Starting phenix.real_space_refine
on Tue Mar  3 11:24:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xdc_22136/03_2026/6xdc_22136.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xdc_22136/03_2026/6xdc_22136.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xdc_22136/03_2026/6xdc_22136.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xdc_22136/03_2026/6xdc_22136.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xdc_22136/03_2026/6xdc_22136.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xdc_22136/03_2026/6xdc_22136.map"
  }
  resolution = 2.9
  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=  -0.001 sd=   0.101
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      16      5.16       5
     C    2094      2.51       5
     N     490      2.21       5
     O     550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3150
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1575
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 4, 'TRANS': 188}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1575
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 4, 'TRANS': 188}
          Chain breaks: 1
  Time building chain proxies: 0.88, per 1000 atoms: 0.28
  Number of scatterers: 3150
  At special positions: 0
  Unit cell: (55.713, 62.535, 94.371, 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      16     16.00
     O     550      8.00
     N     490      7.00
     C    2094      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: 0.22
  Conformation dependent library (CDL) restraints added in 107.2 milliseconds
  

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  732

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 2 sheets defined
      50.5% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 61
      removed outlier: 3.806A  pdb=" N   ILE A  47 " --> pdb=" O   PHE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 100
    Processing helix  chain 'A' and resid 102 through 134
      removed outlier: 3.618A  pdb=" N   LEU A 108 " --> pdb=" O   PRO A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 141
      removed outlier: 3.881A  pdb=" N   LEU A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 224
      removed outlier: 4.067A  pdb=" N   THR A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 61
      removed outlier: 3.825A  pdb=" N   ILE B  47 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 100
    Processing helix  chain 'B' and resid 102 through 133
      removed outlier: 3.716A  pdb=" N   LEU B 108 " --> pdb=" O   PRO B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 141
      removed outlier: 3.831A  pdb=" N   LEU B 140 " --> pdb=" O   LYS B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 224
      removed outlier: 4.074A  pdb=" N   THR B 223 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160
      removed outlier: 5.422A  pdb=" N   LEU A 214 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ASN A 234 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER A 216 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY A 172 " --> pdb=" O   ASP A 183 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ASP A 183 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   TYR A 189 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 160
      removed outlier: 5.387A  pdb=" N   LEU B 214 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ASN B 234 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   SER B 216 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 172 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ASP B 183 " --> pdb=" O   GLY B 172 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   TYR B 189 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)

    199 hydrogen bonds defined for protein.
    585 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: 0.43

  Time building geometry restraints manager: 0.32 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: 912
        1.34 -     1.46: 719
        1.46 -     1.57: 1595
        1.57 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 3244
  Sorted by residual:
  bond pdb=" CB  GLN A 185 "
       pdb=" CG  GLN A 185 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.17e+00
  bond pdb=" CB  CYS B 157 "
       pdb=" SG  CYS B 157 "
    ideal  model  delta    sigma   weight residual
    1.808  1.760  0.048 3.30e-02 9.18e+02 2.09e+00
  bond pdb=" CB  GLN B 185 "
       pdb=" CG  GLN B 185 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.08e+00
  bond pdb=" C   ALA A 103 "
       pdb=" N   PRO A 104 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.28e-02 6.10e+03 2.05e+00
  bond pdb=" CB  CYS A 157 "
       pdb=" SG  CYS A 157 "
    ideal  model  delta    sigma   weight residual
    1.808  1.762  0.046 3.30e-02 9.18e+02 1.96e+00
  ... (remaining 3239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 4249
        1.72 -     3.44: 148
        3.44 -     5.17: 20
        5.17 -     6.89: 4
        6.89 -     8.61: 3
  Bond angle restraints: 4424
  Sorted by residual:
  angle pdb=" CA  TYR A 107 "
        pdb=" CB  TYR A 107 "
        pdb=" CG  TYR A 107 "
      ideal   model   delta    sigma   weight residual
     113.90  120.12   -6.22 1.80e+00 3.09e-01 1.19e+01
  angle pdb=" CA  TYR B 107 "
        pdb=" CB  TYR B 107 "
        pdb=" CG  TYR B 107 "
      ideal   model   delta    sigma   weight residual
     113.90  120.05   -6.15 1.80e+00 3.09e-01 1.17e+01
  angle pdb=" N   ASN A 137 "
        pdb=" CA  ASN A 137 "
        pdb=" C   ASN A 137 "
      ideal   model   delta    sigma   weight residual
     109.81  117.09   -7.28 2.21e+00 2.05e-01 1.08e+01
  angle pdb=" N   ASN B 137 "
        pdb=" CA  ASN B 137 "
        pdb=" C   ASN B 137 "
      ideal   model   delta    sigma   weight residual
     109.81  117.00   -7.19 2.21e+00 2.05e-01 1.06e+01
  angle pdb=" OG1 THR A 170 "
        pdb=" CB  THR A 170 "
        pdb=" CG2 THR A 170 "
      ideal   model   delta    sigma   weight residual
     109.30  102.79    6.51 2.00e+00 2.50e-01 1.06e+01
  ... (remaining 4419 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.27: 1544
       12.27 -    24.53: 191
       24.53 -    36.80: 67
       36.80 -    49.07: 18
       49.07 -    61.34: 10
  Dihedral angle restraints: 1830
    sinusoidal: 684
      harmonic: 1146
  Sorted by residual:
  dihedral pdb=" CA  LEU B 140 "
           pdb=" C   LEU B 140 "
           pdb=" N   TYR B 141 "
           pdb=" CA  TYR B 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.83  -24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  LEU A 140 "
           pdb=" C   LEU A 140 "
           pdb=" N   TYR A 141 "
           pdb=" CA  TYR A 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.88  -24.12     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  TYR B 189 "
           pdb=" C   TYR B 189 "
           pdb=" N   THR B 190 "
           pdb=" CA  THR B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.99  -16.01     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 1827 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 407
       0.071 -    0.141: 83
       0.141 -    0.212: 8
       0.212 -    0.282: 3
       0.282 -    0.353: 1
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" CB  ILE B 236 "
            pdb=" CA  ILE B 236 "
            pdb=" CG1 ILE B 236 "
            pdb=" CG2 ILE B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CB  VAL B 197 "
            pdb=" CA  VAL B 197 "
            pdb=" CG1 VAL B 197 "
            pdb=" CG2 VAL B 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CB  VAL A 197 "
            pdb=" CA  VAL A 197 "
            pdb=" CG1 VAL A 197 "
            pdb=" CG2 VAL A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 499 not shown)

  Planarity restraints: 528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 137 "   -0.053 5.00e-02 4.00e+02   7.92e-02 1.00e+01
        pdb=" N   PRO B 138 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO B 138 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 138 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 137 "    0.053 5.00e-02 4.00e+02   7.89e-02 9.96e+00
        pdb=" N   PRO A 138 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 138 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 138 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 103 "   -0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO B 104 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 104 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 104 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 525 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 831
        2.80 -     3.33: 2598
        3.33 -     3.85: 5072
        3.85 -     4.38: 5521
        4.38 -     4.90: 9971
  Nonbonded interactions: 23993
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 151 "
            pdb=" O   TYR B 154 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG1 THR A 151 "
            pdb=" O   TYR A 154 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   PHE B 114 "
            pdb=" OG  SER B 117 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" O   PHE A 114 "
            pdb=" OG  SER A 117 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" N   ASP A 238 "
            pdb=" OD1 ASP A 238 "
     model   vdw
     2.381 3.120
  ... (remaining 23988 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.030
  Find NCS groups from input model:        0.030
  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:6.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
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   0.065   3244  Z= 0.244
  Angle     :  0.788   8.610   4424  Z= 0.444
  Chirality :  0.062   0.353    502
  Planarity :  0.008   0.079    528
  Dihedral  : 13.654  61.336   1098
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.23 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.72 (0.34), residues: 378
  helix: -1.09 (0.30), residues: 168
  sheet: -1.40 (0.42), residues: 106
  loop : -3.07 (0.45), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 126 
 TYR   0.020   0.002   TYR A 107 
 PHE   0.010   0.001   PHE B  43 
 TRP   0.013   0.002   TRP A 149 
 HIS   0.007   0.002   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 3244)
  covalent geometry    : angle       0.78816 ( 4424)
  hydrogen bonds       : bond        0.20021 (  199)
  hydrogen bonds       : angle       7.17663 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A   61 LYS cc_start: 0.8333 (mttp) cc_final: 0.8072 (mttt)
REVERT: A  134 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7708 (mtp180)
REVERT: A  192 LYS cc_start: 0.8574 (tttt) cc_final: 0.8114 (tttp)
REVERT: A  215 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7043 (m-10)
REVERT: B   61 LYS cc_start: 0.8331 (mttp) cc_final: 0.8046 (mttt)
REVERT: B  113 TYR cc_start: 0.8092 (m-10) cc_final: 0.7876 (m-80)
REVERT: B  134 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7740 (mtp180)
REVERT: B  192 LYS cc_start: 0.8621 (tttt) cc_final: 0.8153 (tttp)
REVERT: B  215 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.6921 (m-10)
  outliers start: 4
  outliers final: 1
  residues processed: 66
  average time/residue: 0.3399
  time to fit residues: 23.3874
Evaluate side-chains
  47 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain B residue  215 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0030
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
B  93 HIS
B 185 GLN
B 204 HIS
B 234 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.167701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.139137 restraints weight = 4134.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.93
r_work: 0.3654 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3244  Z= 0.138
  Angle     :  0.563   9.152   4424  Z= 0.312
  Chirality :  0.044   0.143    502
  Planarity :  0.006   0.064    528
  Dihedral  :  6.336  57.199    428
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.67 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.55 (0.40), residues: 378
  helix:  1.44 (0.38), residues: 168
  sheet: -0.83 (0.46), residues: 96
  loop : -2.71 (0.45), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.022   0.001   TYR B 107 
 PHE   0.006   0.001   PHE A  43 
 TRP   0.008   0.001   TRP B 149 
 HIS   0.002   0.001   HIS B  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3244)
  covalent geometry    : angle       0.56294 ( 4424)
  hydrogen bonds       : bond        0.04507 (  199)
  hydrogen bonds       : angle       4.44611 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   61 LYS cc_start: 0.8054 (mttp) cc_final: 0.7838 (mttt)
REVERT: A  134 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7242 (mmt-90)
REVERT: A  154 TYR cc_start: 0.7546 (t80) cc_final: 0.7287 (t80)
REVERT: A  192 LYS cc_start: 0.8397 (tttt) cc_final: 0.7861 (tttp)
REVERT: A  194 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8060 (mm-30)
REVERT: B   61 LYS cc_start: 0.8094 (mttp) cc_final: 0.7880 (mttt)
REVERT: B  134 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7272 (tpt170)
REVERT: B  192 LYS cc_start: 0.8285 (tttt) cc_final: 0.7783 (tttp)
  outliers start: 12
  outliers final: 10
  residues processed: 60
  average time/residue: 0.3523
  time to fit residues: 22.0229
Evaluate side-chains
  55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  93 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.164369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.135957 restraints weight = 4105.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 2.88
r_work: 0.3624 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3244  Z= 0.157
  Angle     :  0.572   9.154   4424  Z= 0.316
  Chirality :  0.044   0.138    502
  Planarity :  0.005   0.057    528
  Dihedral  :  6.290  57.762    426
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.25 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.43), residues: 378
  helix:  2.20 (0.39), residues: 170
  sheet: -0.85 (0.48), residues: 96
  loop : -2.60 (0.48), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A  68 
 TYR   0.027   0.002   TYR B 107 
 PHE   0.018   0.001   PHE A 207 
 TRP   0.009   0.001   TRP B 149 
 HIS   0.004   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3244)
  covalent geometry    : angle       0.57200 ( 4424)
  hydrogen bonds       : bond        0.04389 (  199)
  hydrogen bonds       : angle       4.34758 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7216 (tpt170)
REVERT: A  192 LYS cc_start: 0.8416 (tttt) cc_final: 0.7914 (tttp)
REVERT: B   61 LYS cc_start: 0.8027 (mttp) cc_final: 0.7812 (mttt)
REVERT: B  134 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7280 (mtp180)
REVERT: B  192 LYS cc_start: 0.8306 (tttt) cc_final: 0.7819 (tttp)
  outliers start: 12
  outliers final: 12
  residues processed: 56
  average time/residue: 0.3581
  time to fit residues: 20.8555
Evaluate side-chains
  49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.166011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.137646 restraints weight = 4086.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.88
r_work: 0.3626 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3244  Z= 0.142
  Angle     :  0.573  10.628   4424  Z= 0.309
  Chirality :  0.043   0.136    502
  Planarity :  0.005   0.056    528
  Dihedral  :  6.137  57.099    426
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.40 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.41 (0.43), residues: 378
  helix:  2.56 (0.40), residues: 170
  sheet: -0.87 (0.49), residues: 96
  loop : -2.38 (0.48), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 122 
 TYR   0.027   0.002   TYR A 107 
 PHE   0.022   0.001   PHE A 207 
 TRP   0.010   0.001   TRP A 193 
 HIS   0.003   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3244)
  covalent geometry    : angle       0.57306 ( 4424)
  hydrogen bonds       : bond        0.04056 (  199)
  hydrogen bonds       : angle       4.16643 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  127 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7275 (mm)
REVERT: A  134 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7216 (tpt170)
REVERT: A  192 LYS cc_start: 0.8284 (tttt) cc_final: 0.7782 (tttp)
REVERT: B   61 LYS cc_start: 0.7996 (mttp) cc_final: 0.7785 (mttt)
REVERT: B  134 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7248 (mtp180)
REVERT: B  192 LYS cc_start: 0.8242 (tttt) cc_final: 0.7775 (ttmp)
  outliers start: 13
  outliers final: 12
  residues processed: 51
  average time/residue: 0.4102
  time to fit residues: 21.6754
Evaluate side-chains
  50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 37
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4016 r_free = 0.4016 target = 0.164652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.136364 restraints weight = 4113.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.88
r_work: 0.3614 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3244  Z= 0.158
  Angle     :  0.578   9.189   4424  Z= 0.316
  Chirality :  0.044   0.136    502
  Planarity :  0.005   0.056    528
  Dihedral  :  6.208  57.875    426
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 20.69 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.43 (0.43), residues: 378
  helix:  2.64 (0.39), residues: 170
  sheet: -0.96 (0.49), residues: 96
  loop : -2.36 (0.48), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 122 
 TYR   0.027   0.002   TYR A 107 
 PHE   0.017   0.001   PHE B 207 
 TRP   0.010   0.001   TRP B 193 
 HIS   0.004   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3244)
  covalent geometry    : angle       0.57792 ( 4424)
  hydrogen bonds       : bond        0.04136 (  199)
  hydrogen bonds       : angle       4.16832 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  127 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7264 (mm)
REVERT: A  134 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7205 (tpt170)
REVERT: A  192 LYS cc_start: 0.8288 (tttt) cc_final: 0.7749 (tttp)
REVERT: A  194 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7977 (mm-30)
REVERT: B   61 LYS cc_start: 0.7977 (mttp) cc_final: 0.7765 (mttt)
REVERT: B  134 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7286 (mmt180)
REVERT: B  192 LYS cc_start: 0.8293 (tttt) cc_final: 0.7795 (ttmp)
REVERT: B  198 LYS cc_start: 0.6283 (mptp) cc_final: 0.5974 (mptm)
  outliers start: 15
  outliers final: 11
  residues processed: 49
  average time/residue: 0.3983
  time to fit residues: 20.2968
Evaluate side-chains
  47 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8986

-------------------------------------------------------------------------------
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 = 0.165627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136610 restraints weight = 4139.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 2.96
r_work: 0.3596 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6749
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3244  Z= 0.172
  Angle     :  0.592   8.683   4424  Z= 0.324
  Chirality :  0.045   0.136    502
  Planarity :  0.005   0.057    528
  Dihedral  :  6.266  57.907    426
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 20.69 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.49 (0.44), residues: 378
  helix:  2.71 (0.39), residues: 170
  sheet: -0.99 (0.49), residues: 96
  loop : -2.33 (0.49), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG A 122 
 TYR   0.027   0.002   TYR A 107 
 PHE   0.021   0.001   PHE A 207 
 TRP   0.013   0.002   TRP B 193 
 HIS   0.005   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 3244)
  covalent geometry    : angle       0.59160 ( 4424)
  hydrogen bonds       : bond        0.04224 (  199)
  hydrogen bonds       : angle       4.16321 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  127 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7214 (mm)
REVERT: A  134 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7184 (tpt170)
REVERT: A  192 LYS cc_start: 0.8259 (tttt) cc_final: 0.7737 (tttp)
REVERT: A  198 LYS cc_start: 0.6296 (mptp) cc_final: 0.6001 (mptm)
REVERT: B   61 LYS cc_start: 0.7924 (mttp) cc_final: 0.7717 (mttt)
REVERT: B  134 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7220 (mtp180)
REVERT: B  192 LYS cc_start: 0.8238 (tttt) cc_final: 0.7776 (ttmp)
REVERT: B  198 LYS cc_start: 0.6293 (mptp) cc_final: 0.6052 (mptm)
  outliers start: 15
  outliers final: 11
  residues processed: 48
  average time/residue: 0.4308
  time to fit residues: 21.4277
Evaluate side-chains
  47 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0020
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.166937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.138546 restraints weight = 4186.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.91
r_work: 0.3643 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3244  Z= 0.132
  Angle     :  0.563   8.710   4424  Z= 0.306
  Chirality :  0.043   0.134    502
  Planarity :  0.005   0.056    528
  Dihedral  :  6.042  56.560    426
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 20.69 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.56 (0.44), residues: 378
  helix:  2.80 (0.39), residues: 170
  sheet: -1.00 (0.50), residues: 96
  loop : -2.28 (0.49), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 122 
 TYR   0.026   0.001   TYR A 107 
 PHE   0.023   0.001   PHE A 207 
 TRP   0.017   0.002   TRP B 193 
 HIS   0.004   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3244)
  covalent geometry    : angle       0.56284 ( 4424)
  hydrogen bonds       : bond        0.03705 (  199)
  hydrogen bonds       : angle       3.99953 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 36
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7210 (tpt170)
REVERT: A  192 LYS cc_start: 0.8284 (tttt) cc_final: 0.7768 (tttp)
REVERT: A  198 LYS cc_start: 0.6187 (mptp) cc_final: 0.5893 (mptm)
REVERT: A  215 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6992 (m-10)
REVERT: A  218 GLN cc_start: 0.7642 (mm110) cc_final: 0.7431 (mm-40)
REVERT: B   61 LYS cc_start: 0.7983 (mttp) cc_final: 0.7770 (mttt)
REVERT: B  134 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7212 (mtp180)
REVERT: B  162 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8244 (p)
REVERT: B  192 LYS cc_start: 0.8323 (tttt) cc_final: 0.7793 (tttp)
  outliers start: 16
  outliers final: 11
  residues processed: 49
  average time/residue: 0.4392
  time to fit residues: 22.2811
Evaluate side-chains
  47 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 34
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.4033 r_free = 0.4033 target = 0.166644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.137264 restraints weight = 4174.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.98
r_work: 0.3624 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3244  Z= 0.135
  Angle     :  0.569   8.562   4424  Z= 0.310
  Chirality :  0.043   0.140    502
  Planarity :  0.005   0.056    528
  Dihedral  :  6.012  56.733    426
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.41 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.62 (0.44), residues: 378
  helix:  2.88 (0.39), residues: 170
  sheet: -1.01 (0.50), residues: 96
  loop : -2.27 (0.49), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 122 
 TYR   0.025   0.001   TYR A 107 
 PHE   0.025   0.001   PHE A 207 
 TRP   0.019   0.002   TRP B 193 
 HIS   0.004   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3244)
  covalent geometry    : angle       0.56855 ( 4424)
  hydrogen bonds       : bond        0.03666 (  199)
  hydrogen bonds       : angle       4.00773 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7194 (mmt180)
REVERT: A  162 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8249 (p)
REVERT: A  192 LYS cc_start: 0.8280 (tttt) cc_final: 0.7769 (tttp)
REVERT: A  194 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7925 (mm-30)
REVERT: A  198 LYS cc_start: 0.6122 (mptp) cc_final: 0.5826 (mptm)
REVERT: B   61 LYS cc_start: 0.7952 (mttp) cc_final: 0.7751 (mttt)
REVERT: B  134 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7199 (mtp180)
REVERT: B  162 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.8084 (p)
REVERT: B  192 LYS cc_start: 0.8276 (tttt) cc_final: 0.7785 (tttp)
  outliers start: 14
  outliers final: 11
  residues processed: 47
  average time/residue: 0.4433
  time to fit residues: 21.6025
Evaluate side-chains
  46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 33
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0170
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6618

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.165507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.136059 restraints weight = 4167.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.96
r_work: 0.3613 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3244  Z= 0.144
  Angle     :  0.577   8.463   4424  Z= 0.316
  Chirality :  0.044   0.139    502
  Planarity :  0.005   0.056    528
  Dihedral  :  6.049  56.874    426
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.28 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.63 (0.44), residues: 378
  helix:  2.92 (0.39), residues: 170
  sheet: -1.00 (0.50), residues: 96
  loop : -2.33 (0.49), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 122 
 TYR   0.026   0.002   TYR A 107 
 PHE   0.012   0.001   PHE B 207 
 TRP   0.017   0.002   TRP B 193 
 HIS   0.003   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3244)
  covalent geometry    : angle       0.57680 ( 4424)
  hydrogen bonds       : bond        0.03770 (  199)
  hydrogen bonds       : angle       4.00333 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  127 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7273 (mm)
REVERT: A  134 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7183 (tpt170)
REVERT: A  162 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8230 (p)
REVERT: A  192 LYS cc_start: 0.8284 (tttt) cc_final: 0.7765 (tttp)
REVERT: A  194 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7923 (mm-30)
REVERT: B   61 LYS cc_start: 0.7938 (mttp) cc_final: 0.7735 (mttt)
REVERT: B  134 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7184 (mtp180)
REVERT: B  162 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.8250 (p)
REVERT: B  192 LYS cc_start: 0.8290 (tttt) cc_final: 0.7763 (tttp)
REVERT: B  194 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7941 (mt-10)
  outliers start: 14
  outliers final: 11
  residues processed: 46
  average time/residue: 0.4427
  time to fit residues: 21.0877
Evaluate side-chains
  46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 32
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0070
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.166638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.137438 restraints weight = 4096.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.93
r_work: 0.3630 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3244  Z= 0.138
  Angle     :  0.578   8.415   4424  Z= 0.317
  Chirality :  0.043   0.138    502
  Planarity :  0.005   0.056    528
  Dihedral  :  5.979  56.428    426
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 22.99 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.68 (0.44), residues: 378
  helix:  2.96 (0.39), residues: 170
  sheet: -0.96 (0.51), residues: 96
  loop : -2.33 (0.49), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 122 
 TYR   0.025   0.001   TYR A 107 
 PHE   0.024   0.001   PHE A 207 
 TRP   0.018   0.002   TRP B 193 
 HIS   0.003   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 3244)
  covalent geometry    : angle       0.57784 ( 4424)
  hydrogen bonds       : bond        0.03640 (  199)
  hydrogen bonds       : angle       3.96979 (  585)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 36
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  127 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7129 (mm)
REVERT: A  134 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7176 (tpt170)
REVERT: A  162 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.8050 (p)
REVERT: A  192 LYS cc_start: 0.8252 (tttt) cc_final: 0.7695 (tttp)
REVERT: A  194 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7913 (mm-30)
REVERT: B   61 LYS cc_start: 0.7934 (mttp) cc_final: 0.7730 (mttt)
REVERT: B  134 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7198 (mtp180)
REVERT: B  162 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.8009 (p)
REVERT: B  192 LYS cc_start: 0.8258 (tttt) cc_final: 0.7702 (tttp)
REVERT: B  194 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7933 (mt-10)
  outliers start: 14
  outliers final: 11
  residues processed: 47
  average time/residue: 0.4378
  time to fit residues: 21.3410
Evaluate side-chains
  48 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 34
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  148 CYS
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  170 THR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  215 TYR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 17 optimal weight:    0.0050
   chunk 11 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4994

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.167104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.137894 restraints weight = 4134.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 3.00
r_work: 0.3634 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3244  Z= 0.129
  Angle     :  0.569   8.369   4424  Z= 0.312
  Chirality :  0.043   0.138    502
  Planarity :  0.005   0.056    528
  Dihedral  :  5.912  56.249    426
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.41 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.73 (0.44), residues: 378
  helix:  3.01 (0.39), residues: 170
  sheet: -0.93 (0.51), residues: 96
  loop : -2.34 (0.49), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 122 
 TYR   0.025   0.001   TYR A 107 
 PHE   0.026   0.001   PHE A 207 
 TRP   0.018   0.002   TRP B 193 
 HIS   0.002   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3244)
  covalent geometry    : angle       0.56908 ( 4424)
  hydrogen bonds       : bond        0.03503 (  199)
  hydrogen bonds       : angle       3.92987 (  585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1075.54 seconds
wall clock time: 19 minutes 7.14 seconds (1147.14 seconds total)