 ASP
Chi-restraints excluded: chain M residue   33 TRP
Chi-restraints excluded: chain M residue   67 ASP
Chi-restraints excluded: chain M residue   69 PHE
Chi-restraints excluded: chain M residue  104 VAL
Chi-restraints excluded: chain M residue  112 VAL
Chi-restraints excluded: chain M residue  125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0270
   chunk 13 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0980
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
M 129 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.130692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.111826 restraints weight = 9267.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.113238 restraints weight = 4647.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.113748 restraints weight = 2643.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.096   3456  Z= 0.143
  Angle     :  0.678   9.493   4674  Z= 0.351
  Chirality :  0.042   0.171    508
  Planarity :  0.004   0.038    603
  Dihedral  :  5.154  64.157    452
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.41 %
    Favored  : 75.77 %
  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:  2.69 (0.42), residues: 413
  helix:  2.73 (0.29), residues: 281
  sheet:  None (None), residues: 0
  loop : -0.36 (0.60), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP M  12 
 HIS   0.002   0.001   HIS K 158 
 PHE   0.012   0.001   PHE M  15 
 TYR   0.022   0.001   TYR K 148 
 ARG   0.003   0.001   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (  235)
  hydrogen bonds       : angle       3.96609 (  699)
  covalent geometry    : bond        0.00329 ( 3456)
  covalent geometry    : angle       0.67798 ( 4674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3382.60 seconds
wall clock time: 62 minutes 48.65 seconds (3768.65 seconds total)